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1. F 2 3 5 7 1 Vart where volumes extracted Vgxr and filtered Vpr are in mL Pheopigment concentrations determined using the standard fluorometric method of Holm Hansen et al 1965 have not been reported in published articles for many years This is based on the fact that i there is always a residual amount of pheopigments in all natural samples Smith and Baker 1978 25 of the summed chlorophyll plus pheopigment ii pheopigment concentrations are 19 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 overestimated in the presence of chlorophyll b Lorenzen and Jeffrey 1980 Vernet and Lorenzen 1987 and iii HPLC measured pheopigments generally contribute very little to the chlorophyll a pigment pool e g Hallegraeff 1981 Everitt et al 1990 and Bricaud et al 1995 Trees et al 2000a assembled an extensive HPLC pigment database 5 617 samples extending over a decade of sampling and analysis and including a variety of environments ranging from freshwater to marine oligotrophic to eutrophic and tropical to polar and found that the average pheopigment to chlorophyll a ratio was only 0 037 This global scale result emphasizes the problems associated with estimating pheopigments using the standard fluorometric method 3 4 In Situ CHLOROPHYLL a FLUORESCENCE PROFILES An in situ fluorometer should be employed to measure a continuous profile of chlorophyll fluorescence The fluoromet
2. at i 1 2 N angles e g using a WET Labs VSF 3 is to fit a polynomial to the N 1 values 2np Ay siny derived from the N measurements and the endpoint 2x8 AX rz e sin 0 and integrate it from 5 tom following Beardsley and Zaneveld 1969 Determination of b X from VSF Measurements at Only One Angle Oishi 1990 used Mie scattering calculations and VSF observations to determine B A y and bp for polydispersions of spheres having different size distributions similar to those observed for marine hydrosols He invoked the mean value theorem to observe from the definition of b X that for each n polydispersion phase function p Q v there must be at least one angle w for which b 4 22 4 87 f sin YAY 22 A 7 5 22 2 Oishi 1990 then futher observed that for a selected common reference angle w he could determine an approximate linear estimate of the backscattering coefficient for each polydispersion as P Recalling that B 4 w 2 X B A w Vol I Ch 2 Sect 2 4 74 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV bf 4 2ay p 4 9 5 23 where the coefficient z v is selected to minimize the uncertainty N 2 Dla 0 amp 0 U j 5 24 v 3 5 24 By varying y Oishi found that the minimum overall uncertainty for the ensemble of N size distributions occurred at w 120 with x 1209 2 1 14 Boss and Pegau
3. max and i max is the weight specific absorption coefficient L g cm of pigment i Values for X are given in Appendix E of Jeffrey et al 1997 Standards stored under nitrogen in the dark at 20 C do not change appreciably over a one month period provided that they are stored in containers proven to prevent evaporation e g glass or Teflon bottles vials b Procedure l 2 Set up and equilibrate the HPLC system with eluant A at a flow rate of 1 mL min Calibrate the HPLC system using working standards prepared on the day of use by diluting the primary standard with the appropriate solvent Jeffrey et al 1997 Appendix E When preparing calibration standards one should only use dilution devices for which the precision and uncertainty have been validated with the solvent to be measured Prepare at least 5 concentrations ug L of working standards for each pigment spanning the concentration range appropriate for the samples to be analyzed For each working standard mix 1000 uL with 300 uL of distilled water shake and equilibrate for 5 min prior to injection diluting the standards and sample extracts with water increases the affinity of pigments for the column in the loading step resulting in an improved separation of the more polar pigments Rinse the sample syringe twice with 300 uL of the diluted working standard and draw 500 uL of the working standard into the syringe for injection Place the syringe i
4. which is a function of the polar scattering angle alone In terms of the VSF measurements as represented in 1 19 we have that 2n B A w B A w do 2x 4 w o 1 20 0 Backscattering Coefficient Determination The backscattering coefficient b Vol I Ch 2 equation 2 23 is an important factor in the physical relationship between the IOP and remote sensing reflectance Vol III Ch 4 Sect 4 3 and references cited therein As is the case for the volume scattering coefficient b A there is no practical way to directly measure b X in the sea If that is true then how can 5b X be determined using the so called backscattering meters in common use within the community These instruments actually measure the VSF PO v at one angle yw or several angles y i L2 N in the backward direction For single angle VSF instruments such as the HOBILABS HydroScat series and WET Labs ECO BB series one uses the fact that most observed phase functions and modeled VSFs show a common crossover angle y at which Bv cc b An empirical linear equation is used to calculate b from Bv where the angle w is selected to minimize the uncertainty in b X associated with a simulated uncertainty in Bs Qv Oishi 1990 Maffione and Dana Boss and Pegau 2001 The approach used to determine 5 4 from measurements of B w i 1 2 N angles e g using a WET Labs VSF 3 is to fit a polynomial to the N 1 v
5. 30 28pp Matlack D E 1974 Deep ocean optical measurements DOM report on North Atlantic Caribbean and Mediterranean cruises Tech Rep Naval Ordnance Lab pp 1 103 Moore C J R V Zaneveld and J C Kitchen 1992 Preliminary results from an in situ spectral absorption meter Ocean Optics XI Proc SPIE 1750 330 337 Mobley C D and OTHERS 1993 Comparison of numerical models for computing underwater light fields Appl Opt 32 36 7484 7504 Nikolayev V P and A A Zhil tsov 1968 Simple photoelectric transparency meter Oceanology U S S R 8 428 432 Pegau W S J R V Zaneveld and K J Voss 1995 Toward closure of the inherent optical properties of natural waters J Geophys Res 100 13 193 13 Pettersson H 1934 A transparency meter for sea water Medd Oceanogr Inst Gothenberg Ser B 4 Petzold T and R W Austin 19686 An underwater transmissometer for ocean survey work In Underwater Photo optical Instrument Applications Proc SPIE 12 133 137 Timofeeva V A 1960 Instrument for determining the attenuation coefficient of directed light in the sea Sov Oceanogr 1962 Ser 4 79 83 25 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Van Zee H D Hankins and C deLespinasse 2002 ac 9 Protocol Document Revision F WET Labs Inc Philomath OR 41pp Voss K J and R W Austin 1993 Beam attenuation measurement error due to s
6. Because of reflections and absorption during transmission through windows and other optical components 4 A 77 0 gt A but assuming the optical throughput is linear 4 7 0 cc A The detector s dark response VS A is any signal output that is present when the source is off and b 2 7 0 0 If the detector s electrical response is linear X v A V 2 and we may write D A 7 0 e 2 C Vn 4 V5 a W nm 2 2 where Cp is a constant with units of w nm V accounting for the combined effects of optical losses and the detector s flux responsivity A measure of the flux 2 0 0 is still required if the transmission is to be determined A beam splitter before the source window can be used to shunt a proportion of the source light to a reference detector to provide a measure of the flux being sent into the water Because of losses associated with the source windows and beam splitter the reference detector receives and responds to a flux proportional to A 0 0 e and we have that D 2 0 0 0 C Va 4 V 2 W nm Q 3 where V A and V r X are the reference detector response and ambient dark signals respectively and Cx is a second system response constant The transmittance may now be written as the ratio of 2 2 and 2 3 17 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV 9 un
7. Directional radiant flux at distance r from a source or from a scattering interaction site within the transmitted beam is denoted A r y In Fig 1 4 for example radiometric flux scattered into direction y at position X is denoted as b 4 0 Yy o and the scattered flux transmitted in that direction to Detector 2 at position X as D A n V 9 Radiometric flux within the beam transmitted to a point on the zg axis at distance r from the source is denoted 4 r 0 9 where the dot indicates that is indeterminate when y 00rw m In particular the flux transmitted from the source to Detector 1 is o A r 0 e Transmittance and Beam Attenuation The shaded rectangle overlaid on the extended z axis in Fig 1 4 schematically illustrates a cylinder of cross sectional area As representing the collimated beam of radiant flux transmitted from the source to Detector 1 The gradient in shading represents the exponential decrease in b A r 0 with increasing distance r as photons interact with the medium and are absorbed and scattered out of the beam During transmission over a path interval from r to r Ar the fraction of radiant flux absorbed in the volume AsAr is spectral absorptance A X and the fraction of flux scattered out of the beam direction in that volume is spectral scatterance B X see Vol I Chapter 2 Sect 2 4 One could envision superimposing a lightly shaded cloud on Fig 1 4 to visuali
8. Ensure proper hydration of the sample by placing the GF F filter on a small drop of 0 2 um FSW Store each filter sample in the dark and refrigerate it 4 deg C until it is to be measured in the spectrophotometer e If the spectrophotometric measurements will be delayed more than 24 hours following sample filtration the filter samples should be prepared for liquid nitrogen storage Samples should be stored in containers that allow the filter to remain flat and which are specifically designed for immersion in liquid nitrogen e g Fisher Histoprep tissue capsules One pair of blank filters should also be prepared each day for use as the reference blank for samples collected that day Samples may be stored in liquid nitrogen for extended periods but it is strongly recommended to analyze them as soon as possible e Non pressurized liquid nitrogen dewars generally retain liquid nitrogen for 2 4 weeks Pressurized liquid nitrogen dewars can be rented at low cost for extended cruises 4 5 weeks so that the sample dewars may be replenished and kept full Care must be taken at sea and in return shipping to ensure that the samples are properly frozen Samples should be shipped in liquid nitrogen dry shippers which will maintain proper temperatures for 2 to 3 weeks if they are properly charged and in good condition e Air transport of liquid nitrogen dry shippers is approved under International Air Transportation Agreement IATA 41 Edition Secti
9. eese 7 1 4 ABSORPTION MEASUREMENT CONCEPTS esee eren etr enenennnnene 9 Reflecting Tube Absorption Meters essent rennen rene 9 Laboratory Methods for Determining Absorption Coefficients eee 10 Absorption Determinations from Radiometric Measurements of Irradiance Flux Divergence 10 Other Methods of Measuring Absorption esee eene ener 10 1 5 SCATTERING MEASUREMENT CONCEPTS esee enenenne een ene nene 11 Scattering Coefficient Determinations esent 1l Volume Scattering Function Measurements eese eene 11 Backscattering Coefficient Determination seen eene entrent 12 CHAPTER perm 15 BEAM TRANSMISSION AND ATTENUATION COEFFICIENTS INSTRUMENTS CHARACTERIZATION FIELD MEASUREMENTS AND DATA ANALYSIS PROTOCOLS 2 INTRODUGTION pectore rrr a n eec dv Sese repere E E ENEN aR e 15 2 2 TRANSMISSOMETER DESIGN CHARACTERISTICS eese 15 Direct and Folded Path Transmissometers essent eene enne 15 Other Types of Transmissometers esses n enne ena tnter enne 16 Source and Detector Characteristics assure renser renerne renere nnne nne 17 Transmissometer Response Temperature Dependence sse 18 Spectral Characteristics a ete eg edetatude attesa 18 Beam Geometry Detector Acceptance Angle and Scattered Light sss 18 Paihlength Considerations 5 0 uenti te
10. the sample is removed and the sample originator is notified V Calibration procedures for chemistry Calibration curves are generally linear and are made up of 4 7 points A full calibration is performed at the beginning of each run a run is generally 40 60 samples with a reduced calibration 3 5 points performed at the end of the run Occasionally calibration data is best fit with a quadratic equation and this is used if it best describes the data within a specific run Standards are made from reagent grade chemicals typically JT Baker that have been dried and are stored in a dessicator Working stock solutions are labeled with the content description concentration initials of the maker and the date the stock solution was made Generally stock solutions are kept less than one week however some stocks Br Na Cl C for DOC can be stored for several months Standard solutions are kept for less than one week from the date they were made Stocks and standards are stored tightly covered in a dark refrigerator Control charts are prepared and printed every few months However data from each run are looked at within days of analyses Calibration curves Laboratory Duplicates Lab Fortified Blanks LFB Lab Fortified Sample Matrices LFM and Lab Page E 4 Reagent Blanks LRB are reviewed and are checked against known concentrations where applicable to ensure QC criteria are met for each run of samples VI Data Reduction valid
11. 0 c a X B A V and QO 3 0 8 0 9 a X Ba V that account for the bidirectional nature of the ocean s reflectance this bidirectionality may be traced directly to the shape of the VSF Bidirectionality of remote sensing reflectance as it arises from the VSF is shown more explicitly in the formulation by Zaneveld 1982 Equation 1 18 could be used directly as a basis for measuring the VSF if an instrument s source and detector were well collimated and there were no flux losses or FOV distortions associated with an its optical elements Some general angle scattering meters Petzold 1972 Lee et al 2003 are designed with a well enough collimated beam and very small detector acceptance angle so that equation 1 18 may be applied directly In terms of equation 1 19 this is equivalent to assuming that the scattering response weighting function W a y c is narrow enough to set it to unity The General Angle Scattering Meter GASM built at the Scripps Institution of Oceanography s Visibility Laboratory Petzold 1972 consists of a lamp focused into a cylindrical beam and a narrow field of view detector mounted to swing in an arc to view the beam at many off axis scattering angles between approximately 10 and 170 Petzold 1972 reported VSF s measured for selected natural waters using the 65 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV GASM This refere
12. 0 0005 OD Save the digital baseline spectrum Ensure the baseline is flat and stable over time and note any anomalies It is common for the baseline to exhibit temperature dependent artifacts 650 800 nm These should be minimized if possible by ensuring the purified water in the sample and reference cuvette are at the same temperature If the baseline reference spectrum OD A is not flat and stable during analysis according to specifications summarized in section 4 3 the precision of any estimate of soluble absorption may be seriously questioned It is the investigator s responsibility to ensure satisfactory performance of the instruments and use of proper methods to ensure that the final result is reasonable Significant deviation from the specifications in section 4 3 or improper consideration of sample preparation protocols may result in estimates of soluble absorption that are not meaningful given the small magnitude of this estimate in the visible spectral region of most interest for ocean color applications 50 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV e Remove the sample cuvette and discard the liquid Rinse the inside of the cuvette three times with 5 mL to 10 mL of the next sample to be measured A copious rinse is desired but sample volume is often limited Several vigorously shaken small sample rinses are recommended if the volume is extremely limited e Fill the sample cuvette w
13. 1983 When water flows through the pores of a Nuclepore filter streamlines are formed that can align small particles longitudinally with the result that cell diameter becomes important with these filters It is known on the other hand that Whatman GF F filters can retain particles much smaller than their rated pore size Generally at small volumes 100 300 mL filter adsorption and electrostatic and van der Waals attractions are important whereas at larger volumes gt 2 000 mL sieving dominates This has been tested in oligotrophic waters off Hawaii in which small 500 mL and large volumes gt 2 4 liters retained similar amounts of chlorophyll a on the two types of filters whereas for intermediate sample volumes the GF F filters showed lower concentrations As a general rule it is recommended that the following volumes be filtered for these water types 0 5 1 0 liter for oligotrophic 0 2 0 5 liter for mesotrophic and 0 1 liter and less for eutrophic water It is recommended to not pre filter seawater samples to remove large zooplankton and particles because this practice may exclude pigment containing colonial and chain forming phytoplankton such as diatoms and Trichodesmium sp Forceps should be used to remove large zooplankton from the GF Fs following filtration 16 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Sample Handling and Storage Samples should be filtered as quickly as po
14. 2 1 INTRODUCTION Beam transmittance T A n over an optical path of length r m and the beam attenuation coefficient c X m are introduced in Chapter 1 Sect 1 3 The two variables are related by equation 1 6 A beam transmissometer is an instrument that combines a source of collimated spectral radiant flux 2 0 0 and a co aligned detector to measure the flux A 7 0 transmitted over distance 7 to measure T A r Fig 1 4 and related text in Sect 1 3 Ch 1 A beam transmissometer is also frequently called a beam attenuation meter or a c meter 2 2 TRANSMISSOMETER DESIGN CHARACTERISTICS In concept a beam transmissometer is a relatively simple instrument to build and the derived beam attenuation coefficient is needed in many optical studies of the sea Therefore instruments of this type have been in use for many years While a great number of different transmissometer designs have appeared most follow one of the two basic designs illustrated in Fig 2 1 Direct and Folded Path Transmissometers Probably the most common transmissometer design uses a collimated light beam with a source in one housing and a detector facing the source Fig 2 1 top panel In such an ideal direct path transmissometer either a white light or a light emitting diode LED source is combined with a pinhole to provide a point source A lens is inserted into the path to collimate the light beam an interference filter is inser
15. 2001 separated the VSF and backscattering coefficient as B A w B QV p 4 V and b X b X b A where the subscripts p and w designate contributions due to particles and water respectively The scaling factor 5 25 X E Is correspondingly partitioned as ABS oe B a 1 E ES qa DE B a Y p w Analyses similar to those of Oishi 1990 and Maffione and Dana 1997 but in this partitioned framework led Boss and Pegau 2001 to conclude that xl Xp g v z 1 1 only when 2117 3 consistent with the results of Oishi 1990 For measurements at other scattering angles they recommend modifying Equation 4 6 to correct for the water scattering contribution as b A 2ay V B A B 4 b A 5 27 They provide equations for estimating B 2 v and b based on the theoretical equations and experimental 5 26 results of Morel 1974 and tabulate estimates of x v in the range 90 lt V lt 170 REFERENCES Beardsley G F and J R V Zaneveld 1969 Theoretical dependence of the near asymptotic apparent optical properties of sea water J Opt Soc Amer 59 373 377 Bohren C F and D R Huffman 1983 Absorption and Scattering of Light by Small Particles Wiley New York 530pp Boss E and W S Pegau 2001 Relationship of light scattering at an angle in the backward direction to the backscattering coefficient Appl Opt 40 55
16. 4 Total Suspended Solids Grab sample and laboratory analysis Act 4 Critical Hyperspectral imagery Low altitude aerial survey Act 2 Critical Water Temperature Near continuous buoy observations Act 1 Near continuous flow through obs Act 3 Measurements with field sensors Act 4 For information only Salinity Near continuous buoy observations Act 1 Near continuous flow through obs Act 3 Measurements with field sensors Act 4 For information only Nutrients 1 e nitrate nitrite orthophosphate Near continuous buoy observations Act 1 Grab sample and laboratory analysis Act 4 For information only Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 18 Sample Process Design for Activity 1 Near Continuous Buoy Observations The stations for this activity are listed on Table 5 The Activity 1 stations will be monitored continuously from 4 1 07 to 12 15 07 for several water quality parameters The water quality parameters to be measured by each buoy are listed in Table 6 Table 5 Sampling Station Summary for Activity 1 D Latitude Longitude ation escription DD MM MMM DD MM MMM Great Bay Central Great Bay 43 0715 70 8677 Coastal Buoy Table 6 Sample Process Design for Field Measurements for Activity 1 Station ID Parameters pampig Pernod pnd Responsible Agency Frequency Water Temper
17. 670 nm transmissometer with a 1 0 acceptance angle is approximately 19 However accurate correction of an apparent Cy measured by that instrument would require knowing both the VSF B A y o over the range b X 0 y Wrov and the single scattering albedo o 4 E Vol I Ch 2 Sect 2 4 To date very few reliable c measurements have been made of B A y o at angles less than 1 Given the extreme rate of increase in the magnitude of the VSF for particles p v o and for turbulence as w 0 Ch 1 Fig 1 3 any estimate of its integrated value over the range 0 y 1 would be highly uncertain That uncertainty would transmit directly into any c X correction algorithm attempting to account for the effects of the near forward VSF 19 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV The best approach to dealing with the effects of scattered light in measured beam attenuation coefficients may be that proposed by both Voss and Austin 1993 and Pegau et al 1995 That is do not try to apply any scattering corrections to the measured determination of ch Simply report the acceptance angle characteristics of the transmissometer used to make the measurements and leave all considerations of how to handle scattering artifacts to the user of the data Internal consistency of IOP is obtained by including light scattered up to a certain acceptance angle Woy in the beam attenua
18. De pigmented Particle and Phytoplankton Absorption Coefficients sss 54 47 DATA REPORTING wy gerne dep t e eee ee Re quete iren visere 54 4 9 PROTOCOL STATUS AND FUTURE DIRECTIONS eese rennen 54 Absorption spectra for particles filtered on GF F filters sss 54 Absorption spectra for particles transferred to glass slides sss 55 Transmission Reflectance T R Method eee eene 55 Absorption spectra for seawater filtered through membrane filters or cartridges 33 Constraints on the estimate of soluble and particle absorption see 56 Go VUINU Hm 65 VOLUME SCATTERING FUNCTION AND BACKSCATTERING COEFFICIENTS INSTRUMENTS CHARACTERIZATION FIELD MEASUREMENTS AND DATA ANALYSIS PROTOCOLS 5 INTIRODU GTION iter teet Ore pato eet pe Y ER SR TER Ee O Pee Poeta S 65 iv Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV 5 2 CHARACTERIZATION AND CALIBRATION OF A VSF SENSOR FROM ITS GEOMETRY AND RESPONSE TO SCATTERING BY POLYSTYRENE BEADS eere 67 Geometric Determination of W w sessi eenren rene 67 Generalized Weighting Functions for Arbitrary Source Beam and Detector FOV Geometries 69 Dependence of the Weighting Functions on the Beam Attenuation Coefficient Cc 70 Calibration with Polystyrene Spheres sese eene ener enne ee 71 5
19. Dore D Karl and L Van Heukelem Authors National Aeronautical and Space administration Goddard Space Flight Space Center Greenbelt Maryland 20771 January 2003 NASA TM 2003 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume V Biogeochemical and Bio Optical Measurements and Data Analysis Protocols James L Mueller CHORS San Diego State University San Diego California Giulietta S Fargion Science Applications International Corporation Beltsville Maryland Charles R McClain Goddard Space Flight Center Greenbelt Maryland J L Mueller and C Trees CHORS San Diego State University San Diego California R R Bidigare D M Karl and J Dore Department of Oceanography University of Hawaii Hawaii L Van Heukelem University of Maryland Center for Environmental Science Maryland National Aeronautical and Space administration Goddard Space Flight Space Center Greenbelt Maryland 20771 January 2003 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Preface This document stipulates protocols for measuring bio optical and radiometric data for the Sensor Intercomparison and Merger for Biological and Interdisciplinary Oceanic Studies SIMBIOS Project activities and algorithm development The document is organized into 7 separate volumes as Ocean Optics Protocols for Satellite Ocean Color Sensor Validation Revision 4 Volume I
20. Figure 3 are clear indicators of impending problems for NH s estuaries NHEP 2006 The NH Department of Environmental Services DES is responsible for developing nutrient criteria for NH s estuaries DES in collaboration with the New Hampshire Estuaries Project NHEP began this process with the formation of a workgroup in 2005 The NHEP Coastal Scientist a DES employee is coordinating the work to undertake this process with input from the workgroup Information from the workgroup meetings is available at www nhep unh edu programs nutrient htm This workgroup adopted eelgrass survival as the water quality target for nutrient criteria development for NH s estuaries Eelgrass survival is largely dependent on light availability The NHEP Coastal Scientist has undertaken a review of the water clarity data for NH s estuaries There are three important constituents in the optically complex coastal waters phytoplankton non algal particulates and colored dissolved organic matter CDOM IOCCG 2000 These constituents by changing the Inherent Optical Properties IOPS affect water clarity or more precisely the magnitude of light attenuation an Apparent Optical Property AOP see Mobley 1994 Preliminary results indicate that CDOM is the major factor controlling water clarity However NHEP is not able to draw strong conclusions from these results because of significant datagaps and a large degree of spatial heterogeneity in NH s estuaries Theref
21. Oceanogr 20 1024 1034 James H R and E A Birge 1938 A laboratory study of the absorption of light by lake waters Trans Wis Acad Sci 31 1 154 Kou L D Labrie and P Chylek 1993 Refractive indices of water and ice in the 0 65 to 2 5 um spectral range Appl Opt 32 3531 3540 Kullenberg G 1968 Scattering of light by Sargasso Sea water Deep Sea Res 15 423 432 Maffione R A and D R Dana 1997 Instruments and methods for measuring the backward scattering coefficient of ocean waters Appl Opt 36 6057 6067 Maffione R A K J Voss and R C Honey 1993 Measurement of the spectral absorption coefficient in the ocean with an isotropic source Appl Opt 32 18 3273 3279 Morel A 1974 Optical properties of pure water and pure sea water In Optical Aspects of Oceanography N G Jerlov and E S Nielson Eds pp1 23 Morel A and S Maritorena 2001 Bio opical properties of oceanic waters A reappraisal J Geophys Res 106 C4 7163 7180 Mueller J L and G S Fargion Eds 2002 Ocean Optics Protocols for Satellite Ocean Color Sensor Validation Revision 3 NASA Tech Memo 2002 210004 NASA Goddard Space Flight Center Greenbelt Maryland 308pp Oishi T 1990 Significant relation between the backward scattering coefficient of sea water and the scatterance at 120 degrees Appl Opt 29 31 4658 4665 Pegau W S and J R V Zaneveld 1993 Temperature dependent absorption of water
22. pigment molecule into the blue regions of the spectrum The ratio of PUB PEB chromophores in the PE pigments synthesized by different Synechococcus strains greatly affects the absorption spectrum of the whole cells Wood et al 1985 Clearly the dependence of a on the PUB PEB ratio of phycoerythrin will affect also Rgs X in water masses dominated by cyanobacteria The PUB PEB ratio for the PE in a given water mass may be characterized using scanning fluorescence spectroscopy Wood et al 1999 Wyman 1992 The measurement of phycoerythrin is not yet as routine nor as accurate as the measurements of chlorophylls and carotenoids The techniques introduced by Stewart and Farmer 1984 work well for measuring biliproteins in freshwater and estuarine species but are less successful for natural populations of marine species Wyman 1992 reported a linear relationship between the in vivo fluorescence emission intensity of PE measured in the presence of glycerol and the PE content of Synechococcus strain WH7803 Scanning spectral fluorescence measurements have been used to estimate PE concentration of extracted bulk samples Vernet et al 1990 Nevertheless there are few direct measurements of separated PE proteins from natural samples High Performance Capillary Electrophoresis HPCE is a powerful analytical tool currently used in clinical biochemical pharmaceutical forensic and environmental research In HPCE high voltages typically 10 30 KV
23. representing the total flux reflected from the plaque into the FOV of the detector If the plaque is moved continuously over z the integral of 5 18 yields the total relative flux reflected from the plaque to the detector from the volume intersection of the source beam and detector FOV as Pa c p 3 og 5 19 A similar integration of 5 1 yields o Sete J B y W x e axayaz B w ymo 5 20 where the angle w is selected so that the equality holds the mean value theorem assures that this must be true for at least one scattering angle Taking the ratio of 5 10 and 5 20 and solving for B w yields the result fr z c dz _ p Pale z P w x c fm zc d 5 21 We refer the reader to Maffione and Dana 1997 for the derivation of the unknown terms in 5 21 from the plaque integral and differential measurements and defer further comparative analysis and description of this method and the explicit approach of Section 5 2 for a future revision to this chapter 5 4 METHODS FOR THE DETERMINATION OF THE BACKSCATTERING COEFFICIENT FROM VSF MEASUREMENTS AT ONE OR MORE SCATTERING ANGLES If the complete VSF is measured at fine angular resolution using a general angle scattering meter then it 1s straightforward to integrate it over the backward hemisphere to determine b directly Determination of b X from VSF Measurements at Three or More Angles The approach used to determine b X from measurements of B A y
24. see also Vol I Chapter 2 Comparisons between absorption profiles measured using Gershun s equation with E z X and E z scalar irradiance data and absorption profiles measured with a reflecting tube instrument agreed within 896 Pegau et al 1994 This level of agreement is well within the calibration uncertainties of the particular prototype instruments used for that experiment which were approximately 1096 uncertainties in both the scalar irradiance radiometer and in the reflecting tube instrument Less than 5 uncertainties in absorption are expected in future experiments assuming the data are properly averaged to remove near surface irradiance fluctuations caused by surface waves Zaneveld et al 2001 In very clear oligotrophic water moreover uncertainty in water absorption values may make it impossible to realize this level of relative agreement Other Methods of Measuring Absorption There are several other measurement concepts that may be used to determine the absorption coefficient of seawater however none of them are currently useful for making routine measurements during daylight conditions at sea One possible exception is the determination of absorption by inverting radiance distribution profiles measured using a camera system Voss 1989 but at present such camera systems are not commercially available In a similar method absorption may be determined by inverting the radiative transfer equation for several measured m
25. the Environment for Visualizing Images is an image processing software package ENVI provides comprehensive data visualization and analysis for multiband and hyperspectral data imagery UNH will use remote sensing techniques to isolate eelgrass and green and red macroalgal areas in the estuary The remote sensing sub tasks are described below e Endmember collection A spectrum representing a spectrally pure feature e g vegetation soil etc is defined as a spectral endmember Following the review of field observations from 2007 and in situ measurements candidate locations will be identified in the hyperspectral imagery and endmember will be created of the macroalgae areas and of bottoms without macroalgae present pure background Macroalgal does not remain permanent in one location and does not usually create a dense bed representing just one species macroalgae like eelgrass beds Therefore UNH will use the regions with most dense macroalgal patches as the best available endmember that can be produced purest feature available e Endmember analysis The endmembers collected will be analyzed according to macroalgal type and bottom mineral type Distinct features along the specra will be used in order to discriminate between the different endmembers e Classification Following the characteristics of the different endmembers a classification technique will be chosen and applied to the data The product will be a thematic map that each
26. 0 086 TT elson et al 1998 Synechococcus WH7803 mwemm m itchell and Kiefer 19882 IDanalislla tertiolecta Field samples D tertiolecta Bricaud and Stramski 1990 Cultures of Mitchell amp Kiefer 19882 Kahru and Mitchell 1998 Mitchell 1990 data Roesler 1998 Assume p 2 0 0 100 61 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV 0 3 Filter Optical Densi I 0 0 poiitirviitiiriirtiiin 300 400 500 600 700 800 Wavelength nm Figure 4 1 Optical density for various spectrophotometers for a diatom culture filtered onto GF F filters The average from 790 800 nm was used for a null value and the same volume was used for all samples The data from the Hewlett Packard diode array system is higher than the other spectrophotometers as discussed in detail in Mitchell et al 2000 Below 400 nm the Hewlett Packard unit was too noisy for the glass fiber filter method 0 045 r 0 16 m r A 0 14 B j 0 12 0 10 0 08 0 06 0 04 3j 4 73 Lra I sf op 0 02 iii pirit aad ao orania 300 400 500 600 300 400 500 600 700 800 Wavelength nm Wavelength nm Figure 4 2 Optical density for fresh Millipore Alpha Q water in the sample cuvette referenced to air in a dual beam spectrophotometer OD determined during the ACE Asia experiment A OD wa plotted for the spectral range 300 nm to 600 nm B
27. 1 Sect 1 3 a detector with a finite acceptance angle or Field of View FOV wy detects photons that are singly scattered in the range 0 y lt Yoy Therefore the flux OY 0 750 e arriving at a 10 A reference detector may be used in a feedback circuit to stabilize an LED source However the reference detector signal is not usually included in the instrument s data output stream in constant source output designs of this type 18 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV transmissometer s detector assembly window and subsequently measured see above exceeds the true flux directly transmitted along the path direction y 0 according to Vrov OF A 7 0 O 4 7 0 9 2 i P3 w o sin vdvy 2 6 0 where B A y is the volume scattering function VSF Ch 1 Sect 1 5 In other words because a transmissometer measures a portion of the forward scattered light its measurement overestimates the transmittance T A n and underestimates the beam attenuation coefficient calculated with equation 1 6 The acceptance angle and thus the scattering error is dependent on the optical elements of the instrument There is no standard specified for transmissometer acceptance angle and each manufacturer may use a different one for each particular instrument design Therefore were the transmittance of a homogeneous water volume to be measured a number of perfectly calibrated beam a
28. 2 hr during an extended series of measurements Other desirable but not absolutely essential spectrophotometer features are variable slit width to allow reducing the FWHM spectral resolution when desired automatic baseline corrections the adequacy of which must nevertheless be verified and automatic spectral calibration during instrument warm up using mercury emission lines supplied by an internal lamp source The spectral accuracy of the spectrometer should be verified by scanning a holmium oxide filter with reference to an air to air baseline This spectral calibration should be repeated each time the instrument is turned on and at 41 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV the conclusion of a series of measurements Alternatively a spectrophotometer s spectral characteristics may be calibrated using an internal line source e g a mercury lamp if the instrument is so equipped but independent checks with the holmium oxide filter are also strongly advised A set of absorbance reference filter standards of known OD must be used to calibrate a spectrophotometer s responses over the range of OD associated with the samples to be measured This calibration together with instrument baseline spectrum determinations should be repeated at intervals necessary to characterize within the noise tolerances given above any measurable drifts in the instrument baseline and or OD response Unles
29. Blough M D DeGrandpre E T Peltzer and R K Nelson 1996 Seasonal variation of CDOM and DOC in the Middle Atlantic Bight Terrestrial inputs and photooxidation Limnology and Oceanography 42 674 686 Waters K J R C Smith and M R Lewis 1990 Avoiding ship induced light field perturbation in the determination of oceanic optical properties Oceanography November 18 21 Yentsch C S 1957 A non extractive method for the quantitative estimation of chlorophyll in algal cultures Nature 179 1302 1304 Yentsch C S 1962 Measurement of visible light absorption by particulate matter in the ocean Limnology and Oceanography 7 207 217 60 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Table 4 1 Published coefficients for determining pathlength amplification effects The suspension optical density OD sp computed for a GF F filter with OD s 0 2 is provided for comparison C ODs 0 2 RO chal 1950 392 0 655 0 392 0 655 0 299 0 105 leveland amp Weidemann 1993 oore et al 1995 halassiosira weissflogii oore et al 1995 Synechococcus WH8103 assan amp Ferrari 1995 Scenedesmus obliqus elson et al 1998 Dunaliella tertiolecta EA lied ed 0304 0 450 0 080 0 40 EM Nelson et al 1998 Phaeodactylum tricornutum Es Een Pl 00 MEET 0 102 0 437 0 088 0 294 0 082 0 055 0 540 0 467 0 082 1 630 0 220
30. Figure 3 2 Same as Figure 3 1 for data collected during the Marine Optical Characterization Experiment MOCE 4 cruise 21 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 y 0 665x 065 r 0 937 logHPLC 1 065logFluor 0 178 r2 0 937 n 300 10 E GoCal 96 H Gulf of California ap og S E 0 1 8 0 01 0 01 0 1 1 10 Fluorometric Chlorophyll a mg m 3 Figure 3 3 Same as Figure 3 1 for data collected during the Gulf of California cruise Gulf of California November 1996 MOBY Mooring amp GoCal Cruises 4 Nov 96 Turner 10 AU 005 Response Turner 10 005R Response Figure 3 4 Comparison of fluorometrically determined chlorophyll a using the VisLab Turner Fluorometer 10 005R and the Moss Landing Marine Laboratory Turner Fluorometer 10 AU 005 Samples were analyzed from a MOBY Nov 96 cruise and a Gulf of California cruise Mueller Nov 96 22 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 0 50 0 45 4 0 40 0 35 4 0 30 025 4 020 0 15 HPLC Chl a mg m 0 10 0 05 000 005 O10 O15 020 025 030 035 040 045 0 50 TD700 Chl a mg m Manufacturer s Calibration Figure 3 5 Comparison between chlorophyll a determined by the TD700 equation supplied by the manufacturer and that measured by HPLC methods 0 40 0 35 0 30 4 0 25 4 020 0 15 H
31. Ocean Color Sensor Validation Revision 4 Volume 5 fluorometric chlorophyll a samples filtered from the flow through system the alongtrack profile of F z lat lon can be calibrated in units of chlorophyll a concentration mg m 1 4 SUSPENDED PARTICLES Suspended Particulate Matter All total suspended particulate material SPM dry weight mg L will be determined gravimetrically as outlined in Strickland and Parsons 1972 In general samples are filtered through preweighed 0 4 um polycarbonate filters The filters are washed with three 2 5 mL 5 0 mL aliquots of DIW and immediately dried either in an oven at 75 C or in a dessicator The filters are then reweighed in a laboratory back on shore using an electrobalance with at least seven digits of precision Particulate Organic Carbon and Particulate Organic Nitrogen Protocols for measuring concentrations in seawater of Particulate Organic Carbon POC and Particulate Organic Nitrogen PON as specified for JGOFS UNESCO 1994 Chapter 15 are also adopted here The units of POC and PON are ugC Kg and ugN Kg respectively Therefore it is mandatory that each of thes measurements be accompanied by Conductivity Temperature and Pressure measurements so that the density of seawater Kg m may be calculated Particle Size Distributions Particle size distributions can potentially provide important information about the shape of the volume scattering function which stron
32. Plotted for the spectral range 300 nm to 800 nm Optical Density Optical Density 62 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV 0 05 CR CI EET hm 0 004 rrr rrr rr 0 04 4 I B B z 1 8 00 5 A E 0 02 8 uz E amp 0 01 e 0 00 0 01 rib re scu peri tiiii tii i ENN EU INS 300 400 500 600 700 800 300 400 500 600 700 800 Wavelength nm Wavelength nm 0 05 rrTTT TTTTTTTTTTTTTTTTTTT po 0 04 C 4 a 0 03 4 A F 4 d 0 02 amp 0 01 0 00 0 01 pot 300 400 500 600 700 800 Wavelength nm Figure 4 3 Typical results for soluble absorption determined during the ACE Asia cruise March April 2001 in the western Pacific according to the protocols recommended here A Raw optical density OD A for samples relative to Millipore Alpha Q water B Blank optical density spectra OD A after null offset gray compared to a global value solid line The global blank is determined by fitting an exponential function to the mean blank for more than 15 cruises from 1998 2001 where the mean for each cruise was determined as the mean of all individual blanks for each cruise A fitted curve to a cruise or global mean for OD X is recommended for correction of the soluble sample blank because individual spectra gray have significant instrument noise Note the scale for 3B is approximately 1
33. RE CE UR DERI UR URS 4 REFERENCES erede eo arem a e EU C CI ERROR 4 CHAPTER 2 21 eerte de eben ON A io sender Sus sepe EAE E EA 5 HPLC PHYTOPLANKTON PIGMENTS SAMPLING LABORATORY METHODS AND QUALITY ASSURANCE PROCEDURES Z ELINTRODUGCTIONS 5 5 oce petrae editi oni bu ERROR 5 2 2 SAMPLING PROTOCOLS FOR PHYTOPLANKTON PIGMENTS eene 6 Water Samples 5 npe ieri ea PN EE oen en ee Dep PER ete EA RU EP eres h 6 FiltEaGlion d d o tei Ro ee toii ee NR ps 6 Sample Handling and Storage eee eee eterne nennen anada teen nns 7 Recordkeepihig s 5 e Ses Stet eet tetro elec see ie ee eats ee niea oase 8 2 3 LABORATORY METHODS FOR HPLC PHYTOPLANKTON PIGMENT ANALYSIS 8 Internal Standard and Solvent Preparation eee eene 8 BEXU CHO ioi ER T Rer ER S ete RE E SEE HERE edes sa aen A A m rine n 8 EIIMAMIISE EET 8 HPLC Eluants and Gradient Programs esee eene ener nentes 9 Determination of Algal Chlorophyll and Carotenoid Pigments by HPLC Wright et al 1991 9 2 4 QUALITY ASSURANCE PROCEDURES eene eene renes 11 2 5 PROTOCOL STATUS AND FUTURE DIRECTIONS FOR RESEARCH 12 REFERENCES 25 ote ort tere ree ee eor ete deti arbo e DIO e a ers 14 CHAPTER Joore irena r en E I EAE E EE E EE ese ER ose Rese Fen Fee iu s ese ERU EN EAA AEAEE 15 FLUOROMETRIC CHLOROPHYLL A SAMPLING LABORATORY METHODS AND DATA ANALYSIS PROTOCOLS 3 T INTRODUCTION ipanen reete
34. Record the digital air baseline This spectrum should be spectrally flat with noise less than 0 0005 OD Place the reference cuvette in spectrophotometer and scan OD A the optical density of purified water relative to air Remove the reference cuvette and repeat the measurement for the sample cuvette Store both spectra noting which file is for the cuvette to be used as reference in subsequent analyses and which is to be used for samples See Figure 4 2 for spectra of OD A determined during ACE Asia Compare the spectra of OD A determined for the reference and sample cuvettes to each other and with a digital library of previous reference water to air optical density spectra Ensure that the two cuvettes are well matched optically and that both conform to tolerance of pure water relative to air Note anomalies and plan to make any needed corrections during data processing If anomalies are associated with poor preparation of the cuvette repeat the preparation and run new water to air baseline reference scans Put both reference and sample cuvettes filled with purified reference water into the spectrophotometer for a double beam unit For a single beam unit this will be done sequentially Run a baseline correction for purified water After the water to water baseline optical density measurement is complete record the pure water baseline as a sample OD A This spectrum should be spectrally flat with magnitude less than
35. Sleeve w Lip fr nno Spectral Sources vee Interference Filters Lower can for 9 Wavelengths Fig 3 3 Schematic illustration of the ac 9 beam attenuation and absorption meter courtesy of WET Labs Inc Pure Water Calibration The procedure for using pure water to calibrate the reflective tube absorption meter side of an ac 9 is identical to that described in Chapter 2 Sect 2 4 for its flow through beam transmissometer side The calibration equation for measured absorption a relative to pure water corresponding to equation 2 9 for c is Vay AJ Ve A V Vr X a a A In Yaw 09 9 02 nw A S JD 09 797 09 p0 p l i 3 11 Vow A r 02 9 6 V 2 where the signal notations on the right hand side are the same as those defined in Chapter 2 and pure water absorption values are listed in Table 1 1 of Chapter 1 Pure Water Preparation The methods for preparation of optical calibration grade pure water were not addressed in Chapter 2 and are included here 32 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV To prepare pure water for instrument calibrations the manufacture uses a commercial de ionization system and filtration system After primary de ionization the water is processed using a Barnstead or equivalent purification unit and stored in a large holding tank To maintain purity water in the holding tank should be re circulated through a ultra violet c
36. Surface PAR PAR at depth units units Station Start Time local End Time Depth m Surface PAR PAR at depth units units Station Start Time local End Time Depth m Surface PAR PAR at depth units units Additional Comments QAPP Addendum Hyperspectral Imagery for Great Bay NH RFA No 07309 July 11 2008 USING MOORED ARRAYS AND HYPERSPECTRAL AERIAL IMAGERY TO DEVELOP NUTRIENT CRITERIA FOR NEW HAMPSHIRE S ESTUARIES Quality Assurance Project Plan Addendum Purpose The New Hampshire Estuaries Project collected hyperspectral imagery and water quality data from the Great Bay Estuary in 2007 Data were collected under the referenced approved QAPP After the data were collected the NHEP and other researchers at the University of New Hampshire received funding from EPA to conduct additional analyses with the hyperspectral imagery data No new data will be collected for this project The purpose of this addendum to the original QAPP is to document the additional analyses that will be conducted using the hyperspectral imagery data Project Description A General Summary Statement of Project Goal amp Justification Increasing nitrogen concentrations Figure 1 and declining eelgrass beds in Great Bay Figure 2 are clear indicators of impending problems for NH s estuaries NHEP 2006 The NH Department of Environmental Services DES is responsible for de
37. This procedure results in sharper peaks allowing greater loading than can be obtained with undiluted samples This method does not separate monovinyl and divinyl chlorophylls a and b The presence of divinyl chlorophylls a and b can cause errors if they are not separated either physically on the column or by a channels ratio method from the monovinyl forms Latasa et al 1996 showed that the use of a single response factor only for monovinyl chlorophyll a could result in a 15 to 25 overestimation of total chlorophyll a concentration if divinyl chlorophyll a was present in significant concentrations Although monovinyl and divinyl chlorophyll a co elute each compound absorbs differently at 436 nm and 450 nm and it is therefore possible to deconvolve the absorption signals due to these pigments Latasa et al 1996 Alternatively these two chlorophyll species can be separated chromatographically and individually quantified using the Cg HPLC techniques described by Goericke and Repeta 1993 and Van Heukelem and Thomas 2001 The latter technique uses a two solvent system and elevated column temperature to achieve desired separations Regardless of the method or column packing material used Ci or Cg it is important that HPLC performance be validated before and during use This would include validation that resolution between peaks is acceptable or when peaks are not chromatographically resolved that equations based on spectral deconvolut
38. Water Quality in Coastal Areas and Shallow Inland Lakes University of Northern Iowa and NASA Kennedy Space Center Iowa Space Grant Final Technical Report January 2005 Available at cosmos ssol iastate edu isgc RES INF VRR2004 Sugu COOP pdf UNH 2006 June 2006 Great Bay Sampling Report UNH Coastal Ocean Observing Center University of New Hampshire Durham NH Available at http ccg sr unh edu pdf June 2006 Great Bay Sampling Report pdf UNH 2005 Great Bay Sampling Methods UNH Coastal Ocean Observing Center University of New Hampshire Durham NH Available at http ccg sr unh edu pdf Great Bay Methods Report pdf Appendix A QAPP for the Water Quality Analysis Lab at the University of New Hampshire Department of Natural Resources Durham NH I Laboratory Organization and Responsibility Dr William H McDowell Director Jeffrey Merriam Lab Manager QA manager Mr Merriam supervises all activities in the lab His responsibilities include data processing and review QA review database management protocol development and upkeep training of new users instrument maintenance and repair and sample analysis Jody Potter Lab Technician Mr Potter s responsibilities include sample analysis logging of incoming samples sample preparation filtering when appropriate daily instrument inspection and minor maintenance All analyses are completed by Jody Potter or Jeffrey Merriam and all data from each sample analys
39. Ww Qov One must know both c X and amp 4 0 0 0 to determine the VSF from 1 17 If the same detector were used at positions shown for detectors 1 and 2 in Fig 1 4 following the method introduced by Kullenberg 1968 and if ly r j n we may substitute from 1 7 and determine the VSF from the two measured detector fluxes as pO y 9 z D A m y 9 A 7 r Anr 0 0 Y Qov 1 18 11 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Equation 1 18 could be used to measure the VSF if the source and detector are well collimated and there were no flux losses or FOV distortions associated with an instrument s optical assembly For most scattering meters however the averaged VSF estimate B A w is related to the true VSF D X w by a weighted integral 2n n BG wo BG wo A we c sin wd wao 1 19 00 where the weighting function W y 9 c accounts for instrumental factors including the divergence and uniformity of the source beam and detector angular response function the working volume geometry variations in attenuation of flux scattered to the detector from different volume elements and optical reflection and absorption losses in the system Practical methods for determining W A y Q c are described in Chapter 5 The VSF of ocean water is usually considered to be azimuthally symmetric about the transmission axis Therefore the VSF is usually reported as p X w
40. X x 5 4 Combining 5 2 and 5 3 and multiplying by the flux transmittance over the pathlength x a7 x leads to A AV 3 c AF uus x AQ AV AQ AV x TURN ed able ka a enol e I 2 65 AxAy x X ofi a where the solid angle subtended by the area AxAy at the detector is AQ AV x reference to 1 18 through 1 20 we may now write SOON stus xs 5 6 and by subsitution we obtain the incremental weighting function for each volume element AV x as W x c an AQ ara A 3 To obtain the desired weighting function W w c for each scattering angle y it is necessary to sum the weights for l x exp c Is x x 5 7 all volume elements at which the scattering angle falls within a discrete angular interval of y i e W wic EW s e 8 w w x Av 5 8 Ko E where A a A L vv x Av 2 2 5 9 0 Otherwise 80 90 100 110 120 130 140 150 160 170 180 Scattering Angle y degrees Figure 5 2 Examples of weighting functions W w calculated for VSF measurements by source detector pairs aligned at nominal scattering angles V V Y 100 125 150 Figs 5 1 and 1 4 68 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Once the weighting functions are computed for all scattering angles v falling within the beam and detector FOV intersection volume they are normalized suc
41. a particular instrument 6 Compute transmittances T X r and beam attenuation coefficients c X c X offsets relative to pure water using the appropriate combination of equations 2 9 2 10 or 2 11 with 1 6 for the instrument type and output data 7 Add pure water c X determined from Table 1 1 to c X c A to obtain the total beam attenuation coefficient c i 24 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Detailed procedures required to carry out each of the above steps for particular instrument are typically provided by the manufacturer WET Labs Inc for example provides both a User s Manual for it s ac 9 absorption and beam attenuation coefficient meter and a detailed ac 9 Protocol Manual Van Zee et al 2002 additional information from the latter document regarding absorption and beam attenuation measurements is outlined in Chapter 3 Many of the steps listed above apply also when a transmissometer is installed and operated on a ship as a component of an along track measurement system The lengthy plumbing path in such a system introduces intake to measurement lags of up to several minutes while a research vessel typically advances approximately one Km in 3 min Therefore accurate temporal and spatial co registration of e g surface water temperature chlorophyll a fluorescence and c X requires accurate determination of the flow rate and lag time between
42. a vacuum or positive pressure with a pressure differential equivalent to 180 200 mm of mercury Large filtration volumes are not required because of the increased sensitivity of the fluorescence measurement Inert membrane filters such as polyester filters may be used when size fraction filtration is required When this is done it is recommended to also filter a replicate sample through a GF F to determine the total concentration Summing the various size fractionated concentrations may not produce an accurate estimate of the total because of the potential for cell disruption during filtration There has been an ongoing discussion on filter types and retention efficiencies for natural samples Phinney amp Yentsch 1985 showed the inadequacy of GF F filters for retaining chlorophyll a in oligotrophic waters as did Dickson and Wheeler 1993 for samples from the North Pacific In response to Dickson and Wheeler 1993 Chavez et al 1995 compared samples collected in the Pacific Ocean using GF F and 0 2 um membrane filters with small filtered volumes 100 540 mL Their results for small volumes showed a very close agreement between the two filter types with GF F filters having only a slightly positive 5 bias Filtration volume can directly affect the retention efficiency for GF F filters Particles can be retained by filters through a variety of ways such as filter sieving filter adsorption electrostatic and van der Waals attractions Brock
43. a water volume s intake usually in a ship s sea chest passage through some debubbler apparatus and its arrival in the measurement cell of each instrument REFERENCES Barth H K Grisard K Holtsch R Reuter and U Stute 1997 Polycromatic transmissometer for in situ measurements of suspended particles and gelbstoff in water Appl Opt 36 30 7919 7928 Bogucki D J J A Domaradzki D Stramski and J R V Zaneveld 1998 Comparison of near forward light scattering on oceanic turbulence and particles Appl Opt 37 21 4669 4677 Duntley S Q 1963 Light in the sea J Opt Soc Amer 53 2 214 233 Gordon H R 1993 Sensitivity of radiative transfer to small angle scattering in the ocean Quantitative assessment Appl Opt 32 36 7505 7511 Gumprecht R O and C M Sliepcevich 1953 scattering of light by large spherical particles J Opt Soc Am 57 90 94 Jerlov N G 1957 A transparency meter for ocean water Tellus 9 229 233 Jones D and M S Wills 1956 The attenuation of light in sea and estuarine waters in relation to the concentration of suspended solid matter J Mar Biol Assoc U K 35 431 444 Kitchen J C J R V Zaneveld and H Pak 1982 Effect of particle size distribution and chlorophyll content on beam attenuation spectra Applied Optics 21 3913 3918 Lundgren B 1975 Measurements in the Baltic with a spectral transmittance meter Univ Copenhagen Inst Phys Oceanogr Rep
44. absorbance falls between 0 1 and 1 0 optical density units Clesceri et al 1998a The concentration of the standard is calculated as A0 4Q STD max bE lem 50901 3 1 where C is the concentration ug L of the chlorophyll a standard A A and A 750 are absorbances at Am and 750 nm b is the pathlength of cuvette cm and E is the specific absorption coefficient L g cm of chlorophyll a in 90 acetone For 90 acetone 87 67 Lg cm and for 100 acetone E 88 15 Lg Jeffrey et al 1997 Appendix E The peak wavelength A must be determined by inspection of the measured spectrum because its location may shift max ax cm cm when applied to the absorption measured at the peak wavelength A max due to interactions between the particular solvent and mixture of pigment compounds in each sample Standards stored under nitrogen in the dark at 20 C do not change appreciably over a one month period provided that they are stored in containers proven to prevent evaporation e g glass or Teflon bottles vials The stock chlorophyll a standard with its concentration measured on a spectrophotometer as described above should be diluted using calibrated gas tight syringes and Class A volumetric pipettes and flasks The minimum number of dilutions of the stock standard for calibrating a fluorometer depends on whether it is a digital model Turner Designs 10 AU 005 or it is an analog model with
45. algal biogenous matter A comparison between the Peru upwelling area and the Sargasso Sea Limnology and Oceanography 35 562 582 Butler W L 1962 Absorption of light by turbid materials Journal of the Optical Society of America 52 292 299 Carder K L S K Hawes K S Baker R C Smith and R G Steward 1989 Remote sensing algorithms for discriminating marine humus from chlorophyll Limnology and Oceanography 30 2 286 298 Carder K L R G Steward G R Harvey and P B Ortner 1989 Marine humic and fulvic acids Their effects on remote sensing of ocean chlorophyll Limnology and Oceanography 34 68 81 Chavez F P K R Buck R R Bidigare D M Karl D Hebel M Latasa L Campbell and J Newton 1995 On the chlorophyll a retention properties of glass fiber GF F filters Limnology and Oceanography 40 2 428 433 57 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Cleveland J S and A D Weidemann 1993 Quantifying absorption by aquatic particles A multiple scattering correction for glass fiber filters Limnology and Oceanography 38 1321 1327 D Sa E J R G Steward A Vodacek N V Blough and D Phinney 1999 Determining optical absorption of colored dissolved organic matter in seawater with a liquid capillary waveguide Limnology and Oceanography 44 1 142 1 148 Duntley S Q 1942 The optical properties of diffusing materials Journal of the Optical Society of Ame
46. and down to clear memory yes no Confirm that clear memory yes is in the window and then press ENTER This may not clear the memory b In the LI 1400 program under the remote menu click CLEAR DATABASE In the clear database window confirm that all is chosen then click OK 9 Under the remote menu click DISCONNECT Unplug the DataLogger from the computer turn it off make sure that there is no dirt or salt on it and put it away Data Processing l Open GBSWMP Light Profile Master Excel File and Save As GBSWMP Light Attenuation MMDDYY Cut and paste the raw light data into the appropriate rows columns in the GBSWMP Light Attenuation MMDDYY file making sure to separate each station as indicated by the station labels in column A Edit the depths Column E so that they reflect the correct depths at which each of the readings at a particular station was taken Runindividual regression analyses for each of the light profiles as follows using APL as an example Click on Tools Data Analysis Regression Select Input Y Range as the range of measured Depth m in Column E Select Input X Range as the range of calculated Quantum LN in Column H Select Output Range as the Yellow Shaded Block in Column J Select OK this should insert the regression statistics to the right of the data Note Do not include data for which the Quantum Raw Water data is 0 1 f SaveFi
47. are used to separate molecules rapidly in narrow bore 25 100 um fused silica capillaries based on differences in the charge to mass ratio of the analytes HPCE is an automated analytical separation system with reduced analysis times and on line quantification of compounds ideally suited to the separation and quantification of water soluble proteins like phycobilins from seawater HPCE methods for separation analyses of phycoerythrin from cyanobacterial cultures and natural samples are currently under development and may be included in a future revision to the ocean optics protocols C Kinkade Pers Comm 1 3 IN SITU CHLOROPHYLL a FLUORESCENCE Protocols for measuring and analyzing profiles of in situ fluorescence by chlorophyll a F z Table 3 1 in Chapter 3 Volume I are described in Chapter 3 When measured together with c z 660 profiles Chapter 2 Volume IV the structure of F z provides valuable guidance for selecting depths of water samples analyses of structure in K z A derived from radiometric profiles and various aspects of quality control analysis It is often useful to digitally record one minute averages of F z lat lon in water pumped from a near surface depth z 3 m to measure horizontal variability while underway steaming between stations especially in water masses where mesoscale and sub mesoscale variability is strong Section 4 2 Chapter 4 Vol I If supplemented by frequent Ocean Optics Protocols For Satellite
48. class will represent a macroalgal density e Data export The classification results will be exported to a vector format that is compliant with the GIS environment shapfile polygons A similar project was able to map macroalgae species in the Venice Lagoon Alberotanza et al 2006 No human subjects or research animals will be used for this study QAPP Addendum Hyperspectral Imagery for Great Bay NH RFA No 07309 July 11 2008 Figure 4 Area of hyperspectral imagery collection C Deliverables and Schedule 1 Summary Report due 9 30 08 The summary report will contain methods results maps and interpretation Specifically the report will contain the following items a Maps of eelgrass and nuisance macroalgae multiple Ulva species Gracilaria e g G tikvahiae epiphytic red algae e g ceramialean red algae and detached entangled QAPP Addendum Hyperspectral Imagery for Great Bay NH RFA No 07309 July 11 2008 Chaetomorpha populations in Great Bay Little Bay Piscataqua River and contiguous tidal tributaries in August 2007 and October 2007 b Calculations of the total cover of eelgrass and the different species of nuisance macroalgae in the NHEP eelgrass assessment zones e g Great Bay Little Bay Oyster River etc in August 2007 and October 2007 c Maps showing the distribution of nuisance macroalgae in August 2007 and October 2007 compared to the areas where eelgrass has been lost relative to
49. continuously measure water temperature salinity chlorophyll a and colored dissolved organic matter Grab samples will be analyzed for physico chemical parameters dissolved nutrients chlorophyll a total suspended solids CDOM and water clarity measured in the field A custom profiling package will measure the vertical distribution of the IOPs with a hyperspectral attenuation absorption meter and nine channel backscattering meter ACS and BB 9 WetLABS Inc Laboratory based measurements of absorption spectra for the optically important constituents from discrete water samples will help with the interpretation and validation of profiler measurements Mitchell et al 2000 The combination of in situ moored measurements flow through measurements and grab samples will be used to ground truth the aerial imagery After calibrating the hyperspectral imagery with the ground truth measurements the UNH Coastal Observing Center will analyze the imagery to map the distributions of chlorophyll a CDOM particulates and benthic light availability throughout the system Output B The combination of aerial imagery and Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 12 ground truth measurements has been proven to be effective at producing accurate maps of water quality parameters Sugumaran et al 2005 and submerged aquatic vegetation Dierssen et al 2003 For the third task of the study UNH Coastal Observing Center will a
50. et bete eim nere 15 3 2 SAMPLE ACQUISITION AND STORAGE 1 rere ennemi ennt 16 Filirationa y eirese na n ashlee 16 Sample Handling and Storage 2 i ht t e reet eade 17 Recordkeeping 1i ite teet E PU i e Hep p eb o D HB E DERE Ra EE DURS 17 33 LABORATORY METHODS FOR FLUOROMETRIC DETERMINATION OF CHL A AND PHEOPIGMENT CONCENTRATIONS GG G Gsvssseeeeeeerreeseese ere sn ere en erne een enne enn en nennen enne entren enne ener sneen 17 Fluorometer Calibrations eese esee eee terere ee hehe res ete tertie ene e esee EEEE neeesser eren 18 Solvent Preparation s oe e oda ee De aleae pee a een e eb t PM de 19 VD 71 7 15112 ERREICHTE ORENSE A SE os is sk bn EE 19 MOedsukemelt uo sec SEN M ON ENS EAM E SDN is Erst Mia A M REN fe ala 19 3 4 IN SITU CHLOROPHYLL A FLUORESCENCE PROFILES see 20 3 5 PROTOCOL STATUS AND FUTURE DIRECTIONS FOR RESEARCH 20 REEERENGCES rb t EE TR d E heec EM Mea patr M M Me e RAD 24 iii Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Chapter I Overview of Biogeochemical Measurements and Data Analysis in Ocean Color Research James L Mueller Center for Hydro Optics and Remote Sensing San Diego State University California 1 1 INTRODUCTION A total of 9 biogeochemical and bio optical observations are listed in Tables 3 1 and 3 2 Phytoplankton pigment concentrations determined by the HPLC method and
51. for radiometric and bio optical measurements from moored and drifting buoys Chapter 3 ocean color measurements from aircraft Chapter 4 and methods and results using LASER sources for stray light characterization and correction of the MOBY spectrographs Chapter 5 In the next few years it is likely that most new additions to the protocols will appear as chapters added to this volume Volume VI also collects appendices of useful information Appendix A is an updated version of Appendix A in Revision 3 summarizing characteristics of past present and future satellite ocean color missions Appendix B is the List of Acronyms used in the report and is an updated version of Appenix C in Revision 3 Similarly Appendix C the list of Frequently Used Symbols is an updated version of Appendix D from Rev 3 The SeaBASS file format information given in Appendix B of Revision 3 has been removed from the protocols and is promulgated separately by the SIMBIOS Project In the Revision 4 multi volume format of the ocean optics protocols Volumes I II and III are unlikely to require significant changes for several years The chapters of Volume IV may require near term revisions to reflect the rapidly evolving state of the art in measurements of inherent optical properties particularly concerning instruments and methods for measuring the Volume Scattering Function of seawater It is anticipated that new chapters will be also be added to Volumes V and VI in Revi
52. further isolated by multiple plastic bags or isolation in separate freezer space This is typically not an issue as we primarily deal with uncontaminated samples We do not pay special attention to holding time of samples as frozen samples are stable indefinitely Avanzino and Kennedy 1993 However we do keep track of the date samples arrive at the WQAL and can report holding times if necessary After samples are analyzed they are returned to the project s manager for safe keeping or they are held for a period of time at the WQAL to allow necessary review and analysis of the data by the interested parties not from a laboratory QC sense but from a project specific viewpoint Once the data is analyzed by the project s manager s the samples are returned or disposed of based on the preference of the project s manager Chain of custody is only implemented when required by a specific project This is usually only when it s required by the funding agency or if the samples could be the basis for an enforcement action Page E 3 Samples that arrive unfrozen with cracked bottles caps or with loose caps are noted in the database and are not analyzed These samples are disposed of to prevent accidental analysis The sample originator is notified generally via e mail of which samples were removed from the sample analysis stream Similarly if while in the possession of the WQAL a sample bottle is broken or improperly stored e g not frozen
53. method e Prepare NaCIO solution e For freshwater samples 0 1 active chlorine in purified water e g Milli Q water e For marine samples 0 1 active chlorine in purified water containing 60 gl Na5SO to match osmotic pressure of sample cells e The volume of 0 1 active chlorine solution needed to bleach pigments from a filter sample has been empirically shown to be approximately 30D 440 mL e Place the sample particle side up on the filtration system closed valves e Gently pour the solution down the sides of the filter funnel e Let the solution act for 5 min to 10 min adding solution as necessary to compensate for loss through the filter e Cover the filtration cup with aluminum foil to prevent contamination during bleaching e Rinse the sample by gentle filtration of 50 mL of water either fresh water or FSW depending on sample source e Complete bleaching of the pigments is indicated by the absence of a 675 nm peak together with a concave shape near 440 nm in the OD 4 spectrum of the bleached filter If evidence of residual pigment absorption persists repeat the NaClO oxidation treatment as indicated above Spectrophotometric Measurement of De pigmented Optical Density Spectra e The OD 4 spectrum of the de pigmented samples should be measured in the spectrophotometer as described above for OD A e Note that methanol extracted sample and blank filters will tend to dry out quickly if the methanol is not
54. metric tons QAPP Addendum Hyperspectral Imagery for Great Bay NH RFA No 07309 July 11 2008 B Project Description Who The project will be completed by the NHEP researchers at the University of New Hampshire UNH and the NH Department of Environmental Services DES The NHEP is part of EPA s National Estuary Program and is coordinating the nutrient criteria development process through its Technical Advisory Committee The NHEP s latest State of the Estuaries report highlighted declines in eelgrass beds and increases in nitrogen concentrations in Great Bay The NHEP Director will manage the funds and will assign staff and committee meeting time to this project The NHEP will coordinate with UNH researchers from the Center for Coastal and Ocean Mapping CCOM Coastal Ocean Observing Center COOC and the Jackson Estuarine Laboratory JEL to conduct the technical tasks of the project The results of the project will be integrated into the nutrient criteria development process and ultimately provided to DES which is responsible for developing nutrient criteria in NH s estuaries The project team will be Jennifer Hunter NHEP Project grant manager Shachak Peeri Ph D UNH CCOM Analysis of hyper spectral imagery Ru Morrison Ph D UNH COOC Optical properties measurements Arthur Mathieson Ph D UNH JEL Macroalgae species and distribution Fred Short Ph D UNH JEL Eelgrass distrib
55. of profiler measurements Mitchell et al 2000 On each sampling date samples for each parameter will be collected during 21 station visits Table 8 Field replicate replicate samples will be collected at station GRBGB and GRBAP by the UNH Coastal Observing Center Table 7 Sampling Station Summary for Activity 4 Station ID Description ODD FEER GRBGB Central Great Bay 43 0722 70 8694 GRBSQ Mouth of Squamscott River 43 0417 70 9222 GRBLR Lamprey River 43 0800 70 9344 GRBOR Oyster River 43 1340 70 9110 GRBAP Great Bay at Adams Point 43 0919 70 8636 GRBCL Squamscott River at Chapman s Landing 43 0394 70 9283 GRBSF Salmon Falls River 43 2142 70 8172 NH 0049A Oyster River 43 1270 70 8805 NH 0052A iBellamy River 43 1340 70 8470 NH 0057A Upper Piscataqua River 43 1589 70 8302 NH 0058A Cocheco River 43 1950 70 8580 NH 0062A Salmon Falls River 43 1970 70 8210 GB4A Great Bay in channel leading to the Squamscott River 43 0695 70 8819 GB16 Great Bay in channel leading to the Winnicut River 43 0600 70 8559 NH00 0035A Great Bay in northwestern eelgrass beds 43 0786 70 8831 NH01 0026A Great Bay in southern eelgrass beds 43 0620 70 8890 NH00 0027B Great Bay in southeastern eelgrass beds 43 0639 70 8590 NH 0070A Great Bay in northeastern eelgrass beds 43 0769 70 8653 NH04 0245C Upper Little Bay 43 10894 70 85962 NH04 0235C Entrance to Great Bay near
56. of pure water is dependent on water temperature T C Pegau and Zaneveld 1993 and the absorption coefficient of seawater is also dependent on its salinity S PSU Pegau et al 1997 These variations affect the measured coefficients of absorption a X and attenuation c in the following ways 35 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV 1 The difference T 7 between the water temperature T during a measurement at sea and the temperature 7 of the pure water reference standard at the time the instrument was calibrated changes the water absorption baseline value a A This change affects a A and c A equally because scattering by pure water is not significantly temperature dependent 2 The absorption of seawater varies with salinity S and of course S 20 PSU for the pure water reference standard used to calibrate the ac 9 This additional shift in the water absorption baseline also affects a X and c 4 equally 3 The salinity dependent variations in the refractive index of seawater affect the transmission of the optical windows and the effects are different for the windows of the absorption and beam transmission sides of the instrument This effect may also vary slightly between instruments Van Zee et al 2002 0a X Oc 4 Therefore separate coefficients al and el os os combine salinity dependent instrument characteristics and water absorption
57. of water in the red and near infrared portions of the spectrum Limnol Oceanogr 38 1 188 192 Pegau W S D Gray and J R V Zaneveld 1997 Absorption and attenuation of visible and near infrared light in water dependence on temperature and salinity Appl Opt 36 24 6035 6046 Twardowski M S J M Sullivan P L Donaghay and J R V Zaneveld 1999 Microscale quantification of the absorption by dissolved and particulate material in coastal waters with an ac 9 J Atmos Oceanic Tech 16 691 707 Van Zee H D Hankins and C deLespinasse 2002 ac 9 Protocol Document Revision F WET Labs Inc Philomath OR 41pp Zaneveld J R V J C Kitchen A Bricaud and C Moore 1992 Analysis of in situ spectral absorption meter data Ocean Optics XI G D Gilbert Ed SPIE 1750 187 200 Zaneveld J R V J C Kitchen and C Moore 1994 The scattering error correction of reflecting tube absorption meters Ocean Optics XII Proc SPIE 2258 44 55 38 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Chapter 4 Determination of spectral absorption coefficients of particles dissolved material and phytoplankton for discrete water samples B Greg Mitchell Mati Kahru John Wieland and Malgorzata Stramska Scripps Institution of Oceanography University of California San Diego California 4 1 INTRODUCTION The spectral absorption coefficient is one of the inherent optical properties
58. overestimate chlorophyll a concentrations because of the overlap of the absorption and fluorescence bands of co occurring chlorophylls b and c chlorophyll degradation products and accessory pigments Trees et al 1985 Smith et al 1987 Hoepffner and Sathyendranath 1992 Bianchi et al 1995 Tester et al 1995 The application of HPLC to phytoplankton pigment analysis has lowered the uncertainty for measuring chlorophyll a and pheopigments as well as the accessory pigments since compounds are physically separated and individually quantified HPLC has provided oceanographers with a powerful tool for studying the processes affecting the phytoplankton pigment pool Pigment distribution is useful for quantitative assessment of phytoplankton community composition phytoplankton growth rate and zooplankton grazing activity For low uncertainty determinations of chlorophylls a 5 and c chlorophyll degradation products and carotenoid pigments HPLC techniques are recommended It should be noted however that the reverse phase Ci HPLC method recommended by the Scientific Committee on Oceanographic Research SCOR Wright et al 1991 is not capable of separating monovinyl chlorophyll a from divinyl chlorophyll a nor monovinyl chlorophyll b from divinyl chlorophyll 5 This method therefore only provides concentration estimates for these co eluting pigment pairs methods for optically resolving monovinyl chlorophyll a and divinyl chlorophyll a are given
59. proved to be a source of confusion and debate within the ocean color community Furthermore the JGOFS protocols UNESCO 1994 specified that pigment concentrations should be reported in units of pigment mass per mass of seawater ng Kg rather than in units of pigment mass per volume of seawater either ug L or mg m The use of volumetric concentrations is critical because radiative transfer in the ocean and absorption by pigments are volumetric processes One could use the mass concentration values preferred by JGOFS but it would be essential to supplement them with densities computed from CTD data and make the conversion to volumetric concentrations Therefore a complete set of protocols for HPLC measurement of phytoplankton pigment concentrations was added as Chapter 13 of Revision 2 0 to the Ocean Optics Protocols Fargion and Mueller 2000 updated as Chapter 16 of Revision 3 Mueller and Fargion 2002 and updated here again as Chapter 2 of the present volume Chapter 2 provides complete protocols for obtaining water samples filtering them freezing the filtered samples in liquid nitrogen sample handling and storage extraction HPLC calibrations and measurements data analysis and quality control A new HPLC solvent program in Chapter 2 replaces that specified in the previous version of the protocols Bidegare et al 2002 Fluorometric Measurement of Chlorophyll a Concentration Chapter 3 For reasons similar to those described above
60. range 400 700 nm is reported in Mitchell et al 2000 for that specific model The Hewlett Packard data is reported only for wavelengths greater than 400 nm because the instrument performs poorly at short wavelengths with the glass fiber filter method If a user chooses such optical geometry for the determination of particle absorption they should carefully assess the potential issues illustrated in Figure 4 1 We recommend that the user compare several spectrophotometers for raw optical density of properly hydrated samples relative to blank filters and ensure the unit they use does not deviate from the typical result of most systems for which amplifications factors B have been determined Table 4 1 Alternatively one must determine the pathlength amplification for the 54 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV instrument of choice a laborious and unnecessary procedure if a spectrophotometer is selected that does not cause the bias illustrated in Figure 4 1 Absorption spectra for particles transferred to glass slides An alternative method developed by Allali et al 1995 to estimate absorption coefficients of cultures and seawater samples is to freeze transfer the particles to transparent microscope slides following the protocols of Hewes and Holm Hansen 1983 The investigator must have an integrating sphere or equivalent scattered transmission accessory to implement this method This proc
61. tasses senses sense ene 7 AG Project Task Description m 9 AT Quality Objectives and Criteria eee essens sinet s sns Esser suse tassa se taste seen stes sons stan 14 AS Special Training Certification aeree e eee eee eee eese eene en sete seen atta stt sensns sn netus esu senses ease ease tosta sets sensns se 15 A9 Documents and Records ae 16 B1 Sampling Process Design 17 B2 Sampling Methods 22 B2 Sampling Methods udseender serende LEE eee drer eres rides beses rese Ende es 22 B3 Sample Handling and Custody screeningen eee essen setenta seta seta stis sens sins suns enne suse es ss reen dere 24 hALPVDLBUDIDn 25 B5 Quality Control P M 25 B6 Instrument Equipment Testing Inspection Maintenance ccssccssssssssccsscsssscsessssssssssesessessesessssssseees 27 B7 Instrument Equipment Calibration and Frequency sscssccssccssessssssesssscsssssssesesecsssessssssssssesesesessesssees 29 B8 Inspection Acceptance Requirements for Supplies and Consumables ssssscssscssssecscscesseessseesseeeeeee 29 B9 Non direct Measurements m ser osso
62. that influence the reflectance of aquatic systems The absorption coefficient a 4 in m at any point within a natural water body can be described in terms of the additive contribution of its components as a A a A a A a A m 4 1 where a A a A and a A are the spectral absorption coefficients of water particles and soluble components respectively The spectral absorption coefficients of pure water adopted for the protocols are given in Table 1 1 Ch 1 and combine the results of Pope and Fry 1997 Sogandares and Fry 1997 Fry 2000 and Kou et al 1993 The depth z dependence of the absorption coefficients is omitted for brevity The particle absorption coefficient may be further decomposed as a A a A a A m 4 2 where a 4 and 4 are the spectral absorption coefficients of phytoplankton and de pigmented particles respectively Laboratory methods are described for determining operational estimates of these fractions It is conceptually possible to further separate a A into absorption fractions due to de pigmented organic and inorganic particles but at present there are no well established protocols for separately determining the absorption coefficient for inorganic particles To interpret aquatic spectral reflectance and better understand photochemical and photobiological processes in natural waters it is essential to quantify the contributions of the individual constituents to t
63. the western Pacific However below 500 nm the values for ACE Asia are near 1 0 and below 400 nm they exceed 1 0 For AMLR values approach 1 0 for wavelengths less than 350 nm The ratio of a A a 4 where a a a a is also plotted in Figure 4 4 filled symbols The trend clearly illustrates that the soluble component dominates at short wavelength There are several hypotheses that should be considered to understand the overestimates of 4 A below 400 nm These could include underestimate of K 2 4 or overestimates of any of the absorption components A combination of these factors may prevail 56 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV The filter radiometer in the profiler has good out of band blocking but the spectrum of surface irradiance is rapidly changing in the region 350 nm and this may cause a red shift in the effective band center of the channels with an associated underestimate of K z 4 There may be small particles or colloids that pass the 0 2 um filters causing a spectrally dependent scattering error Aas 2000 The particle absorption we estimate is based on Mitchell 1990 which results in higher estimates compared to some other published methods Table 1 Also there has not been adequate attention paid to determination of the pathlength amplification factor for the region below 400 nm It is also possible that the values for pure water absorptio
64. then immersed in a test tank containing the pure water standard Care must be taken to prevent bubbles from collecting on the instrument s optical windows It is ordinarily not practical to carry out this calibration procedure at sea 2 To calibrate an enclosed path instrument a volume of the pure water standard is pumped through the flow through measurement cell as described in detail in Chapter 3 for the ac 9 as an example Procedures to assure bubbles do not form within or be introduced into the flow through measurement cell Ch 3 must be followed carefully This pure water calibration procedure can be carried out at sea and it is recommended to do so daily whenever possible In either case after allowing suitable time for the instrument to warm up the instrument signal outputs in response to flux transmitted in the pure water standard and dark ambient background V X and V5 and if appropriate also V and V A are recorded over a several minute sampling period and averaged For pure water the forward scattering is sufficiently small that the acceptance angle has little effect on the calibration From equation 1 7 Ch 1 the transmittance of the pure water standard is 7 A Hh e U Foran instrument with a source reference detector we substitute from 2 4 to write Vay A Ve X c 0 T un gt re i s A Vow 2 or for an instrument with a constant source output we substitute from
65. thoroughly rinsed from the filters prior to spectrophotometric measurements e NaClO oxidized sample and reference filters must be thoroughly rinsed with FSW or fresh water for inland water samples to extend the spectral range below 400 nm 4 5 SOLUBLE ABSORPTION SAMPLE PREPARATION AND ANALYSIS The measurement methods described in this section are used to determine a 4 the spectral absorption coefficient spectrum of gelbstoff often referred to as dissolved organic matter CDOM Water samples are collected and particulate material is removed by filtration The absorption of the filtrate is measured relative to purified water using a spectrophotometer All equipment utilized to prepare soluble absorption samples must minimize contamination by organic or otherwise colored material Samples must be protected from photo degradation during preparation and measurements Plastic or glass filtration apparatus may be used provided that the units are equipped with mesh filter supports made either of stainless steel or plastic and not with ground glass frits Glass frits tend to become clogged over time and may cause uneven distribution on the filter reduce the rate of filtration and may contaminate the sample filtrate 47 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Membrane filters with 0 2 um pore size e g Nuclepore polycarbonate filters are recommended for this procedure The membrane
66. time and doing multiple profiles or by connecting a single filter and pump to both sides of the ac 9 When connecting to both sides using a single filter you are reducing an already low flow which makes it more difficult to remove bubbles from the system but it requires fewer casts to complete an instrument test A degassing Y may be used on the outflow side of the combined plumbing arrangement to facilitate bubble removal 37 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV The noise level in the measurements should be gt 0 005 m at all channels Measurements with noise exceeding this criterion indicate instruments with large measurement noise a rough check of quality of the calibration and pressure or temperature dependencies that may exist Assuming that there is no measurable scattering by particles that pass through the filter then the filtered a and c measurements should be equal and departures 70 005 m are symptoms of drift in pure water calibration offsets or calibration errors due to optical impurity of the reference water Comparisons of profiles between successive down and up casts may help in separating suspected temperature effects from pressure dependencies Evidence of hysteresis in different up and down profile responses to gradient features is symptomatic of a problem with an instrument s internal temperature compensation Care must be taken in this interpretation however beca
67. to the data from the entire 5 or more concentrations and a single Fp factor is determined for the instrument With a mechanical fluorometer the regression is applied to the data from the 3 or more concentrations of the standard and a separate Fp factor is determined for each door setting As a means of monitoring an instrument s performance Fg factors from successive calibrations should be charted as functions of time Clesceri et al 1998b These quality control graphs should be retained with the data analysis logbooks to document the quality of each data set for which that fluorometer is used Solvent Preparation It is recommended that 90 acetone by volume be used to extract pigments for the fluorometric analysis Richard and Thompson 1952 were the first to propose 90 acetone as a solvent to extract pigments from marine phytoplankton Their results indicated improved extraction efficiencies and also showed that the procedure minimized the activity of the naturally occurring chlorophyllase enzyme which degrades the pigment With a graduated cylinder make up 90 acetone by first pouring in distilled water followed by 100 acetone Using volumetric pipettes or auto pipettes accurately measure 8 mL to 10 mL of 90 acetone and place it in a centrifuge tube Record this volume as Vgxr A number of such tubes containing acetone are then stored in a freezer and individually removed as filter samples are collected Pre chilling the solv
68. variations Pegau et al 1997 Van Zee et al 2002 and must be applied separately to correct to a and c X The temperature and salinity corrections are applied to measured absorption as 8a X 0a X TS A Y T T S 3 12 a 0 a 2 Pr 7 55 G2 and to measured beam attenuation as Oa X 6c X TS A x d T T S 3 13 cB A 0 r r EE 63 The temperature dependence coefficients are listed in Table 1 1 Pegau and Zaneveld 1993 Pegau et al 1997 and the salinity dependence coefficients are provided by the manufacturer Van Zee et al 2002 Temperature and salinity must be measured using a CTD concurrently with an ac 9 profile to apply these corrections using 3 12 and 3 13 Therefore it is strongly recommended that the ac 9 be mounted on the same profiling package as an accurate CTD and from this perspective the priority of CTD measurements is higher than is implied in Table 3 1 Vol I Chapter 3 These corrections become directly significant only at red and near infrared wavelengths see Table 1 1 However the methods of the next section depend on accurate values of a Aym and c Ayr at a near infrared reference wavelength Anr 2715 nm to determine scattering corrections at all wavelengths Moreover the temperature correction in 3 12 must also be applied to laboratory spectrophotometric measurements of absorption by CDOM Chapter 4 if the temperatures of the pure water reference blank and filtere
69. volumes 100 mL to 540 mL Their results showed a very close agreement between the two filter types with GF F filters having only a slightly positive 5 bias Filtration volume can directly affect the retention efficiency for GF F filters Particles can be retained by filters through a variety of ways such as filter sieving filter adsorption electrostatic and van der Waals attractions Brock 1983 When water flows through the pores of a Nuclepore filter streamlines are formed that can align small particles longitudinally with the result that cell diameter becomes important with these filters It is known on the other hand that Whatman GF F filters can retain particles much smaller than their rated pore size Generally at small volumes 100 mL to 300 mL filter adsorption and electrostatic and van der Waals attractions are important whereas at larger volumes 72 000 mL sieving dominates This has been tested in oligotrophic waters off Hawaii in which small 500 mL and large volumes gt 2 L to 4 L retained similar amounts of chlorophyll a on the two types of filters whereas for intermediate sample volumes the GF F filters showed lower concentrations During several cruises off the Hawaiian Islands differences in retention efficiencies were found for GF F filters to be a function of sample volume large sample volumes 2 L and 4 L retained about 18 more chlorophyll a than replicate 1 L samples Filtration volumes are usually limited
70. w The first integral on the right hand side of 3 2 represents flux scattered at angles less than the critical over the optical path and the second integral represents flux reaching the detector following scattering by angles greater than the critical angle In either case the pathlength to the detector from a scattering interaction at or distance r is and both types of scattered reflected paths are attenuated by absorption over this elongated cosy path The second term also is reduced by incomplete reflectance in N r r v 21 interactions with the reflective tube The measured absorption coefficient is therefore greater than the true absorption coefficient since NE DEAE i za S683 om X 0 r 0 T T and the two may be related as a a 2n W y B y sinydy 3 3 where the weighting coefficients W w account for the absorption and wall reflection losses in the two integral terms of 3 2 and for the exclusion of backscattering in the measured flux In other words the weighting coefficient W wy may be interpreted as the fraction of light that is scattered at angle w that does not reach the absorption detector it may take values from 0 indicating all light scattered at that angle reaches the detector to 1 indicating that none of the light reaches the detector The uncertainty of absorption coefficients determined from measurements with a reflective tube instrument is largely determined by the unc
71. water temperature provides the basis for any temperature compensation adjustments that may be required 2 Apply lag corrections to account for the time interval between when water enters the intake port and when it enters the beam attenuation measurement optical path in a flow through transmissometer 3 Subtract the depth offset between the pressure transducer used to measure package depth and either a the intake port of a flow through transmissometer or b the midpoint of the optical path in an open path transmissometer 4 Field calibration adjustments should be applied by the methods specified by the manufacturer of a particular instrument In many cases this will involve entering the changes in an instrument calibration file used by the computer software that implements and applies 2 9 or 2 10 to calibrate the data a Pure water calibration results are the preferred source of these adjustments for flow through instruments b Air calibration for tracking drift corrections should be applied using only data from calibrations carried out under dry laboratory conditions and showing insignificant variations between replicated calibrations When the manufacturer represents the calibration coefficients in terms of a reference signal to be applied using 2 11 the corrected air calibration factor is computed using 2 13 5 Instrument Internal Temperature Compensation factors should be applied in the manner specified by the manufacturer of
72. where a L a v Bv Y a 1 a r B w a X andy 9 dark x Lay 1 mon K By y Multiplying both sides of 3 9 by X the transpose of the matrix X we obtain X a X x 7 leading to the normalized least squares solution for the three coefficients as 7 X x x 3 10 where Xx is the inverse of the 3 x 3 matrix X x Having thus described the conceptual basis for determining the absorption coefficient from measurements with a HOBILabs a beta instrument or a similar instrument time constraints on the publication schedule for this document preclude exploring more detailed protocols for its calibration and use or the uncertainty budgets associated with this approach These considerations must be deferred to a possible future revision to this protocol volume 3 2 CHARACTERIZATION and CALIBRATION OF REFLECTIVE TUBE SPECTRAL ABSORPTION METERS Perhaps the best known version of a reflective tube absorption meter is the ac 9 manufactured by WET Labs Inc This instrument measures both the spectral beam attenuation coefficient c X in an enclosed flow through non reflective optical path and the spectral volume absorption coefficient a A using parallel enclosed flow through reflective tube optical paths one of which the absorption side 1s a reflective tube Fig 3 1 Many aspects of the characterization calibration field measurements and data analysis protocols relating to this type of instru
73. www seabird com products spec sheets 37sipdata htm CDOM is measured using a WET Labs ECO FLCDS open path fluorometer http www wetlabs com products eflcombo fl htm Chlorophyll a is measured using a WET Labs ECO FLNTUS open path fluorometer http www wetlabs com products eflcombo fl htm Turbidity is measured using a WET Labs ECO FLNTUS open path fluorometer http www wetlabs com products eflcombo fl htm Nitrate is measured using a Satlantic ISUS http www satlantic com details asp ID 1 1 amp CategoryID 2 amp SubCategoryID 0 Light levels are measured at the surface and at 1 and 2 m below the surface using Satlantic HyOCR sensors From these measurements light attenuation can be calculated http www satlantic com details asp ID 9 amp CategoryID 1 amp SubCategoryID 0 Sampling Methods for Activity 2 Hyperspectral imagery collection SpecTIR proposes an airborne data collection with the VNIR sensor with a spatial resolution of 2 5 meters with 30 sidelap for the area of interest The imagery will have a nominal spectral resolution of 10nm or 64 spectral channels from approximately 430 nm to 1000 nm The delivered product will consist of calibrated radiance and geographic lookup tables with navigation Navigation will be performed with high speed airborne DGPS integrated with a laser ring gyro Specifications for the SpecTIR VNIR sensor are listed in Appendix B The planned flight lines are shown in Figu
74. 0 Figure 6 Area for hyperspectral imagery collection shown in red ssssssssss 11 Figure 7 Sampling Stations for Activity 74 enne 20 Figure 8 Flight lines for hyperspectral imagery collect esee nnne 24 Great Bay Nutrient Criteria Study QAPP A3 Distribution List Draft No 1 August 24 2007 Page 4 Table 1 shows the individuals and their respective agency affiliations that will receive the approved QAPP the QAPP revisions and any amendments Table 1 QAPP Distribution List QAPP Recipient toe Telephone number Name Project Role Organization and Email address i i Ru morrison unh edu Ru Morrison Project Manager UNH 603 862 4354 Tom gregory unh edu Tom Gregory UNH Research Staff UNH 603 862 4397 mnovak cisunix unh edu Mike Novak UNH Research Staff UNH 603 862 1348 WBernard SpecTIR com William Bernard SpecTIR Program Manager SpecTIR 410 820 5591 775 329 6660 775 722 7701 cell AJ Markow SpecTIR Project Manager SpecTIR aimarkow SpecTIR hostpilot com i Oweatherbee spectir com Oliver Weatherbee SpecTIR Project Staff SpecTIR 410 820 5592 Chris Joyce SpecTIR Project Staff SpecTIR 702 526 1322 cell 1 Jeff merriam gjunh edu Jeff Merriam Laboratory QA Officer UNH 603 862 2341 i Jennifer hunter unh edu Jennifer Hunter NHEP Program Manager NHEP 603
75. 0 2 um pore size The use of Nylon filters is not recommended as they may bind certain hydrophobic pigments Apparatus The HPLC system consists of solvent pumps sample injector guard and analytical columns absorption and fluorescence detector and a computer A temperature controlled autosampler is optional but highly recommended to chill the samples chilled prior to injection and to reduce uncertainties during sample preparation and injection A variety of companies manufacture HPLC systems e g Agilent Technologies Beckman ThermoQuest Waters Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Associates For a review of hardware and software requirements for measuring chlorophylls and their degradation products as well as carotenoids see Jeffrey et al 1997 HPLC Eluants and Gradient Programs There are several currently recognized HPLC methods for separating chlorophylls chlorophyll derivatives and taxonomically important carotenoids The Cig method of Wright et al 1991 is recommended by SCOR and separates more than 50 chlorophylls carotenoids and their derivatives using a ternary gradient system This HPLC method is described in detail below The separation of the various pigments requires about 30 minutes Prior to injection 1000 uL of the aqueous acetone pigment extract is diluted with 300 uL HPLC grade water to increase the affinity of pigments for the column during the loading step
76. 03 5507 Mie G 1908 Beitrage zur Optic truber Medien speziell kolloidalen Metallosungen Ann Phys 25 377 442 Maffione R A and D R Dana 1997 Instruments and methods for measuring the backward scattering coefficient of ocean waters Appl Opt 36 6057 6067 Mobley C D L K Sundman and E Boss 2002 Phase function effects on oceanic light fields Appl Opt 41 6 1035 1050 Oishi T 1990 Significant relation between the backward scattering coefficient of sea water and the scatterance at 120 degrees Appl Opt 29 31 4658 4665 Petzold T J 1972 Volume scattering functions for selected ocean waters Contract No N62269 71 C 0676 UCSD SIO Ref 72 78 75 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Stramska M D Stramski B G Mitchell and C D Mobley 2000 Estimation of the absorption and backscattering coefficients from in water radiometric measurements Limnol Oceanogr 45 628 641 Zaneveld J R V 1982 Remotely sensed reflectance and is dependence on vertical structure a theoretical derivation Appl Opt 21 22 4146 4150 76 Appendix D NASA TM 2003 21621 Rev Vol V Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume V Biogeochemical and Bio Optical Measurements and Data Analysis Protocols James L Mueller Giulietta S Fargion and Charles R McClain Editors J L Mueller R R Bidigare C Trees J
77. 0x smaller than the scale in 3A C Estimates of sample optical density spectra after subtraction of the null value average of raw values 590 600nm and after subtraction of a global blank according to Equation 4 3 Temperature effects are evident 650 800 nm in the individual spectra 63 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV 1 5 0 5 0 0 300 400 500 600 700 Wavelength nm Figure 4 4 Median values for pa the mean cosine for downwelling irradiance open symbols see text for definition determined for the upper mixed layer Values are plotted at each wavelength of the PRR 800 reflectance radiometer deployed during 2001 cruises to the Southern Ocean AMLR and the Western Pacific ACE Asia The ratio of a X a for the same data set are shown in solid symbols and plotted to the same scale For both sets of spectra AMLR data are circles and ACE Asia data are triangles 64 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Chapter 5 Volume Scattering Function and Backscattering Coefficients Instruments Characterization Field Measurements and Data Analysis Protocols J Ronald V Zaneveld Scott Pegau and James L Mueller College of Oceanographic and Atmospheric Sciences Oregon State University Corvallis Center for Hydro Optics and Remote Sensing San Diego State University California 5 1 INTRODUCTION
78. 2 5 to write 2 7 21 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Ty A r Pow 4 Fatt QJ 2 8 as appropriate By straightforward combinations of 1 6 2 4 and 2 7 it is easy to show that for a transmissometer with a source reference detector Vra 4 Ve A Po 4 V2 2 Vow 4 Y 2 Va 4 Vee pue wal at T srp Tw A r 2 9 V VE A V Vs X e e A Lin e 0 a Yo af dark 2 Do 09 2709 Pa 02 7 QJ or combining 1 6 2 5 and 2 8 for a transmissometer with a constant source output V x sp r x TOAST A5 Y A and Pow AJ Yo 2 2 10 Yow Vow 2 JJ The essential calibration factors to be reported therefore are the detector response and ambient dark offset in pure n AORA water Vj X and V3 X and if a source reference detector is used also its response and ambient offset Vaw X and V R A The total beam attenuation coefficient c X may be easily determined by adding c from Table 1 1 Ch 1 to the difference calculated with equation 2 9 or 2 10 An alternative approach to determining the total beam attenuation coefficient directly from the measured voltage response is to determine from the pure water calibration a calculated offset reference voltage V and dark offset V 2 such that the total transmittance may be calculated dire
79. 3 CHARACTERIZATION AND CALIBRATION OF A VSF SENSOR USING A REFLECTING PLAQUE T M 73 5 4 METHODS FOR THE DETERMINATION OF THE BACKSCATTERING COEFFICIENT FROM VSF MEASUREMENTS AT ONE OR MORE SCATTERING ANGLES esee 74 Determination of b X from VSF Measurements at Three or More Angles sss 74 Determination of b X from VSF Measurements at Only One Angle sss 74 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Chapter I Inherent Optical Property Measurement Concepts Physical Principles and Instruments Scott Pegau J Ronald V Zaneveld and James L Mueller College of Oceanographic and Atmospheric Sciences Oregon State University Corvallis Center for Hydro Optics and Remote Sensing San Diego State University California 1 1 INTRODUCTION The Inherent Optical Properties IOP of a medium which describe absorption and scattering interactions that modify a vector light field propagating through it are defined in Vol I Ch 2 Sect 2 4 of this protocol document Geometric conventions and notation underlying definitions of and relationships between IOP and radiative transfer in the medium are described in Section 2 2 of Vol I Ch 2 The roles of the IOP in radiative transfer descriptions and models of light propagation in the sea are also introduced in Vol I Ch 2 and appear elsewhere in
80. 56 25 32 Bidigare R R 1991 Analysis of algal chlorophylls and carotenoids In Marine Particles Analysis and Characterization D C Hurd and D W Spencer Eds Am Geophys Union Washington DC 119 123 12 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Bidigare R R and M E Ondrusek 1996 Spatial and temporal variability of phytoplankton pigment distributions in the central equatorial Pacific Ocean Deep Sea Res II 43 809 833 Brock T D 1983 Membrane filtration a user s guide and reference manual Science Tech Madison WI 381 pp Chavez F K R Buck R R Bidigare D M Karl D Hebel M Latasa L Campbell and J Newton 1995 On the chlorophyll a retention properties of glass fiber GF F filters Limnol Oceanogr 40 428 433 Clesceri L S A E Greenberg and A D Eaton editors 1998 Part 10000 Biological Examination Section 1020 B in Standard Methods for the Examination of Water and Wastewater 20 ed Balitmore MD American Public Health Association American Water Works Association Water Environment Federation Dickson M L and P A Wheller 1993 Chlorophyll a concentrations in the North Pacific Does a latitudinal gradient exist Limnol Oceanogr 38 1813 1818 Gibb S W R G Barlow D G Cummings N W Rees C C Trees P Holligan and D Suggett 2000 Surface phytoplankton pigment distribution in the Atlantic an assessment of basin scale variab
81. 862 3948 NHEP ptrowbridge des state nh us 603 Phil Trowbridge NHEP QA Project Officer NHDES 271 8872 603 340 5220 cell Clark arthur epa gov Arthur Clark EPA QA Officer EPA 617 918 8374 Basile alfred epa gov Al Basile EPA Project Officer EPA 617 918 1599 M Jonathan pennock unh edu Jonathan Pennock Water Quality Field Sampling UNH 603 862 2921 shj cisunix unh edu Steve Jones Water Quality Field Sampling UNH 603 862 5124 Colin Edwards Water Quality Field Sampling UNH 603 862 5124 i re Jeremy LeClair unh edu Jeremy LeClair Water Quality Field Sampling UNH 603 862 5136 cnash des state nh us Chris Nash Water Quality Field Sampling NHDES 603 559 1509 603 568 6741 cell Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 5 A4 Project Task Organization The project will be completed by a partnership of the University of New Hampshire and the New Hampshire Estuaries Project with the assistance of subcontractors using funds from the US Environmental Protection Agency The University of New Hampshire will manage the field data collection and data analysis tasks for this project Specifically Ru Morrison of the UNH Coastal Observing Center will be the overall Project Manager and will oversee all data collection and data analysis activities The UNH Coastal Observing Center an IOOS pilot project funded through the NOAA Coastal Services Center has deployed an instr
82. 99 confidence that the analyte concentration is greater than zero L 8 o 5 Hn B 3 E S s xe E B z S m 22 O08 pE 3 mes E eIBegSEUBo E g a o gt c5 o g O SZ oO 5 TOS B 7 amp X E o 2 Hy a os E a E 3 gc 2 a B3 SAR e EST ko Hee Ka SiO2 mg 0 40 Linear 4 7 0 3 3 5 15 0 92 8 15 0 SiO2 L PO ug P L 0 200 Linear 4 7 2 3 1 5 7 8 15 0 95 5 15 0 93 7 15 0 NH ug N L 0 200 Linear 4 7 2 3 1 5 7 1 15 0 103 9 15 0 95 0 15 0 NO FIA mg N L 0 10 Linear 4 7 0 05 0 003 4 6 15 0 100 9 15 0 102 6 15 0 Na mg Na L 0 15 Quadrati 4 7 0 1 0 9 15 0 112 7 c K mg K L 0 7 Quadrati 4 7 0 05 10 4 15 0 97 8 c Mg mg Mg L 0 7 Quadrati 4 7 0 1 4 5 15 0 89 7 c Ca mg Ca L 0 10 Quadrati 4 7 0 1 4 0 15 0 98 2 c Cr mg CI L 0 15 Quadrati 4 7 0 2 0 02 1 6 15 0 92 7 c NO mg N L 0 3 Quadrati 4 7 0 002 0 002 0 3 15 0 96 3 c SO mg S L 0 8 Quadrati 4 7 0 1 0 04 2 2 15 0 86 5 c TDN mg N L 0 10 Linear 4 7 0 1 0 029 7 8 15 0 100 3 15 0 102 1 15 0 DOC mg C L 0 20 Linear 4 7 0 1 0 048 4 9 15 0 100 5 15 0 97 0 15 0 Page E 12 References Avanzino R J and V C Kennedy 1993 Long term frozen storage of stream water samples for dissolved orthophosphate nitrate plus nitrite and ammonia analysis Water Resources Research 29 10 3357 3362 Merriam J L W H McDowell W S Currie 1996
83. A high temperature catalytic oxidation technique for determining total dissolved nitrogen Soil Science Society of America Journal 60 4 1050 1055 Page E 13 Appendix B Spectrograph Spectral range Spectral resolution Slit width it of spectral bands Operating modes Spectral sampling bands Image rate Spatial swath pixels High efficiency imaging spectrograph Smile and keystone lt 2 microns F 2 4 400 990 nm 2 3 20 nm 30 microns 1 256 Hyperspectral and multispectral 4 6nm 128 9 2nm 64 2 3nm 256 18 4nm 32 4 100 Hz 960 pixels Fore optics options Focal length FOV IFOV Swath width Ground resolution 1 000 m altitude Integration time Shutter dm ui 1 1320 Freeport Blvd Suite 106 Sparks NV 89431 775 329 6660 FAX 775 329 6668 Conrad SpecTIR com user controllable by software User selectable on the fly 9mm 63 degrees 0 062 degrees 1 22 x altitude 1 2m 7 8626 Brooks Drive t SpecTIH Suite 103 x Easton MD 21601 410 820 5001 WBemard SpecTIR om WWW SpecTIR com Appendix C NASA TM 2003 211621 Rev4 Vol IV Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Inherent Optical Properties Instruments Characterizations Field Measurements and Data Analysis Protocols James L Mueller Giulietta S Fargion and Charles R McClain Editors Scott Pegau J Ronald
84. C DETERMINATION OF CHL a AND PHEOPIGMENT CONCENTRATIONS Chlorophyll and pheopigments can be determined using either a Turner Designs or Sequoia fluorometers equipped with the standard light sources and Corning excitation and emission filters following the manufacture s recommendation for measuring extracted chlorophyll The fluorometric instrument should be warmed up for at least 30 to 45 minutes prior to making measurements Because of the acidification requirement for the standard fluorometric method Holm Hansen et al 1965 differences in excitation and emission wavelength bands between fluorometers can produce uncertainties Trees et al 1985 The sensitivity with which a particular instrument is able to differentiate between chlorophyll and pheopigment is a function of the excitation wavelength This effect is measured during calibration of the fluorometer and is called the tau factor x Saijo and Nishizawa 1969 have shown that t can vary from 1 to 11 5 depending upon the excitation wavelength in the range between 410 nm and 440 nm For example a comparison between a Turner Designs Model 10 005R analog fluorometer and a Turner Designs Model 10 AU 005 digital fluorometer showed statistically significant differences for 42 oceanic samples slope 1 06 even though both were calibrated with exactly the same standards Figure 3 4 The departure from a unit slope is attributable to differences in the excitation bands for the two fluo
85. EP QA Officer to determine an appropriate response Incomplete field sampling data may require re sampling of the questionable location 2 Conflicting or poor quality data When results do not meet the prescribed quality control QC goals the available data will be reviewed by the Project Manager and the NHEP QA Officer Upon examination all or some of the following actions may be applied a Systems audit for analyte in question b Determination of matrix interference c Re sampling of the questionable sample d Reconsideration of acceptable limits with statements explaining the results of the action rationale taken Rejection of data and exclusion from the report with written explanation and or Rejection of the entire sample site location with recommendation for relocation of sample site or reconsideration of results mo Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 33 If the Project Manager determines that any data are invalid the invalid results will be flagged as Not Valid in the EMD in order to communicate this determination to all data users or deleted from the dataset altogether D3 Reconciliation with User Requirements If the project objectives from Section A7 are met the user requirements have been met If the project objectives have not been met corrective action as discussed in D2 will be taken by the Project Manager The overall reconciliation with user requirements will b
86. Furber Strait 43 0844 70 86374 Figure 7 Sampling Stations for Activity 4 Bounding Box for Hyperspectral Collect a NH 0052A GRBOR H00 0035A GB4A GRBLR NH 0C Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 20 NH 00624 NH 0057A NH04 0245C Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 21 Table 8 Sample Process Design for Field Measurements for Activity 3 Station ID Parameters Sampling Peripd and Responsible Agency Frequency Water Temperature Salinity GRBGB Light Attenuation Oue samp ie Oued GRBSQ Chlorophyll a measurement on each date of GRBLR CDOM hyperspectral imagery UNH GBNERR System GRBCL TSS collection Wide Monitoring Program SEBAE b a field measurement Orthophosphate Water Temperature Salinity Light pm SIUS Reap leer HEN GRBOR Chlorophyll a measurement on each date of NH 0049A EDON y hyperspectral imagery UNH National Coastal NH 0052A TSS collection Assessment Program RET ita field measurement Orthophosphate Water Temperature Salinity One sample or field NH 0057A Chlorophyll a measurement on each date of NH 0058A CDOM hyperspectral imagery NH 0062A TSS collection DES eur eee GRBSF Absorption spectra Nitrate nitrite field measurement Orthophosphate Water Temperature T Salinity GRBOB Held fep Light attenuation GRBAP field rep Turbiditv GB4A U Mens and One sample or field GB16 e me
87. Hydrologic optics 1 Introduction 2 Foundations 3 Solutions 4 Imbeddings 5 Properties 6 Surfaces 1450 Quickenden T I and J A Irvin 1980 The ultraviolet absorption spectrum of liquid water Journal of Chemical Physics 72 4 416 4 428 Reynolds R A D Stramski and B G Mitchell 2001 A chlorophyll dependent semianalytical reflectance model derived from field measurements of absorption and backscattering coefficients within the Southern Ocean Journal of Geophysical Research 106 C4 7 125 7 138 Roesler C S 1998 Theoretical and experimental approaches to improve the accuracy of particulate absorption coefficients derived from the quantitative filter technique Limnology and Oceanography 43 1 649 1 660 Shibata K 1958 Spectrophotometry of intact biological materials Absolute and relative measurments of their transmission reflection and absorption spectra Journal of Biochemistry 45 599 623 Shifrin K S 1988 Physical Optics of Ocean Water New York American Institute of Physics 285 Sogandares F M and E S Fry 1997 Absorption spectrum 340 640 nm of pure water I Photothermal measurements Appl Opt 36 8699 8709 Sosik H M 1999 Storage of marine particulate samples for light absorption measurements Limnology and Oceanography 44 1 139 1 141 Sosik H M and B G Mitchell 1991 Absorption fluorescence and quantum yield for growth in nitrogen limited Dunaliella tertiolecta Limnology and Oceanog
88. ITION Water samples should be taken using Niskin or similar bottles at the site of and simultaneously with the surface in water optical measurements and at depth increments sufficient to resolve variability within at least the top optical depth When possible samples should be acquired at several depths distributed throughout the upper 300m of the water column or in turbid water up to seven diffuse attenuation depths for PAR irradiance In E 0 E z 7 to provide a basis for relating the spectroscopic measurements of absorption to in situ profile measurements Samples should be drawn immediately from the in situ sampling bottles into clean sampling bottles using clean silicon rubber or Tygon tubing or by directly filling the sample bottles from the Niskin bottle spigot If Niskin bottles will not be sampled immediately precautions must be taken to ensure large particles that settle are re suspended This can be done by transferring all water from the Niskin to a bottle or carboy larger than the total volume of the Niskin so that the entire water sample can be mixed invert bottle numerous times to mix by turbulence or by draining a small amount of water from the Niskin and manually inverting the entire Niskin prior to sub sampling Sample bottles should be kept cool ideally near in situ temperatures and dark prior to sample preparations Preparations should be completed as soon as possible after sampling but no later than several hours after
89. Introduction Background and Conventions Volume II Instrument Specifications Characterization and Calibration Volume III Radiometric Measurements and Data Analysis Methods Volume IV Inherent Optical Properties Instruments Characterization Field Measurements and Data Analysis Protocols Volume V Biogeochemical and Bio Optical Measurements and Data Analysis Methods Volume VI Special Topics in Ocean Optics Protocols Volume VII Appendices The earlier version of Ocean Optics Protocols for Satellite Ocean Color Sensor Validation Revision 3 Mueller and Fargion 2002 Volumes 1 and 2 is entirely superseded by the seven Volumes of Revision 4 listed above The new multi volume format for publishing the ocean optics protocols is intended to allow timely future revisions to be made reflecting important evolution of instruments and methods in some areas without reissuing the entire document Over the years as existing protocols were revised or expanded for clarification and new protocol topics were added the ocean optics protocol document has grown from 45pp Mueller and Austin 1992 to 308pp in Revision 3 Mueller and Fargion 2002 This rate of growth continues in Revision 4 The writing and editorial tasks needed to publish each revised version of the protocol manual as a single document has become progressively more difficult as its size increases Chapters that change but little must nevertheless be rewritten for each revision to reflect re
90. Kiefer and SooHoo 1982 following the nomenclature of Butler 1962 This symbol should not to be confused with the volume scattering coefficient B A V used in other chapters of this Technical Memorandum Kiefer and SooHoo 1982 reported a constant to scale the red peak of chlorophyll absorption for natural particles retained on GF C filters to the diffuse absorption coefficients determined on suspensions by Kiefer et al 1979 The diffuse absorption coefficient is double the value of the volume absorption coefficient of interest here Preisendorfer 1976 Mitchell and Kiefer 1984 1988a made direct estimates of volume absorption coefficients for phytoplankton suspensions and absorbance on glass fiber filters with the same particles to develop empirical equations that relate the amplification factor to the glass fiber sample optical density This procedure is the basis of most laboratory methods for determining particle absorption in water samples Field applications of these quantitative estimates of a 4 were reported by Mitchell and Kiefer 1984 1988b and Bricaud and Stramski 1990 More detailed empirical results to correct for pathlength amplification were reported by Mitchell 1990 for various filter types and diverse cultures coccoid cyanobacteria nanochlorophytes diatoms chrysophytes and dinoflagellates with sizes ranging from 2 um to 20 um Cleveland and Weidemann 1993 and Tassan and Ferrari 1995 found that the empirical rel
91. ND STORAGE Water samples should be taken using e g Niskin bottles at the site of and simultaneously with the surface in water upwelled radiance and reflectance measurements and at depth increments sufficient to resolve variability within at least the top optical depth The K z profiles over this layer will be used to compute optically weighted near surface pigment concentration for bio optical algorithm development Gordon and Clark 1980 When possible samples should also be acquired at several depths distributed throughout the upper 200 m of the water column or in turbid water up to seven diffuse attenuation depths i e In E 0 E z 7 to provide a basis for relating fluorescence signals to pigment mass concentration Samples should be filtered as soon as possible after collection If processing must be delayed for more than an hour hold the samples on ice or in a freezer at 4 C and protect them from exposure to light For delays longer than several hours the samples should be stored in liquid nitrogen Use opaque sample bottles because even brief exposure to light during sampling and or storage might alter pigment values Filtration Whatman GF F glass fiber filters with approximately 0 7 um pore size are preferred for removing phytoplankton from water The glass fibers assist in breaking the cells during grinding and no precipitate forms after acidification Twenty five mm diameter GF F glass fiber filters should be used with
92. PLC Chl 6 mg m 0 10 4 0 05 4 0 00 T T T T T T T 0 00 0 05 0 10 0 15 020 025 0 30 0 35 0 40 TD700 Chl b mg m Manufacturer s Calibration Figure 3 6 Same as Figure 3 5 for chlorophyll b 23 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 0 10 0 08 0 06 0 04 HPLC Chl c mg m 0 02 0 00 T T T T 0 00 0 02 0 04 0 06 0 08 0 10 TD700 Chl c mg m Manufacturer s Calibration Figure 3 7 Same as Figure 3 5 for chlorophyll c REFERENCES Bianchi T S C Lambert and D C Biggs 1995 Distribution of chlorophyll a and pheopigments in the northwestern Gulf of Mexico a comparison between fluorometric and high performance liquid chromatography measurements Bull Mar Science 56 25 32 Brock T D 1983 Membrane filtration a user s guide and reference manual Science Tech Madison WI 381 pp Campbell J W 1995 The lognormal distribution as a model for bio optical variability in the sea J Geophys Res 100 13237 13254 Chavez F K R Buck R R Bidigare D M Karl D Hebel M Latasa L Campbell and J Newton 1995 On the chlorophyll a retention properties of glass fiber GF F filters Limnol Oceanogr 40 428 433 Clesceri L S A E Greenberg and A D Eaton eds 1998a Part 10000 Biological Examination Section 10200 H in Standard Methods for the Examination of Water and Wastewater 20th ed Baltimore MD A
93. Plan for this laboratory is attached as Appendix A The analytical methods for each parameter are listed in Table 9 A laboratory turn around time of 30 days is needed for the sample analyses in order to meet grant contract deadlines The UNH Laboratory QA Officer will be responsible for responding to all non standard situations pertaining to the WQAL laboratory analyses The Project Manager will be responsible for responding to non standard situations at the Jackson Estuarine Laboratory Table 9 Method Reference Parameter Method Laboratory Chlorophyll a See Appendix D JEL CDOM See Appendix C JEL TSS SMI7 2540 D JEL EPA Method 160 2 Absorption spectra See Appendix C JEL Nitrogen NO2 NO3 EPA Method 353 3 WQAL Phosphorus PO4 EPA Method 365 2 WQAL B5 Quality Control The quality control tests for this study and the frequency at which they will be performed are listed in Table 10 The acceptance criteria for each test are listed on Table 2 Quality control will be achieved through frequent cleaning and maintenance of sensors see section B6 at least annual recalibration of sensors comparison of field replicate samples and traditional laboratory QC samples Preliminary laboratory and field data will be reviewed by the UNH Research Staff Results that do not meet the data quality objectives from Section A7 will be flagged as needing corrective action The corrective action taken will range from rej
94. QA QC procedures rely on well documented atmospheric features such as the Oxygen fraunhaufer line at 760nm to ensure that accurate wavelength mapping is maintained Navigation and Boresighting SpecTIR s instruments incorporate 3 ring laser gyro based Inertial Navigation Systems INS to provide for the accurate georeferencing of the data The IMU is coupled with a 12 channel GPS system which utilizes Omnistar HP realtime differential corrections to feed the tightly coupled Kalman filter of the INS The capabilities of this navigation system are as stated Position Accuracy 0 10 m CEP Velocity Accuracy 0 02 m s Pitch Accuracy 0 015 deg RMS Roll Accuracy 0 015 deg RMS Azimuth Accuracy 0 05 deg RMS Data Rate 100Hz In order to ensure the optimal translation of the INS positional data to the image the INS and camera must be boresighted To achieve this SpecTIR has established a boresight calibration site south of the Stead NV airport As control 6 inch orthophotography and matching 2 foot contour data was obtained from Washoe County The positional accuracy of the orthophotography is 9 inches In order to provide orthocorrected hyperspectral imagery SpecTIR has the entire 10m resolution NED DEM database for the continental United States If improved accuracies are required client provided DEMs from such sources as Lidar can be incorporated into the processing stream During processing georeferencing
95. Quality Assurance Procedures Robert R Bidigare Laurie Van Heukelem and Charles C Trees Department of Oceanography University of Hawaii Hawaii Horn Point Environmental Laboratory University of Maryland Maryland Center for Hydro Optics and Remote Sensing San Diego State University California 2 1 INTRODUCTION Marine phytoplankton utilize chlorophyll a as their major light harvesting pigment for photosynthesis Other accessory pigment compounds such as chlorophylls b and c carotenoids and phycobiliproteins also play a significant role in photosynthesis by extending the organism s optical collection window thereby improving absorption efficiencies and adaptation capabilities The important chlorophyll degradation products found in the aquatic environment are the chlorophyllides phaeophorbides and phaeophytins The presence or absence of the various photosynthetic pigments is used to separate the major algal groups and to map the chemotaxonomic composition of phytoplankton in the oceans The unique optical properties of chlorophyll a have been used to develop spectrophotometric Jeffrey and Humphrey 1975 and fluorometric Holm Hansen et al 1965 measurement techniques With the commercial availability of fluorometers for routine measurements of chlorophyll a this pigment became a universal parameter in biological oceanography for estimating phytoplankton biomass and productivity These optical methods can significantly under or
96. RED ARRAYS AND HYPERSPECTRAL AERIAL IMAGERY TO DEVELOP NUTRIENT CRITERIA FOR NEW HAMPSHIRE S ESTUARIES Quality Assurance Project Plan Prepared by New Hampshire Estuaries Project Marine Program University of New Hampshire Durham NH 03824 August 24 2007 Ru Morrison Date Jennifer Hunter Date Project Manager NHEP Program Manager Tom Gregory Date Phil Trowbridge Date UNH Research Staff NHEP QA Officer AJ Markow Date Al Basile Date SpecTIR Project Manager EPA Project Officer Jeff Merriam Date Arthur Clark Date Laboratory QA Officer EPA QA Project Officer Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 2 A2 Table of Contents LvLMrlrqd 2 List of Appendices P 2 List of Tables SEERE SES ETS oreet steer rae vo ede dun voee oe oe ce iiia tosi eK Voisit SE ESE Sia E TaK SES E EE i 3 List of Fig r CS pee siscsdeesseusesesievscccustesesectsesteotssenesesdsadescevsetenesvectdecsvoces 3 A3 Distribution List M E es 4 A4 Project Task Organization e eaae eee eee eene ene tn sn tn staat tn sts sts sins suns tuse suse s evo vseen ivo ET ANT Eve RS IR eve ds seede bes 5 AS Problem Definition Background eese eee ee eese eese testen sensns tns sees ennen enes sneen en sense
97. Reflecting Tube Figure 3 1 Schematic illustration of light interactions and transmission in a reflective tube absorption meter Ray paths ending in the water represent absorption and those extending directly from the source to detector represent beam transmittance Other ray paths indicate scattering interactions 1 backward scattered paths do not reach the detector 2 paths with forward scattering at an angle less than the critical angle i e y y experience total internal reflection by the tube and reach the detector over an elongated optical path and 3 forward scattered ray paths at angles in the range T Vy Ww experience partial losses from the tube at the quartz air interface and may or may not reach the detector depending on whether the internally reflected path survives the absorption process In the single scattering approximation the flux measured by the detector of a reflective tube absorption meter may be written iat P w e PEE sin ydydr ot ous Dn r 7 2n 0 3 2 Pa F B w e To um o v sin yd ydr 210 0 RE i where p v is net reflectance of the quartz tube beyond the critical angle and the exponent N r r w is the average number of wall reflections required for a ray path to reach the detector following a scattering event at 28 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV distance r and angle
98. SSURANCE TRACKING PURPOSES PLEASE ADD THE FOLLOWING TRACKING NUMBER TO ALL CORRESPONDENCE RELATING TO THIS DOCUMENT EPA RFA 07309 UNITED STATES ENVIRONMENTAL PROTECTION AGENCY EPA New England Office of Environmental Measurement amp Evaluation 11 Technology Drive North Chelmsford MA 01863 MEMORANDUM DATE July 14 2008 RFA No 07309 SUBJ Approval of Hyperspectral Imagery QAPP Addendum FROM Arthur E Clark Chemist Quality Assurance Office EQA TO Al Basile EPA Water Quality Branch OEP CWQ On September 17 2007 we approved the following quality assurance project plan Using Moored Arrays and Hyperspectral Aerial Imagery to Develop Nutrient Criteria for New Hampshire s Estuaries by New Hampshire Estuaries Project Marine Program University of New Hampshire August 24 2007 On July 11 2008 I received an addendum to the QAPP entitled Hyperspectral Imageryfor Great Bay NH July 11 2008 It proposes to use the imagery already gathered to produce additional information No new monitoring will occur I find the addendum to be satisfactory If you have any comments or questions please contact me at any time I may be reached by phone at 617 918 8374 and by fax at 617 918 8274 FOR QUALITY ASSURANCE TRACKING PURPOSES PLEASE ADD THE FOLLOWING TRACKING NUMBER TO ALL CORRESPONDENCE RELATING TO THIS DOCUMENT EPA RFA 07309 cc N Conlon M Lataille V Perelli DES G Sotolongo P Trowbridge NHEP USING MOO
99. Spectra 5 edu CR dette e Te eea ee cet Eve eure dp DE nate OS 44 b Spectrophotometric Measurement Procedure sese 45 Sample Filter Preparation for De pigmented Particle Absorption see 46 a Methanol Extraction method sse eee 46 b Sodium Hypochlorite oxidation method eee 47 Spectrophotometric Measurement of De pigmented Optical Density Spectra sc 47 4 5 SOLUBLE ABSORPTION SAMPLE PREPARATION AND ANALYSIS see 47 Purified water for soluble absorption measurements eene 48 Pre cruise preparations usus eee eene trennen renere eee eee ette tene tret tret tret tree tr etre etre nein en 48 Soluble Absorption Sample Preparation Storage and Analysis sse 49 Determination of Optical Density of Soluble Absorption Preparations sss 49 4 6 DATA PROCESSING AND ANALYSIS sese ennt enne nennen 51 Soluble Absorption Coefficients esee eene trennen rre 5l a Filtered pure water blank spectra esee eene nenne 52 b Null point corrections to soluble absorption spectra eee 32 Particle Absorption Coefficients eese reete eene entretient entren ennt 52 a Particle absorption blank spectra sese eee 53 b Null point corrections to particle absorption spectra eee 53 c Pathlength amplification corrections esee tenen 53 d
100. The volume scattering function VSF B A w sr m and the volume absorption coefficient a A m provide the most fundamental description of a medium s inherent optical properties IOP as all other IOP can be derived from them In particular the volume scattering coefficient b and volume backscattering coefficient b 2 may be derived by integrating B A w over the unit sphere and backward hemisphere respectively In terms of determining the complete IOP from in situ measurements a useful combination is a X the beam BG v c X a 4 referred to Vol I Chapter 2 Sect 2 4 and to Chapter 1 of the present volume for further details regarding these definitions and relationships attenuation coefficient c X and the volume scattering phase function Bw E The reader is Knowledge of the VSF is a critical prerequisite to accurate radiative transfer modeling of remote sensing reflectance and water leaving radiance In Vol III Chapter 4 and references cited there it is shown that irradiance reflectance R X is approximately proportional to the ratio of the backscattering to absorption coefficients and that upwelled radiance just beneath the sea surface is proportional to R A so that b X L 07 5 0 9 E o 09 Q a n This relationship is completely general and exact but it does not express a linear proportionality to the IOP ratio because the factors f and Q are not simply coefficients They are functions f 3
101. UNITED STATES ENVIRONMENTAL PROTECTION AGENCY EPA New England Office of Environmental Measurement amp Evaluation 11 Technology Drive North Chelmsford MA 01863 MEMORANDUM DATE September 17 2007 RFA No 07309 SUBJ Approval of Hyperspectral Imagery QAPP FROM Arthur E Clark Chemist Quality Assurance Office EQA TO Al Basile EPA Water Quality Branch OEP CWQ On August 28 2007 we received the following quality assurance project plan Using Moored Arrays and Hyperspectral Aerial Imagery to Develop Nutrient Criteria for New Hampshire s Estuaries by New Hampshire Estuaries Project Marine Program University of New Hampshire August 24 2007 I have reviewed the QAPP and found that it includes the necessary elements provided in our Agency guidance document EPA Requirements for Quality Assurance Project Plans EPA QA R 5 March 2001 I have signed a copy of the title page it is enclosed Please sign it and forward it to Phil Trowbridge of the NHEP When everyone has signed it please send me a photocopy for my files This approval covers the 2007 sampling season If minor changes occur our office should be informed by email or letter but approvals of such changes are not required If major changes occur a revised QAPP should be submitted for review and approval If you have any comments or questions please contact me at any time I may be reached by phone at 617 918 8374 and by fax at 617 918 8274 FOR QUALITY A
102. URING SPECTRAL ABSORPTION COEFFICIENTS WITH REFLECTIVE TUBE METERS ELLE 33 Filtering the Water Intake Port of an ac 9 for Measurements of Absorption by CDOM and Particles Abre dr SAC ApS p eir a ee eee d RM C E HE SERENE M eren 34 3 6 DATA ANALYSIS METHODS eese entente nennen eterne sene reen trennt nnns 35 Temperature and Salinity Corrections eese eene ener eere enne 35 Scattering Corrections fs 0 leks ae I ete nep ete eg taie rng e ege ee eet eeepc 36 3 7 QUALITY CONTROL PROCEDURES eese enne eene rre nrenne trente nene 37 CHAPTER cccssstuscestaspesessatensesssuecussessosses cuts coevensvoves seeswnsuhsuesesdenersevascieiessesseseseescrsuste ceeceaseeseestsursuccepensouse 39 DETERMINATION OF SPECTRAL ABSORPTION COEFFICIENTS OF PARTICLES DISSOLVED MATERIAL AND PHYTOPLANKTON FOR DISCRETE WATER SAMPLES A TINTRODUCTION teet ert Ht et ee dive remove te hte devotion E EE eee 39 42 SAMPLE ACQUISITION eerte pen ERO PO RTI PERPE BEDERREREES 41 4 3 SPECTROPHOTOMETER CHARACTERISTICS AND CALIBRATION eee 41 4 4 PARTICLE ABSORPTION SAMPLE FILTER PREPARATION AND ANALYSIS 42 Filtration ds o sm E e rtc e c lec n tete to eer E iere get 42 a Sample Filter Preparation sese eee 43 b Sample Filter Siorages 2 3 e d ete cepa nii e EDU Roe qp etie Boe aeieea 44 Determination of spectral optical density of sample filters eee 44 az Reference Blank
103. V v2 A TU 2 0 0 8 HAORA 2 C where C NE R If the source output is constant the constant Ye A v may be absorbed in Cx and 2 4 reduces to o 4 0 e 2 0 0 0 and there is no need to use a reference detector output to calculate transmittance PUES C V 4 Vs 2 2 5 Depending on a transmissometer s design we must determine the coefficient Cr in either 2 4 or 2 5 It is not practical to determine the system response constants based on first principles because they are dependent on the optical component throughputs the combined response s of the detector s and electronic circuits Instead a system s calibration constant Cr dimensionless in 2 4 or in V in 2 5 is typically determined by measuring the instrument s output in a standard medium having a known beam attenuation coefficient c For oceanographic transmissometers the standard medium is highly purified water Sect 2 3 below and Cs A c 4 Ch 1 Sect 1 2 Transmissometer Response Temperature Dependence The source output responsivity of the detector and performance of other electronic components tend to be temperature dependent This causes the calibration constants to be temperature dependent Two approaches are used to remove the temperature dependence 1 add compensating electronics that allow the voltage output to remain constant over a temperature range or 2 measure the temperatu
104. V Zaneveld B Gregg Mitchell James L Mueller Mati Kahru John Wieland and Malgorzat Stramska Authors National Aeronautical and Space administration Goddard Space Flight Space Center Greenbelt Maryland 20771 May 2002 NASA TM 2003 211621 Rev4 Vol IV Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Inherent Optical Properties Instruments Characterizations Field Measurements and Data Analysis Protocols J L Mueller CHORS San Diego State University San Diego California Giulietta S Fargion Science ApplicationsInternational Corp Beltsville Maryland Charles R McClain NASA Goddard Space Flight Center Greenbelt Maryland Scott Pegau and J Ronald V Zaneveld COAS Oregon State University Corvallis B Gregg Mitchell Mati Kahru John Wieland and Malgorzat Stramska Scripps Institution of Oceanography University of California San Diego California National Aeronautical and Space administration Goddard Space Flight Space Center Greenbelt Maryland 20771 May 2003 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Preface This document stipulates protocols for measuring bio optical and radiometric data for the Sensor Intercomparison and Merger for Biological and Interdisciplinary Oceanic Studies SIMBIOS Project activities and algorithm development The document is organized into 7 separate volumes as Ocean Optics Protoc
105. a mechanical mode for changing sensitivity e g Turner Designs 10 005 A minimum of 5 dilutions is required for calibrating a digital fluorometer Analog fluorometers with a variety of door settings such as the Turner Designs Model 10 005 must be calibrated for each door setting using at least three standard concentrations per door The diluted standard pigment concentrations used in calibrating the fluorometer must bracket the range of concentrations found in the samples being analyzed Each diluted chlorophyll a standard is placed in the fluorometer and the signal F is recorded after waiting a short period of time 60 seconds for it to stabilize The standard is removed and diluted HCL acid 2 drops of 5 96 or 1 drop of 10 both concentrations by volume is added and mixed within the test tube The tube is then placed back into the fluorometer and after stabilization the acidified fluorescence signal F is recorded Following acidification of the chlorophyll a standard the fluorescence signal stabilizes relatively quickly This 1s not the case for natural samples that contain a mixture of pigment compounds however and stabilization time may vary from sample to sample Stabilization time has to be the same for both pigment standards and for natural samples To minimize this source of uncertainty and to standardize this measurement technique it is recommended that both acidified natural sample and acidified pigment standards be allowed to r
106. air and the adjusted pure water response and dark values are substituted into 2 10 to calibrate field measurements If the manufacturer instead provides a factory reference voltage for calibrating the instrument using equation 2 11 the adjusted pure water and dark values should be substituted in 2 12 to determine V be Air calibration adjustments of this type are usually recommended only for instruments with constant LED source output such as the WET Labs C Star older SeaTech red transmissometers and other similar instruments by different manufacturers Field water calibrations are the recommended basis for correcting drifts in closed path flow through cell instrument such as the ac 9 Instrument Temperature Dependence The change in a transmissometer s response and dark values are usually determined by measuring response variations with the optical path in air or in a dry inert gas such as Nitrogen or Argon as the instrument temperature is varied The response and dark values at each internal instrument temperature an ancillary measurement and data output needed for temperature corrections are recorded and reported either as a lookup table of correction factor and temperature pairs or as the coefficients of a polynomial function of temperature that has been fit to the correction factors Instruments that have a closed flow through optical cell are usually characterized in a water bath the temperature of which is cycled ov
107. al realization would measure only losses due by absorption as per equations 1 9 and 1 10 a 3 1 The transmittance absorption scattering and reflection interaction processes that occur in a real reflective tube absorption meter are illustrated schematically in Fig 3 1 A source emits collimated flux with a cross sectional area slightly less that that of the reflective tube and flux reaching the other end of the tube is measured by a detector that covers its entire cross sectional area Ray paths extending directly from the source to the detector indicate direct transmittance of flux Ray paths that terminate within the water volume enclosed by the tube indicate absorbed flux ll Certain commercial equipment instruments or materials are identified in this chapter to foster understanding Such identification does not imply recommendation or endorsement by the National Aeronautics and Space Administration nor does it imply that the materials or equipment identified are necessarily the best available for the purpose 27 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV In natural waters a large fraction of scattered photons are only slightly deflected in the near forward direction Fig 1 3 and proceed directly to the large area detector without encountering the tube walls Ray paths with scattering angles large enough to encounter the water quartz interface where refraction and reflec
108. alls River Cocheco River Bellamy River Oyster River Lamprey River Squamscott River and the Winnicut River The area covered by the hyper spectral imagery is approximately 200 square kilometers QAPP Addendum Hyperspectral Imagery for Great Bay NH RFA No 07309 July 11 2008 Figure 3 The Great Bay Estuary l 2 0 2 4 6 8 10 Kilometers When Project will commence on July 1 2008 and will end by December 31 2008 DES has set a deadline of December 31 2008 for delivering recommendations to the Water Quality Standards Advisory Committee on the formulation of numeric nutrient criteria for NH s estuaries Information on impairments of eelgrass beds due to nuisance macroalgae must be provided before this deadline Therefore the summary report for the project will be due by September 30 2008 Deliverables related to presentations data management and outreach will be completed between October 1 2008 and December 31 2008 Why Nitrogen concentration in Great Bay have increased by 59 in the past 25 years NHEP 2006 Since the 1940s 29 of the historic eelgrass cover has been lost Nitrogen loading rates in Great Bay 182 kg ha yr are higher than estuaries for which dramatic eelgrass loss has occurred 760 kg ha yr Hauxwell et al 2003 However observations by the UNH Ocean Observing Center in 2007 show that phytoplankton only accounts for 8 of the total light attenuation in the bay While there is evidence for nitrog
109. als other than phytoplankton pigments Finally laboratory methods are also described for measuring the absorption spectrum of CDOM in filtered seawater samples The material in this chapter derives from the results of recent experimental intercomparison workshops in which the authors participated as well as from the published literature Chapter 4 of this volume is a reformatted but otherwise unchanged version of Chapter 15 in Revision 3 to the ocean optics protocols Mueller and Fargion 2002 Absorption Determinations from Radiometric Measurements of Irradiance Flux Divergence In situ spectral absorption coefficient profiles can also be measured with spectral radiometers conforming to the performance specifications listed in Vol IL Chapter 2 if the radiometric package is extended to measure E z A and E z X as well as scalar irradiances E z X and E z 4 This combination may be approached either using hemispherical collectors to measure upwelling and downwelling hemispherical irradiances Hojerslev 1975 or by using cosine collectors on one radiometer in tandem with spherical collectors on another radiometer Given these irradiance components spectral absorption is then computed using Gershun s equation Gershun 1939 as e E z A PO der ean 1 11 E z A where E z X E z X E z X is vector irradiance K z A is the vertical attenuation coefficient for vector irradiance and scalar irradiance E z A E z X E z X
110. alues 2np v 9 sin v derived from the N measurements and the endpoint 2np A v e sin x 2 0 and integrate it from 5 to x following Beardsley and Zaneveld 1969 REFERENCES Beardsley G F and J R V Zaneveld 1969 Theoretical dependence of the near asymptotic apparent optical properties of sea water J Opt Soc Amer 59 373 377 Boss E and W S Pegau 2001 Relationship of light scattering at an angle in the backward direction to the backscattering coefficient Appl Opt 40 5503 5507 Bogucki D J J A Domaradzki D Stramski and J R V Zaneveld 1998 Comparison of near forward light scattering on oceanic turbulence and particles Appl Opt 37 21 4669 4677 Bricaud A A Morel and L Prieur 1981 Absorption by dissolved organic matter of the sea yellow substance in the UV and visible domains Limnol Oceanogr 26 1 43 53 Buiteveld H J H M Hakvoort and M Donze 1994 The optical properties of pure water Ocean Optics XII SPIE Vol 2258 174 183 12 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Gordon H R and A Morel 1983 Remote Assessment of Ocean Color for Interpretation of Satellite Visible Imagery a Review Lecture Notes on Coastal and Estuarine Studies Vol 4 Springer Verlag New York 114pp Gershun A 1939 The light field J Math Phys 18 51 151 Hojerslev N K 1975 A spectral light absorption meter for measurements in the sea Limnol
111. alyzed A system blank consists of a filter reagents and the glassware and hardware utilized in the analytical scheme The system blank is quantified under identical instrumental conditions as the samples and is analyzed by appropriate quantitative methods The system blank may not contain any of the analytes of interest above the MDL or corrective action must be taken A spiked blank is defined as a system blank plus an authentic external standard containing the analytes of interest Each set of samples should be accompanied by a spiked blank and is quantified under the same instrumental conditions as the samples 2 5 PROTOCOL STATUS AND FUTURE DIRECTIONS FOR RESEARCH Recent studies have identified the presence of novel bacterial phototrophs in coastal and oceanic waters These include proteorhodopsin containing Bacteria B ja et al 2000 2001 and aerobic anoxygenic phototrophic Bacteria Kolber et al 2000 2001 Sequence analysis of BAC clone libraries prepared from Monterey Bay Station ALOHA and the Southern Ocean revealed that numerous uncultivated members of the y Proteobacteria contain genes that code for proteorhodopsin This membrane bound pigment contains trans retinal absorbs at blue green to green wavelengths and functions as a light driven proton pump In an unrelated study Kolber et al 2000 used an infrared fast repetition rate IRFRR fluorometer to document the widespread occurrence of aerobic anoxygenic phototrophs AAPs in th
112. ample of polystyrene microsphere beads must be obtained and prepared for use in the calibration procedure The following procedures are recommended 1 Assume the bead diameters D in the sample are distributed as a Gaussian probability density function pdf p D with the mean D and standard deviation S provided by the manufacturer normalize the pdf to unit area a It is good practice to occasionally verify the reported mean diameter and standard deviation using a Coulter Counter or other particle size counting device for randomly selected samples received from a manufacturer Calculate the refractive index of the polystyrene spheres relative to pure water ne x n A P i n 2 where the particle refractive index relative to air is determined according to a relationship provided by the manufacturer e g from Duke Scientific as 5 11 ng 1 5663 0 00785A 0 000334X7 A in um 5 12 and the refractive index of water relative to air is Austin and Halikas 1976 EOE EEA in am 5 13 137 1924 Note carefully the different wavelength units in the empirical equations 5 12 and 5 13 71 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Calculate the particle scattering phase function for each diameter D in 500 equally spaced intervals spanning 3 standard deviations about the mean diameter i e AD d using a Mie 1908 scattering model code e g B
113. amples in each sample analysis batch to assure accuracy The response unit concentration is also used to monitor day to day variation in instrument performance A difference from the certified concentration of more than 10 requires further investigation of that run A difference greater than 15 is failure unless the average of the two samples is less than 10X the MDL and results in re analysis of the Page E 6 entire sample queue unless there is a very reasonable and supported explanation for the inconsistency Table 2 lists historical average recoveries At least 2 QCS are analyzed on each run Standards and reagents are prepared from reagent grade chemicals typically JT Baker or from pre made stock solutions All glassware is acid washed 10 HCI and rinsed 6 times with ultra pure low DOC water 18 2 mega ohm All analyses except CHN use multi point calibration curves 4 7 points which are analyzed at the beginning and the end of each run A Laboratory Reagent Blank LRB Laboratory Fortified Blank LFB a standard run as a sample and Laboratory Duplicate are analyzed every 10 to 15 samples during each run At least one Laboratory Fortified Sample Matrix LFM is analyzed during each run to insure that sample matrices do not affect method analysis efficiency Field Duplicates are not required by our lab and are the responsibility of the specific project s manager Laboratory Duplicates must fall within 1596 relative percent dif
114. asurement on each date of NH00 0035A irradi B 8 hyperspectral imagery UNH Coastal Observing NH01 0026A Hee collection Center Chlorophyll a NH00 0027B CDOM NH04 0245C TSS field measurement E Absorption spectra NHS Nitrate nitrite Orthophosphate Procedure for Responding to Non Standard Situations The sample process design outlined in this section should be followed However in the event of a non standard situation in which the sample process designs cannot be followed the field sampling staff of any agency should contact the Project Manager for direction on how to proceed Possible responses to non standard situations include Relocating sampling stations altering sampling schedules and modifying the sampling design Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 22 B2 Sampling Methods Water sampling for Activities 1 3 and 4 will be conducted using three approaches 1 Continuous measurements with in situ sensors and dataloggers 2 Instantaneous measurements with hand held sensors and 3 Grab samples Hyperspectral imagery will be collected from low altitude aerial surveys These approaches have been successfully used for past studies Sampling Methods for Activity 1 Near Continuous Buoy Observations Water quality parameters are measured by in situ sensors on a deployed buoy Temperature and Salinity are measured using a Sea Bird MicroCAT C T Model SBE 37 SIP http
115. asurements depends largely on the combination of measured variables the uncertainty of each measurements and a judgment of how likely the assumption that a Ayr Anr amp 0 is true in a given water mass l It is strongly recommended to use Method 3 to apply the scattering correction if all variables in 3 16 have been measured with acceptable uncertainty and there 1s no reason to suspect that particle absorption is significant at the near infrared reference wavelength A4 Method 2 is recommended if both a A and c7 A are available at one or more visible wavelengths but a Anr and ch Ayr either were not measured with acceptable uncertainties or there is reason to suspect that a Anr a A44 gt 0 Method 1 must be used if only a7 A and a A44 are measured as for example when a laboratory benchtop spectrophotometer is used to measure a in filtered water samples Chapter 4 This situation might also occur if the c side data of an ac 9 were lost due to an electronic failure or blockage of its flow tube and one wished to salvage the absorption profile measured with that instrument 3 7 QUALITY CONTROL PROCEDURES There are several quality assurance tests that can be made to check how well an ac 9 is operating When using intake filters for quality control measurements in tests of instrument performance it is best to filter both sides of an ac 9 This can be done by filtering one side at a
116. at the internal standard employed is not a naturally occurring analyte in the field samples to be analyzed by HPLC Canthaxanthin is recommended as an internal standard because it has a restricted distribution in ocean waters and it is readily available in high purity from commercial sources For additional background on the use of internal standards see Snyder and Kirkland 1979 The internal standard should be added to the sample prior to extraction and used to correct for the addition of GF F filter retained seawater and sample volume changes during extraction When new external and internal standards are prepared they should be verified against previous standards and a standard reference solution 1f available An internal standard with an HPLC peak removed from those of all the pigments canthaxanthin is added at a fixed concentration to the HPLC grade acetone solvent used to extract the pigments from the filtered samples A sample of canthaxanthin spiked acetone solvent is injected into the HPLC system and its peak area AZ is recorded to provide a baseline internal standard for monitoring the solvent concentration in each extracted sample Extraction Filters are removed from the liquid nitrogen briefly thawed 1 min and placed in glass centrifuge tubes for extraction in acetone Three mL HPLC grade acetone is added to each tube followed by the addition of a fixed volume of internal standard typically 50 uL canthaxanthin in acetone Alterna
117. ation Revision 4 Volume IV This carefully prepared standard water sometimes must be used as the reference material for actual sample analysis If this is planned the investigator should determine the optical density of the standard water preparations before and after a cruise relative to fresh purified water drawn directly into the quartz cuvettes An assessment of the change in this water over time may indicate a need to use a time dependent reference water correction As a precaution even if the investigator intends to have high quality purified water at sea it is wise to determine the standard water optical density relative to freshly purified water before a cruise and as a time series to understand the quality of the purified water system used for reference Soluble Absorption Sample Preparation Storage and Analysis Wash hands with soap and water to avoid contaminating the samples Use 0 2 um polycarbonate filters e g Nuclepore or equivalent Do not use irgalan black stained low fluorescence background polycarbonate filters for this preparation Other membrane filters or Sterivex cartridges may also be used but the investigator must then test for any contamination by the filter and ensure that no artifacts are introduced The filtration system used should be equipped with control of vacuum for each individual filtration funnel and with a provision for direct filtration into clean bottles An example of a suitable soluble absorpt
118. ation reporting and verification Data reduction and validation are performed in a spreadsheet MS Excel The Raw data page of the spreadsheet lists the date of analysis user analysis performed project any issues or problems noted with the instrument on that date and the sample queue and the raw data exported from the instruments Most raw data is exported as an area or an absorbance value A second page typically named Calculations is added to the spreadsheet where known concentrations of standards check standards and reference solutions are added The calibration curve s is calculated and the concentrations are calculated on this page Calculated concentrations for all standards LFB LFM and IPC are compared to the known or prepared values If these are acceptably close 10 of the known no further changes to the calculated concentrations are made If there is evidence of drift in the response of the instrument during a run we try to correct for the drift using the responses from the front end calibration curve and the set of standards analyzed at the end of the run All reference solutions and replicates must meet certain QC criteria described below for a run to be accepted Data are then exported to the WQAL database Exported information includes the unique 5 digit code calculated concentration the analysis date the user the filename the raw data and calculations are saved in and any notes from the run regarding th
119. ations Chapter 3 and general protocols for field measurements metadata logbooks sampling strategies and data archival Chapter 4 Chapters 1 2 and 3 of Volume I correspond directly to Chapters 1 2 and 3 of Revision 3 with no substantive changes Two new variables Particulate Organic Carbon POC and Particle Size Distribution PSD have been added to Tables 3 1 and 3 2 and the related discussion in Section 3 4 protocols covering these measurements will be added in a subsequent revision to Volume V see below Chapter 4 of Volume I combines material from Chapter 9 of Revision 3 with a brief summary of SeaBASS policy and archival requirements detailed SeaBASS information in Chapter 18 and Appendix B of Revision 3 has been separated from the optics protocols Volume II The chapters of this volume review instrument performance characteristics required for in situ observations to support validation Chapter 1 detailed instrument specifications and underlying rationale Chapter 2 and protocols for instrument calibration and characterization standards and methods Chapters 3 through 5 Chapters 1 through 5 of Volume II correspond directly to Revision 3 chapters 4 through 8 respectively with only minor modifications Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Volume III The chapters of this volume briefly review methods used in the field to make the in situ radiometric measurements for ocean co
120. ationships of Mitchell 1990 were consistent with similar types of phytoplankton but Moore et al 1995 reported large differences in the amplification factor for Synechococcus sp WH8103 and Prochlorococcus marinus that were about half the size of the smallest cells studied by Mitchell 1990 Similar results were obtained by Allali et a 1997 for natural populations of the Equatorial Pacific dominated by picoplankton For samples with substantial turbidity and scattering due to inorganic matter coastal shelf coccolithophore blooms methods to correct for resulting artifacts have been described by Tassan and Ferrari 1995a 1995b Table 4 1 provides a summary of various published results for pathlength amplification factors Separation of the particle fraction into phytoplankton and other components is of considerable ecological and biogeochemical interest Early efforts to separate absorbing components for natural particles included treatment with organic solvents UV radiation and potassium permanganate references can be found in Shifrin 1988 and Bricaud and Stramski 1990 The most widely used chemical method is based on methanol extraction Kishino et al 1985 1986 A recent method consists of bleaching the phytoplankton pigments by sodium hypochlorite Tassan and Ferrar 1995a Ferrari and Tassan 1999 Spectral fluorescence methods to estimate the fraction of photosynthetically active absorption if separate total particulate absorp
121. aturated with FSW are used to measure the reference spectrum and one is left in the reference beam during sample measurements For typical single beam instruments generally the reference is scanned and then samples are placed into the beam and scanned Most modern spectrophotometers whether single or double beam automatically store the instrument s reference spectrum and recorded sample spectra are automatically corrected to yield OD s 4 relative to the reference blank filter A new instrument reference baseline scan should be measured each time the spectrophotometer is powered up and whenever its configuration has been changed The baseline should also be checked regularly every 1 hr to 2 hr during extended periods of analysis Frequency of baseline verification will depend on the performance and stability of each instrument and should be determined by the investigator prior to executing routine work Uncorrected baseline drift and changes in sorting filters or lamp source can cause systematic measurement anomalies Wavelength accuracy and measurement precision should also be checked during the analyses Sect 4 3 above 44 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV b Spectrophotometric Measurement Procedure Warm up the spectrophotometer for 30 minutes Measure the initial instrument baseline and wavelength calibration If using frozen samples remove the filters from the storage containe
122. ature Salinity Chlorophyll a Great Bay Coastal Buoy CDOM 4 1 07 12 15 07 UNH Coastal Observing ut Every 30 minutes Center Turbidity Light Attenuation Nitrate Sample Process Design for Activity 2 Hyperspectral imagery collection On two dates between 7 1 07 and 10 31 07 hyperspectral imagery will be collected across the study area Details regarding the hyperspectral imagery will be presented in section B2 The overflights will be conducted by SpecTIR www SpecTIR com The flights will be conducted within 2 hours of either low or high tide at Adams Point preferably one flight at high tide and one flight at low tide Flights will be conducted during the morning or afternoon to avoid sun glint For each flight the target altitude and speed will be 12 500 feet 3 800 meters at 160 knots respectively Imagery over the entire study area will be collected during a 1 5 hour period Imagery will be collected from the estuarine area within the area shown in Figure 6 Sample Process Design for Activity 3 Near Continuous Flow Through Surveys Two flow through surveys will conducted in the study area between 7 1 07 and 10 31 07 The surveys will coincide with the date of hyperspectral imagery collection The flow through surveys will cover Great Bay and Little Bay during the overflights in order to document optical properties in the water near and directly above eelgrass beds The flow through surveys collect data on temperature
123. avelengths between 340 nm and 380 nm Pope and Fry 1997 for wavelengths between 380 nm and 700 nm and Smith and Baker 1981 for wavelengths between 700 nm and 800 nm Here for wavelengths gt 700 nm we recommend values calculated by Van Zee et al 2002 from the imaginary part of the refractive indices for pure water measured by Kou er al 1993 The composite a X spectrum derived from these sources is listed in Table 1 1 together with the linear temperature dependency da X r i X m m c reported by Pegau and Zaneveld 1993 and Pegau et al 1997 Absorption by Suspended Particulates and Colored Dissolved Organic Material CDOM Variations in the spectral absorption of natural waters result directly from variantions in the concentrations and chemical compositions of material substances distributed within the water volume These absorbing materials may be present in seawater either in suspended particulates such as pigment bearing phytoplankton or as solutes i e CDOM Fig 1 1a illustrates qualitative comparisons between the absorption spectrum of pure water a A Table 1 1 a non dimensional Ch specific absorption spectrum of phytoplankton pigment concentration a Prieur and Sathyendranath 1981 and a typically exponential absorption spectrum of CDOM a Bricaud et al 1981 The amplitude of each absorption spectrum in Fig 1 1a is arbitrarily scaled to illustrate the characteristic difference in shapes betwe
124. baseline conditions from the Great Bay Estuarine Restoration Compendium 1949 1981 d Calculations of the how much of the area of former eelgrass beds was covered by nuisance macroalgae in August 2007 and October 2007 2 Transfer of GIS files to New Hampshire GRANIT Repository due 12 31 08 GIS files of eelgrass and nuisance macroalgae distributions will be converted to ESRI shapefiles with FGDC metadata The files will be transferred to the New Hampshire GRANIT repository at UNH from which they will be made available to the public 3 Presentations on results to NH nutrient criteria work group due by 12 31 08 Progress on the project will be presented to the NHEP Technical Advisory Committee at a meeting in the fall of 2008 E Cost The total cost of the project will be 14 798 An itemized budget is attached QAPP Addendum Hyperspectral Imagery for Great Bay NH RFA No 07309 July 11 2008 References Alberotanza L et al 2006 Classification of submerged aquatic vegetation of the Venice lagoon using MIVIS airborne data Annals of Geophysics 49 1 271 276 Hauxwell et al 2003 Eelgrass Zostera marina loss in temperate estuaries relationship to land derived nitrogen loads and effect of light limitation imposed by algae Marine Ecology Progress Series 247 59 73 NHEP 2004 Monitoring Plan New Hampshire Estuaries Project University of New Hampshire Durham NH June 30 2004 Available at www nhep unh edu r
125. below Divinyl chlorophyll a the major photosynthetic pigment found in Prochlorococcus accounts for 10 to 60 of the total chlorophyll a in subtropical and tropical oceanic waters Goericke and Repeta 1993 Letelier et al 1993 Andersen et al 1996 Bidigare and Ondrusek 1996 Gibb er al 2000 Divinyl chlorophyll a is spectrally different from normal monovinyl chlorophyll a and its presence results in a significant overestimation of total chlorophyll a concentration as determined by the conventional HPLC methods Goericke and Repeta 1993 Letelier et al 1993 Latasa et al 1996 To avoid these errors it is recommended that monovinyl and divinyl chlorophyll a be spectrally resolved or chromatographically separated to obtain an unbiased determination of total chlorophyll a for ground truthing satellite ocean color algorithms and imagery Total chlorophyll a TChl a 1s the sum of divinyl chlorophyll a monovinyl chlorophyll a chlorophyllide a and chlorophyll a epimers and allomers These co eluting chlorophyll species can be resolved spectrally following Cis HPLC chromatography Wright et al 1991 and quantified using dichromatic equations at 436 nm and 450 nm Latasa et al 1996 Alternatively these two chlorophyll species can be separated chromatographically and individually quantified using Cg HPLC techniques see below Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 The protocols specified be
126. ble to the public through the EMD and GRANIT which are publicly accessible Turnaround times for laboratories are specified in section B4 Great Bay Nutrient Criteria Study QAPP B1 Sampling Process Design Draft No 1 August 24 2007 Page 17 Data for this study will be collected through four activities 1 Near continuous buoy observations 2 Low altitude aerial surveys for hyperspectral imagery 3 Near continuous flow through surveys of water quality and 4 Point measurements with field sensors and grab samples The parameters for the study are shown in Table 4 The rationale for the sampling efforts is described in Section A6 The sample process design for each of the activities is described in the following sections Table 4 List of Parameters Parameter Measurement Type Priority Light attenuation backscatter and Near continuous buoy observations Act 1 Critical irradiance at various wavelengths Measurements with field sensors Act 4 Near continuous buoy observations Act 1 Chlorophyll a Near continuous flow through obs Act 3 Critical Grab sample and laboratory analysis Act 4 Colored Dissolved Organic Matter New COBHBBONS dd AREA acto tical CDOM Near continuous flow throug obs Act 3 Critica Grab sample and laboratory analysis Act 4 Near continuous buoy observations Act 1 Turbidity Near continuous flow through obs Act 3 Critical Measurements with field sensors Act
127. by the concentration of particles present in each sample For HPLC analysis it is important to filter as large a volume as possible so as to accurately measure most of the major pigments A qualitative check to determine whether a large enough volume has been filtered is to count the number of accessory pigments chlorophylls b ci c cs and carotenoids quantified excluding chlorophyll degradation products Trees et al 2000 Most algal groups excluding phycobiliprotein containing groups contain at least four HPLC measurable accessory pigments see Jeffrey et al 1997 Therefore pigment samples that do not meet this minimum accessory pigment criterion may have detection limit problems related to low signal to noise ratios for the HPLC detectors and or inadequate concentration techniques e g low filtration volumes It is generally recommended that the following volumes be filtered for HPLC pigment analyses 3 L to 4 L for oligotrophic waters 1 L to 2 L for mesotrophic waters and 0 5 L to 1 L for eutrophic waters It is recommended to not pre filter seawater samples to remove large zooplankton and particles because this practice may exclude pigment containing colonial and chain forming phytoplankton such as diatoms and Trichodesmium sp Forceps may be used to remove large zooplankton from the GF Fs following filtration Sample Handling and Storage Samples should be filtered as quickly as possible after collection and stored immediately in
128. cally important See Footnote 2 in Vol 1 Chapter 2 regarding the usage of the variable z in Fig 2 2 and Sect 2 4 of that chapter Here we have substituted the symbol r for the optical pathlength along the z axis in Fig 1 3 compare with Fig 2 2 of Vol 1 Ch 2 5 The transmission of the illustrated beam of scattered photons to Detector 2 will be further considered as a starting point in the discussion of scattering measurement concepts in Sect 1 5 below The question What pathlength limit is short enough to avoid multiply scattered photons from reaching a transmissometer s detector is considered in Chapter 2 of this Protocol Volume Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Xm Collimated Source zi AN T WNNNNAAAA DL Detector 1 r Figure 1 4 The local Instrument Coordinate framework describing optical beam transmission and scattering geometry A collimated beam of radiometric flux A 0 0 e is emitted from a source at the origin x The flux within the collimated beam shown schematically as a gradient shaded rectangle extending along the z axis to Detector 1 is reduced by scattering and absorption as it is transmitted along the Zm axis and a reduced flux o A r 0 is measured by Detector 1 at position X At the intermediate location x some fraction of the flux D 4 7 0 0 that reaches that location is scat
129. chniques shall be addressed and any changes deemed necessary shall be made to ensure consistency and quality of subsequent sampling Assessment frequencies and responsible personnel are shown in the following table Table 12 Project Assessment Table Assessment Type Frequency Person responsible for performing assessment Person responsible for responding to assessment findings Person responsible for monitoring effectiveness of corrective actions Field sampling audit effectiveness of grab sample collection Once after first sampling day Ru Morrison Project Manager Ru Morrison Project Manager Ru Morrison Project Manager Field analytical audit Once after first Ru Morrison Ru Morrison Ru Morrison effectiveness of field sampling day Project Manager Project Manager Project Manager sensor operations UNH JEL Fixed Lab Weekl Ru Morrison Ru Morrison Ru Morrison Audit i i Project Manager Project Manager Project Manager UNH WQAL Fixed Weekl Jeff Merriam Jeff Merriam Jeff Merriam Lab Audit d Lab QA QC Officer Lab QA QC Officer Lab QA QC Officer i Once at end of Phil Trowbridge Phil Trowbridge Phil Trowbridge Data Quality Audit 6 30 08 NHEP QA Officer NHEPQA Officer NHEP QA Officer Based on EPA NE Worksheet 27b Field Sampling Audit QAPP deviations and project deficiencies determined during the field sampling assessment will be evaluated for source of
130. cience Vol 35 UNESCO 20 pp Phinney D A and C S Yentsch 1985 A novel phytoplankton chlorophyll technique Toward automated analysis J Plankton Res 7 633 642 Richards F A and T G Thompson 1952 The estimation and characterization of plankton populations by pigment analysis II A spectrophotometric method for the estimation of plankton pigments J Mar Res 11 156 172 Saijo Y and S Nishizawa 1969 Excitation spectra in the fluorometric determination of chlorophyll a and phaeophytin a Mar Biol 2 135 136 Smith R C and K S Baker 1978 The bio optical state of ocean waters and remote sensing Limnol Oceanogr 23 247 259 Smith R C R R Bidigare B B Prezelin K S Baker and J M Brooks 1987 Optical characterization of primary productivity across a coastal front Mar Biol 96 575 591 Strickland J D H and T R Parsons 1972 A Practical Handbook of Sea Water Analysis Fisheries Research Board of Canada 310 pp Tester P A M E Geesey C Guo H W Paerl and D F Millie 1995 Evaluating phytoplankton dynamics in the Newport River estuary North Caroline USA by HPLC derived pigment profiles Mar Ecol Prog Ser 124 237 245 Trees C C R R Bidigare D M Karl and L Van Heukelem 2000a Fluorometric chlorophyll a sampling laboratory methods and data analysis protocols Chapter 14 in Fargion G S and J L Mueller Eds Ocean Optics Protocols for Satellite Ocean Color Sens
131. cs amp Remote Sensing San Diego State University California Department of Oceanography University of Hawaii Hawaii Horn Point Laboratory University of Maryland Center for Environmental Science Horn Point Maryland 3 1 INTRODUCTION In addition to HPLC analyses it is recommended that the standard fluorometric methodology used for measuring chlorophylls and pheopigments also be applied to 1 the same extracted pigment samples used for HPLC analysis and ii additional independent samples Analysis of fluorometric chlorophyll a concentration is a far simpler procedure than HPLC analysis especially at sea On a given research cruise therefore it is economically feasible to acquire and process many more fluorometric than HPLC samples and to statistically relate fluorometric and HPLC chlorophyll a concentrations using linear regression analysis This additional analysis will also enable a direct link to the historical bio optical algorithms and database development during the CZCS validation experiments Protocols for fluorometric determination of the concentrations of chlorophyll and pheopigments were developed initially by Yentsch and Menzel 1963 and Holm Hansen et al 1965 and are described in detail by Strickland and Parsons 1972 Holm Hansen et al 1965 and Strickland and Parsons 1972 used first principles of fluorescence spectroscopy to derive these fluorometric equations The equation proposed by Yentsch and Menzel 1963 is o
132. ctly as V X Va 0 To eee Dw ref 4 Vow 2 where it is assumed that V3 A V5 X varies very slowly over time and may be treated as an instrument 2 11 constant This approach is only used with transmissometers assumed to have a constant source output examples of which include the former SeaTech red transmissometers The value of V X is calculated by combining 2 11 ref with the transmittance relationship 2 10 as 10 Gne OI 09 8 0 Vow Vose Q9 V 09 709 from which it easily follows that y 4 Vow A Vow ref Te 5 The Sea Tech transmissometers were calibrated to read c 650 0 364 m in pure water This representation and tV A V 2 12 approach perhaps simplifies the determination of c A for the inexperienced user but at the same time obscures the value of c used to determine the offset reference voltage 22 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Air Calibrations The sensors output signal response V and dark offset VS are recorded in air by the manufacturer at the time of each factory water calibration These values are typically reported with the calibration records as factory air calibration and dark values and thus the superscript f to allow the user to periodically record air calibration or air tracking data as a check on instrument stability Air
133. d in Mitchell et al 2000 It is important to address a few salient issues that are routinely asked by investigators interested in implementing the method First most modern dual beam spectrophotometers that have a grating before the sample and illuminate the sample with spectrally resolved light have negligible differences a few percent in terms of determining the raw GF F filter OD y 4 of the particles relative to a properly hydrated blank filter 1f the protocols are carefully followed Thus it is not essential to determine the pathlength amplification factor for each different spectrophotometer that is used as long as the investigator makes an appropriate choice of instrumentation However some spectrophotometers have limited spectral range limited dynamic range more noise and inferior stability so the investigator should evaluate the unit to be used to ensure suitability by following the recommendations in section 4 3 Second diode array systems that illuminate with broad band light and then disperse the post sample light using a spectral photodiode array may have significantly different raw OD for the filtered sample Example OD spectra estimated for a diatom culture for various systems used at the Scripps Workshop are shown in Figure 4 1 see also details in Mitchell et al 2000 Note the Hewlett Packard spectral diode array system has a significantly higher OD than the other instruments An empirical relation for this offset in the
134. d samples to room temperature before beginning optical density measurements If it is practical to do so control the samples and the reference water to equal temperatures during the spectrophotometric measurements Absorption by water is strongly temperature dependent at red and near infrared wavelengths Pegau and Zaneveld 1993 Qorpak bottles can be re used at sea After spectrophotometric analysis is completed thoroughly rinse each bottle and its cap three times with purified water pour in 20 mL of 10 HCI acid and close the cap Before the bottle is reused shake it well discard the 10 HCl rinse the bottle and cap copiously with purified water and fill the bottle with purified water to be used later to rinse a new sample filter Purified water should be drawn directly from the pure water system Determination of Optical Density of Soluble Absorption Preparations If samples have been refrigerated allow them to warm to room temperature 49 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Allow the spectrophotometer to warm up for 30 min Confirm that the optical windows of the spectrophotometer are clean If necessary clean them with purified water and ethanol sequentially and dry them thoroughly with lint free laboratory tissues Verify the instrument s spectral characteristics and precision as described in Section 4 3 Wash hands with soap and water to avoid contamination Between us
135. d seawater sample differ significantly Scattering Corrections The systematic scattering offsets between true absorption and absorption measured with a reflective tube instrument as described in equations 3 2 and 3 3 and related text in Sect 3 1 were evaluated by Zaneveld et al 1994 They recommended a hierarchy of three alternative methods for correcting the scattering offsets to the temperature and salinity corrected measured absorption a A 1 Subtract the measured absorption at a near infrared reference wavelength e g Anr 2 715 nm for an ac 9 Or Anr 750 nm for measurements with a laboratory spectrophotometer Chapter 4 After first applying the temperature and salinity corrections using 3 12 and 3 13 assume that the a Ayr a Anr 0 and that the entire measured signal at the reference wavelength is due to wavelength independent scattering errors so that a X a A 2 a5 X a5 Ayr 3 14 36 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV The value of a7 Ayr should be reported with the corrected absorption values when this method is used Assuming a wavelength independent scattering phase function appropriate for the type of particulates in a given water mass and a weighting function W v based on instrument characteristics see equation 3 3 and the preceding discussion in Sect 1 1 above estimate the scattering error as a fraction amp of the mea
136. d the c intake on the other The filtered and unfiltered measurements from the two casts are combined as above The approach yielding the lowest instrumental uncertainty of the particulate absorption is to derive it from filtered and unfiltered measurements with the same instrument on successive casts Calibration offsets whether known or not are identical in the filtered and unfiltered measurements on each side and therefore the offsets cancel when particle absorption is determined as the difference between the two measurements On the other hand potentially larger uncertainty may result from possible changes in the IOP profiles between casts due to horizontal advection and or vertical displacement of IOP features by internal waves 3 6 DATA ANALYSIS METHODS The initial steps in processing absorption measurements using an ac 9 reflective tube absorption meter are identical to those presented for processing beam transmissometer measurements in Chapter 2 Sect 2 5 substituting equation 3 11 for 2 9 in Step 4 This information will not be repeated here Two additional analysis steps are necessary to obtain accurate absorption coefficients from combined ac 9 or similar instrument measurements of a A and c X 1 corrections for water temperature and salinity induced offsets in water absorption and attenuation and 2 corrections for scattering errors equation 3 3 in a X Temperature and Salinity Corrections The absorption
137. deviation and corrected with verbal communications in the field and documented in field log books Any necessary written structural changes will be made through a revision of the SOP for that activity and this QAPP Field sampling activities will be monitored to determine compliance Field Analytical Audit QAPP deviations and project deficiencies determined during the field analytical assessment will be evaluated for source of deviation and corrected with verbal communications in the field and documented in field log books Any necessary written structural changes will be made through a revision of the SOP for that activity and this QAPP Field analytical activities will be monitored to determine compliance Fixed Laboratory Audit QAPP deviations and project deficiencies determined during the fixed laboratory assessments will be addressed immediately Replicates and critical range tables will be checked with data to determine if sources of error exist Any deviations in results will be addressed in both written and verbal formats and future sampling will be monitored to verify that compliance is reached Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 32 Data Quality Audit The NHEP Project QA Officer will review the quality assurance reports provided by each of the agencies Non conformances with this QAPP will be compiled The NHEP Project QA Officer will be responsible for responding to any systemic non co
138. dure is to average OD bs 4 spectra over the entire cruise and to then fit a smoothed exponential function over wavelength to the overall mean the bold line in Figure 4 3B A separate OD see discussion below should be determined for the averaged and smoothed OD 4 spectrum before it is substituted in Equation 4 3 Because the signals are small instrument noise is a large fraction of the signal even for high quality spectrophotometers Therefore subtraction of an individual blank spectrum including its noise is strongly discouraged as this effectively doubles the noise of an already noisy signal Instead it is recommended that a smoothed blank be determined from many individual blank spectra provided that the investigator can demonstrate as in Figure 4 3B that there 1s consistency among the population of blank spectra that are determined The procedure of determining blanks at least each day during routine sampling provides an important quality control on the sample preparation protocols If the blank is found to deviate considerably from the norm the investigator should immediately determine the cause of the discrepancy b Null point corrections to soluble absorption spectra The absorption spectrum of pure water varies strongly with temperature especially in the wavelength region between 650 nm and 750 nm but at other wavelengths as well Pegau and Zaneveld 1993 To avoid temperature related measurement artifacts the sample and re
139. e 10 cm quartz window spectrophotometer cuvettes should be stored with purified water For analysis discard the purified water in the cuvettes rinse inside and outside of cuvettes twice with 10 HCl twice with ethanol then rinse them inside and outside using copious volumes of purified water After the cuvettes have been cleaned use laboratory tissues to handle them Avoid contacting the cuvettes with bare hands and do not contaminate their optical windows by touching them Fill both cuvettes with purified water drawn directly from the water preparation system Use of purified water stored in containers 1s not recommended However if freshly purified water is not available at sea the carefully prepared standard water in combusted bottles can be used as a reference but the investigator must document its degradation over time relative to air see above Carefully dry the cuvettes Bulk dry with paper towels but dry the quartz optical windows with lint free laboratory wipes only e g Kimwipes Inspect cuvettes carefully especially along their optical paths to ensure that they are clean Make sure there are no bubbles floating dust or contaminants on the optical windows or in suspension Looking through the cuvette against a black background can usually identify any problems in the samples Repeat cleaning and drying procedures as needed to obtain a clean sample Run an air to air baseline reference spectrum for the spectrophotometer
140. e absorption coefficient of dissolved material may be measured by attaching a 0 2 um pore size filter to the intake of an ac 9 The recommended practice is to locate the intake filter below the instrument at the bottom of the cage Measurements in the filtered intake configuration are also very useful for testing the operational performance of ac 9 quality control procedures using dissolved measurements are discussed in Sect 3 5 Examples of suitable filters are the Gelman Suporcap 100 and Gelman Maxi cap 0 2 um filters These filters have high flow rates at low differential pressure and don t adsorb or leach materials The outer housings of these commercial filter cartridges may be cut off to allow some flushing of the filter and increase the flow rate Make sure you don t handle the filter material or lay a filter on the deck where it can be exposed to oil and grease Hose clamp the filter to the tubing and make sure any vents on the filter are closed Before use a filter should be either flushed for several minutes with DI water or soaked several hours in DI water to remove air pockets in the filter membrane As a note of caution never flush a filter in the reverse direction There are alternative ways to plumb the filters into the ac 9 instrument The preferred arrangement is to filter the a and c sides separately using two filters and two pumps so that each side is plumbed independently This approach is expensive however and is not nece
141. e data from the in situ sensors are GBNERR in situ operates six observation buoys be helpful in quality assured by sensors available at in the study area At each ground truthing UNH Only data http cdmo baruch sc e station water depth the hyperspectral points that pass du QueryPages data m temperature salinity dissolved imagery the UNH QA etadata select cfm oxygen pH and turbidity are recorded every 30 minutes The review will be used for this None data are collected as part of a study The national monitoring program accuracy of the temperature salinity and turbidity sensors are 0 15 deg C 1 and 5 respectively B10 Data Management The laboratory data will be transmitted to the Project Manager as Microsoft Excel spreadsheets After QA checks the data will be permanently archived in the DES Environmental Monitoring Database with all relevant metadata Hyperspectral imagery data will be permanently archived in the NH GIS repository GRANIT with all relevant metadata Data from the buoy will be transmitted to the shore station at JEL using wireless telemetry The shore station routinely copies this data to a server Morse Hall on the UNH Durham campus and archives the data at JEL Where appropriate raw count data is converted to calibrated engineering units on this server and both raw and converted data are archived This server is backed up daily In a final step the con
142. e documented in the technical memorandum written after the conclusion of the project References Dierssen HM et al 2003 Ocean color remote sensing of seagrass and bathymetry in the Bahamas Banks by high resolution airborne imagery Limnol Oceanogr 48 1 part 2 2003 444 455 IOCCG 2000 Remote Sensing of Ocean Color in Coastal and Other Optically Complex Waters International Ocean Color Coordinating Group Report 3 Edited by Shubha Sathyendranath pp 140 Available at http www ioccg org reports_ioccg html Mitchell B G et al 2000 Determination of spectral absorption coefficients of particles dissolved material and phytoplankton for discrete water samples In G S Fargion and J L Mueller eds Ocean optics protocols for satellite ocean color sensor validation revision 2 NASA Technical Memoradum 2000 209966 NASA Mobley C D 1994 Light and water radiative transfer in natural waters Academic Press Inc NHEP 2004 Monitoring Plan New Hampshire Estuaries Project University of New Hampshire Durham NH June 30 2004 Available at www nhep unh edu resources pdf nhepmonitoringplan nhep 04 pdf NHEP 2006 State of the Estuaries Report New Hampshire Estuaries Project University of New Hampshire Durham NH June 30 2004 Available at www nhep unh edu resources pdf 2006 state of the nhep 06 pdf Sugumaran R et al 2005 Hyperspectral Remote Sensing and Geographical Information Systems Tools to Assess
143. e filtered and absorbance spectra of the filter OD A are estimated for the retained particles using a laboratory spectrophotometer After measurement the sample filters are soaked in chemical solvents to extract or bleach phytoplankton pigments Kishino et al 1985 Tassan and Ferrari 1995a then rinsed to remove the chemicals and pigments from the material retained on the filter The OD 4 spectrum of the filter is then determined in the spectrophotometer to obtain the absorption component of the de pigmented particles which are sometimes referred to as detritus or tripton Depending on the method used to de pigment the samples this fraction also includes bleached cells and phycobilipigments that are not extractable in methanol and also inorganic minerals that may be important absorbers in some water samples The raw OD s 4 and OD 4 data are used to calculate total particulate and de pigmented absorption coefficients a 4 and a 4 respectively The absorption coefficient of phytoplankton a 4 is then calculated as the difference a 4 ag A Filtration The Whatman GF F filter which is binder free and combustible with a nominal pore size of 0 7 um is recommended for particle absorption sampling This type of filter is also recommended by JGOFS 1991 for 42 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV various particulate and pigment analyses Some authors hav
144. e natural light field varies slowly and is not part of the alternating signal This approach may have difficulties when the ambient light also varies rapidly such as with indoor lights that have a 60 Hz fluctuation or near the ocean surface where waves may rapidly modulate the light field Even with good electronic rejection of ambient light it is wise to reduce the possible influence of ambient light by using baffles and careful positioning of the instrument 2 3 CHARACTERIZATION and CALIBRATION OF BEAM TRANSMISSOMETERS Calibration With Pure Water As explained above the calibration constant C1 for a transmissometer is determined by measuring its response to a standard medium having a known value of c A The optical standard medium commonly used to calibrate oceanographic transmissometers and absorption meters Ch 3 is pure water so that C A 2 e A a X b The recommended values of a 4 and b X are taken from Table 1 2 as explained in Ch 1 Sect 1 2 Pure water of optical calibration grade is freshly prepared by methods described in Chapter 3 This difficult step is critical because residual traces of particles and or dissolved organic material introduce serious calibration offsets and relative uncertainties between calibrations The pure water standard is introduced into the optical path by one of two methods 1 An open path transmissometer must be thoroughly cleaned and rinsed in purified water and
145. e reported that particulate material less than 0 7 um in size will not be retained by the GF F filter and that this fraction may contain up to 10 or 15 of the phytoplankton biomass as measured by chlorophyll concentration Chavez et al 1995 however found no statistical difference between GF F and 0 2 um filters for chlorophyll and productivity measurements The absorption of particles having diameters between 0 22 um and 0 7 um may be selectively determined by filtering the GF F filtrate again through a 0 22 um Millipore cellulose acetate membrane filter and measuring its absorbance with a spectrophotometer Ferrari and Tassan 1996 Note that Mitchell 1990 reported pathlength amplification factors for cellulose acetate filters that are substantially different than those for GF F filters and also described the relative difficulty of keeping cellulose acetate filters properly hydrated The optical transparency of the GF F filter relative to air decreases significantly below 380 nm but many spectrophotometers can still make optical density determinations to 300 nm with these filters The transparency of the filter also increases with hydration so all samples must be fully but not excessively hydrated for proper performance of analytical procedures and accurate optical corrections Pre soaking GF F filters 1 to 2 hrs before use can lead to less variability between individual filters Bricaud and Stramski 1990 For oceanic water samples seawater
146. e specific sample Data are sent to sample originators upon completion of all requested sample analyses and following review by the WQAL lab manager Generally the data include Page E 5 the 5 digit code the sample name collection date and concentrations in row column format Any information entered into the database can be included upon request Data transfer is typically via e mail or electronic medium CD or floppy disk All data corrections are handled by the lab manager Corrections to data already entered into the database are very infrequent Typically they involve reanalysis of a sample In this case the old data is deleted from the database and the new value is imported along with a note indicating that it was re analyzed the dates of initial and secondary analysis and the reason for the correction Hand written or computer printed run sheets are saved for each run and filed based on the project and the analysis Spreadsheet files with raw data and calculations are stored electronically by analysis and date Information in the database allows easy cross reference and access from individual samples to the raw data and the runsheets This provides a complete data trail from sample log in to completion of analysis VII Quality Control All analyses conducted at the WQAL follow approved or widely accepted methods Table 1 Quality Control Samples QCS from Ultra Scientific are analyzed periodically approximately every 20 s
147. e world oceans These microbes possess low amounts of bacteriochlorophyll a Amax 358 nm 581 nm and 771 nm and unusually high levels of bacteriocarotenoids Ama 454 nm 465 nm 482 nm and 514 nm They require molecular oxygen for growth One of us RRB has initiated HPLC pigment analysis of these latter clones and retinal related compounds to determine if the Wright et al 1991 method can be used for their separation and quantification REFERENCES Abramowitz A and LA Segun 1968 Handbook of Mathematical Functions Dover New York 5 Printing 1046pp Andersen R A R R Bidigare M D Keller and M Latasa 1996 A comparison of HPLC pigment signatures and electron microscopic observations for oligotrophic waters of the North Atlantic and Pacific Oceans Deep Sea Res IT 43 517 537 B j O L Aravind E V Koonin M T Suzuki A Hadd L P Nguyen S B Jovanovich C M Gates R A Feldman J L Spudich E N Spudich and E F DeLong 2000 Bacterial rhodopsin Evidence for a new type of phototrophy in the sea Science 289 1902 1906 B j O E N Spudich J L Spudich M LeClerc and E F DeLong 2001 Proteorhodopsin phototrophy in the ocean Nature 411 786 789 Bianchi T S C Lambert and D C Biggs 1995 Distribution of chlorophyll a and pheopigments in the northwestern Gulf of Mexico a comparison between fluorometric and high performance liquid chromatography measurements Bull Mar Science
148. eact with the acid for one minute prior to recording the acidified fluorescence signal F Two drops of 5 by volume hydrochloric acid is added to each of the pigment standards and natural samples Once the acid 1s added the sample in the test tube should be mixed by inverting the tube several times using parafilm as a stopper All fluorometric measurements for both pigment standards and natural samples should be carried out at room temperature A 90 by volume acetone blank B k and an acidified acetone blank B k should also be measured even though the acidified blank B k is frequently found to be equal to the non acidified blank B k The fluorometer s sensitivity to pheopigments t is calculated as 18 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 UB Blk F Blk and is averaged over all concentrations of the chlorophyll a standard For the mechanical door model fluorometers data from the higher gain door settings will often become noisy and computed values will begin to decrease These data should be excluded from the average The fluorometer s response factor Fr ug L per fluorescence signal is determined as the slope of the simple linear regression equation 32 Corp F F Blk 3 3 calculated for the sample of diluted concentrations of the pigment standard and forcing a zero intercept With a digital fluorometer the regression analysis is applied
149. ecial circumstances and with further development may eventually supercede the presently recommended transmission protocol Absorption spectra for seawater filtered through membrane filters or cartridges For most ocean regions the optical density of dissolved organic material relative to purified water in a typical 10 cm pathlength cuvette is very small in the 400 600 nm region of most interest to ocean color satellite investigations To ensure a common frame of reference for the global data collected by diverse investigators we recommend OD 4 spectra 250 850 nm be determined relative to air for purified water directly introduced to properly cleaned quartz cuvettes The purpose of such spectra is to obtain an independent reference of the quality of the purified water OD 4 spectra for the sample cuvette used during ACE Asia are shown in Figure 4 2 OD 4 should be determined daily for the sample and reference cuvettes used in analyses The investigator should keep careful records of this data and assess any bias in final estimates that may be attributed to problems with the reference water By plotting in the range of minimal absorption by water 250 600 nm Figure 4 2A one can assess whether or not the reference water on a ship has seriously degraded Production of impure water by commercial systems is a relatively common problem on ships where the feed water may have serious contamination If the purified water system fails at sea t
150. ecommend that more careful research should be carried out on the methods for soluble absorption which appears to have a potentially dominating influence on the overestimates of z 4 less than 400 nm In particular the influence of scattering by small particles organic or mineral and the role of salt absorption must be more carefully assessed REFERENCES Aas E 2000 Spectral slope of yellow substance problems caused by small particles Proceedings of Ocean Optics XV Monaco 16 20 October 2000 Allali K A Bricaud M Babin A Morel and P Chang 1995 A new method for measuring spectral absorption coefficients of marine particulates Limnology and Oceanography 40 1 526 1 523 Allali K A Bricaud and H Claustre 1997 Spatial variations in the chlorophyll specific absorption coefficients of phytoplankton and photosynthetically active pigments in the Equatorial Pacific Journal of Geophysical Research 102 12 413 12 423 Blough N V O C Zafiriou and J Bonilla 1993 Optical absorption spectra of waters from the Orinoco River outflow terrestrial input of colored organic matter to the Caribbean Journal of Geophysical Research 98 2 271 2 278 Bricaud A A Morel and L Prieur 1981 Absorption by dissolved organic matter of the sea yellow substance in the UV and visible domains Limnology and Oceanography 26 43 53 Bricaud A and D Stramski 1990 Spectral absorption coefficients of living phytoplankton and non
151. ection Expanded reviews of protocols using instruments based on other design concepts are deferred for possible consideration in future revisions to this volume Reflective Tube Absorption Meter Concepts In Sect 1 4 it was observed that to determine the absorption coefficient associated with transmission over an optical pathlength r Fig 1 4 it would be necessary to measure the sum of transmitted and scattered flux at the detector r D r b r Neglecting backscattering it was suggested that perhaps one might redirect all forward scattered flux to the detector using an ideal reflective tube and determine the absorption coefficient as ERE T Of course a perfectly reflecting tube cannot be realized in a real instrument Nevertheless because the scattering phase function of suspended particles in natural waters is strongly peaked in the forward direction Fig 1 3 it is possible to use this approach to retain more than approximately 85 of scattered photons in the beam reaching the detector of such an instrument James and Birge 1938 built a laboratory version of such an instrument to measure absorption spectra of lake waters and Zaneveld et al 1992 introduced an instrument of this type for in situ absorption measurements In essence such an instrument is simply a poor transmissometer Chapter 2 that fails to exclude all of the singly scattered photons from its beam transmittance measurement and therefore in its ide
152. ection of data to adjustment of values with new calibration values After the field sampling is complete the NHEP Project QA Officer will conduct a data completeness check for valid data in the EMD The data quality objectives for data completeness are provided in Section A7 The NHEP Project QA Officer will also compile all of the quality control results for each parameter listed in Table 10 and determine the percentage of quality control samples that met the data quality objectives If this percentage falls below 80 the NHEP Project QA Officer will investigate the possibility of systematic error in the measurements Table 10 Quality Control Test Frequency QC Sample and or Activity Used Parameter Condition to Assess Measurement Frequency Performance Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 26 QC Sample and or Activity Used Parameter Condition to Assess Measurement Frequency Performance Field replicate measurements with Weekly Precision an independently calibrated meter Activity 1 or grab samples Buoy sensor Calibration check with known Twice per year Accuracy measurements standards Complet Data completeness check by QA Once at the end of the project Ee S Officer 6 30 08 D Accuracy Calibration with a NIST traceable Before and after each deployment Activity 2 irradi tral radi Boa al irradiance spectral radiance i as Comparison of ima
153. educe water clarity to any great degree Therefore the NHEP is proposing research to test the hypothesis that alternatively the eutrophication response to nutrient increases in the Great Bay has been the proliferation of nuisance macroalgae which has reduced the amount of area where eelgrass can reestablish from seed i e the potential eelgrass habitat The hyper QAPP Addendum Hyperspectral Imagery for Great Bay NH RFA No 07309 July 11 2008 spectral imagery collected in August and October 2007 will be used to map eelgrass and nuisance macroalgae throughout the estuary The distribution of nuisance macroalgae will be compared to areas where historic eelgrass beds have been lost to determine whether nuisance macroalgae correlates with eelgrass loss in the Great Bay Estuary The research outputs will contribute to the development of numeric nutrient criteria for NH s estuaries The research will benefit other states in New England because eutrophication responses in Great Bay can be used as a model for other northern macrotidal estuaries Figure 1 Dissolved inorganic nitrogen concentrations in Great Bay NHEP 2006 0 6 r 0 5 04 0 3 DIN mg N L 0 2 0 1 0 0 1974 1981 1997 2004 Period Figure 2 Eelgrass cover and biomass in Great Bay NHEP 2006 3 000 2 500 2 000 1 500 1 000 Eelgrass Habitat 500 0 1985 1990 1995 2000 2005 e Cover acres a Biomass
154. edure produced results comparable to the GF F filter method in comparisons reported by Mitchell et al 2000 but sufficient uncertainties remain that the GF F method continues to be recommended for the present Transmission Reflectance T R Method Tassan and Ferran 1995a described a modification of the light transmission method that corrects for backscattering This technique combines light transmission T and light reflection R measurements carried out using an integrating sphere attached to a dual beam spectrophotometer The data analysis is performed by a theoretical model that eliminates the effect of light backscattering by the particles At the Scripps workshop the global error of the T R method was comparable to the error yielded by the simpler T method for monocultures Subsequent modifications of the T R experimental routine Tassan and Ferrari 1998 Ferrari and Tassan 1999 yielded a significant reduction of the experimental error Tassan and Ferrari 1995 reported that for case 1 waters that have negligible inorganic particle load the amplification factor for GF F filters determined with the T R methods is similar to those determined by Mitchell 1990 The T R method is particularly suited for applications to samples containing highly scattering mineral particles that are commonly found in Case 2 waters Despite the more complicated procedure including an instrument with an integrating sphere this method should be considered in sp
155. el 1974 The linear temperature 0a X dependence of pure water absorption au is due to Pegau and Zaneveld 1993 and Pegau et al 1997 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV an exponential function of wavelength Bricaud et al 1981 scaled as a function of Chl Fig 1 1b shows the sum a A Chl a 4 Chl a 4 Chl calculated for Ch 1 3 and 10 mg m using this simple model as implemented in one of the standard IOP spcification options within the HYDROLIGHT radiative transfer model Mobley and Sundman 2000 The subscript m indicates that the spectra shown in Fig 1 1b are those that would be measured by an instrument that was calibrated using pure water as a standard reference medium Chapter 3 The absorption of pure water a X is compared with a X Chl in Fig 1 1b and the corresponsding total absorption coefficient spectra a X Chl a X a 4 Chl are illustrated in Fig 1 1c The illustrated examples are admittedly an oversimplification but they are adequate as a basis for considering the nature of IOP components of the signal measured by an absorption meter or transmissometer at individual wavelengths Scattering by Pure Water The spectral values of the pure water volume scattering coefficient b A recommended in Vol I Chapter 2 Sect 2 4 are those of Morel 1974 as reported by Smith and Baker 1981 Following Van Zee et al 2002 h
156. eld measurements metadata logbooks sampling strategies and data archival Chapter 4 Chapters 1 2 and 3 of Volume I correspond directly to Chapters 1 2 and 3 of Revision 3 with no substantive changes Two new variables Particulate Organic Carbon POC and Particle Size Distribution PSD have been added to Tables 3 1 and 3 2 and the related discussion in Section 3 4 protocols covering these measurements will be added in a subsequent revision to Volume V see below Chapter 4 of Volume I combines material from Chapter 9 of Revision 3 with a brief summary of SeaBASS policy and archival requirements detailed SeaBASS information in Chapter 18 and Appendix B of Revision 3 has been separated from the optics protocols Volume II The chapters of this volume review instrument performance characteristics required for in situ observations to support validation Chapter 1 detailed instrument specifications and underlying rationale Chapter 2 and protocols for instrument calibration and characterization standards and methods Chapters 3 through 5 Chapters 1 through 5 of Volume II correspond directly to Revision 3 chapters 4 through 8 respectively with only minor modifications Volume III The chapters of this volume briefly review methods used in the field to make the in situ radiometric measurements for ocean color validation together with methods of analyzing the data Chapter 1 Ocean Optics Protocols For Satellite Ocean Color Sensor Validatio
157. eld measurements of temperature and salinity will be made with YSI 30 or similar unit Field measurements of light attenuation will follow the Ocean Optics Protocols Appendix C or for the GBNERR and NCA field crews following the UNH Marine Program SOP Appendix E The field data sheet to be used by field crews is attached as Appendix F Profiles of inherent optical properties will be made with a custom profiling package WetLABS Inc This contains a variety of instruments that are powered by two rechargeable waterproof batteries and the data is logged with a WetLABS DH 8 http www wetlabs com products pub specsheets dh4sse pdf Conductivity temperature and pressure with a Seabird Fastcat 49 http www seabird com products spec sheets A9data htm Chlorophyll a and CDOM fluorescence with a WetLABS ECO triplet fluorometer http www wetlabs com products pub specsheets flssu pdf Optical backscatter is measured at 9 wavelengths with a WetLABS BB 9 Absorption and attenuation is measured at over 80 wavelengths with a WetLABS acs http www wetlabs com products pub specsheets acsssc pdf Vertical profiles of the light field both upwelling radiance and downwelling irradiance at approximately 150 wavelengths between 350 and 850 nm will be measured using a Hyperpro II Satlantic Inc http www satlantic com documents 419671 Specifications pdf Procedure for Responding to Non Standard Situations The methods outlined in t
158. en enrichment in the estuary the expected response of high phytoplankton blooms has not been observed due to the light limited water column environment caused by suspended sediments and rapid water column mixing QAPP Addendum Hyperspectral Imagery for Great Bay NH RFA No 07309 July 11 2008 Thus the contribution of phytoplankton blooms to decreased water clarity is unexpectedly low Instead eelgrass takes up a large portion of nitrogen from the water column in Great Bay but as nitrogen levels have risen researchers have observed a proliferation of green and red nuisance macroalgae Macroalgae can eliminate potential eelgrass habitat when it forms dense mats on the sediment Short and Burdick 1996 but evidence of this interaction is limited to the upper intertidal areas of Great Bay The hypothesis of this research is that the eutrophication response in the Great Bay has been the proliferation of nuisance macroalgae which has reduced the amount of area where eelgrass can reestablish from seed i e the potential eelgrass habitat How The NHEP with EPA funding obtained high quality hyper spectral imagery of the Great Bay Estuary at low tide in August 2007 and October 2007 Figure 4 The imagery consisted of radiance reflectance and georeference in 64 spectral bands between 390 nm and 950 nm with a 2 5 mresolution The delivered data was provided in ENVI readable format which will be the main processing software for this study ENVI
159. en the constant water background absorption and two varying absorption components associated with Chl and CDOM concentrations The unique shape and magnitude of the specific absorption spectrum for each individual constituent allows measured values of e g Chl and CDOM concentrations to be determined from measurements of a A at several appropriate wavelengths The strong inverse depencence of remote sensing reflecance on a X Vol III Ch 4 together with the distinctive shape and magnitude characteristics of the constituents similarly provides the physical basis for ocean color algorithms for determining their concentrations from satellite measurements of water leaving radiance at several wavelengths In Case 1 waters it is often useful to assume Gordon and Morel 1983 Morel and Maritorena 2001 Mobley and Sundman 2000 that particle absorption a X is dominated by phytoplankton pigments and may be expressed as a function of Chl concentration mg m and a Chl specific absorption spectrum as 2 Prieur and Sathyendranath 1981 and that CDOM concentration is correlated with Chl so that a X may also be calculated as Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV a 2 a 3 H T S g S E S 5 lt 350 400 450 500 550 600 650 700 750 Wavelength nm b 1 0 0 9 0 8 i cd ME E 0 6 am Chl 1 mg ni 205 a Chl 3 mg m J 5 0 4 a Chl 10 mg m i ras 2 03
160. ence offsets should be measured on deck before and after each cast the optical windows should be shaded to avoid contamination of the zero offset value by ambient light Before each cast the fluorometer windows should be cleaned following the manufacturer s instructions 3 5 PROTOCOL STATUS AND FUTURE DIRECTIONS FOR RESEARCH In order to minimize interferences caused by the overlapping excitation and emission wavebands of chlorophylls a b c and pheopigments Turner Designs Sunnyvale CA manufactures the multi spectral fluorometer TD 700 This instrument was recently tested using samples collected at the US JGOFS Hawaii Ocean Time series Station ALOHA 22 75 N 158 W A set of replicate monthly May Dec 2000 pigment samples collected between the surface and 175 m were analyzed by HPLC using the protocols described in Chapter 2 Duplicate samples were subsequently analyzed in 100 acetone with the TD 700 using the manufacturer s calibration The results of these comparisons are illustrated in Figures 3 5 3 6 and 3 7 for chlorophylls a 6 and c respectively The Model I regression equations predicting each HPLC pigment in mg m from the equivalent TD700 estimate are e HPLC Chl a 0 729 TD 700 Chl a 0 0144 r 0 894 e HPLC Chl b 0 607 TD 700 Chl b 0 0163 r 0 816 e HPLC Chl c 1 083 TD 700 Chl c 0 00249 r 0 906 These equations differ significantly from a one to one relationship The present comparisons dif
161. ended to prepare a set of standard purified water samples prior to a field deployment as a reference to check daily for pure water system degradation e g due to poor quality feed water Even though bottled purified water standards have been found to deteriorate slightly over time especially from 250 nm to 325 nm they provide invaluable quality control and an alternative source of reference water in situations when the purification system performance degrades dramatically Pre cruise preparations e Sample bottles clear borosilicate Qorpak with polyethylene lined caps used to collect sample filtrate or to store standard reference water need to be thoroughly cleaned in advance to remove any potential organic contaminants Sequential soaks and rinses in dilute detergent purified water and 10 HCI followed by a final copious rinse in purified water are recommended e Rinse plastic caps with 10 HCI twice with freshly prepared purified water e g using a Millipore Alpha Q system and dry them at 70 C for 4 hr to 6 hr e Combust bottles with aluminum foil covers at 450 C for 4 hr to 6 hr e Fill clean combusted bottles with fresh purified water drawn directly from the purification unit e Assemble the combusted bottles and clean caps Store in the dark e These standards are used daily during cruises to evaluate the quality of purified water freshly prepared at sea 48 Ocean Optics Protocols For Satellite Ocean Color Sensor Valid
162. ent in this way reduces the possibility of temperature induced pigment degradation Extraction Filters are removed from liquid nitrogen and placed in the chilled centrifuge tubes for extraction in Vexr mL of 90 acetone Samples are disrupted by sonication placed in a freezer and allowed to extract at 0 C for 24 h Alternatively the cells can be mechanically disrupted using a glass Teflon tissue grinder and allowed to extract at 0 C for 24 h If after disrupting the cells it is necessary to rinse the tissue grinder or mortar and pestle then a known volume of 90 acetone measured using a Class A volumetric pipette should be used The ease at which the pigments are removed from the cells varies considerably with different phytoplankton In all cases freezing the sample filters in liquid nitrogen improves extraction efficiency Prior to analysis pigment extracts are swirled into a vortex to remove particles from the sides of the tube and then centrifuged to minimize cellular debris Measurement Following the same measurement procedure described above under Fluorometer Calibration each extracted sample is placed in the fluorometer and its non acidified and acidified responses Fb and Fa are measured and recorded The concentration of chlorophyll Chl ug L in the sample is calculated as Cal F F Blk Blk NER 3 4 FILT and pheopigments concentration Pheo ug L as Pheo F Blk c F Blk
163. ents of particles concentrated on filters and for materials dissolved in water differ primarily in the determination of optical pathlength and in the treatment of reference blanks Soluble Absorption Coefficients For soluble absorption the calculations are directly proportional to the sample optical density relative to the pure water reference after correction for the pure water blank and specification of a null absorption a 4 T0D 4 OD 2 OD 43 where is the cuvette pathlength usually 0 1 m OD A is the optical density of the filtrate sample relative to purified water OD bs 4 is optical density of a purified water blank treated like a sample relative to purified water see below and OD absorption by dissolved materials is assumed to be zero Note that as long as the null wavelength region is the same for sample and blank the sample and blank spectra can be set to zero at the null wavelength independently or after they are subtracted from each other as indicated in Equation 4 3 Equation 4 3 assumes use of a spectrophotometer that automatically references the sample and blank optical density to freshly purified water Most modern commercial single or double beam units will compute this optical density directly relative to the reference The user must record both raw sample and blank optical densities relative to purified water and assess the stability of the purified water OD lai reference by routine determinatio
164. er a range typically from 5 C to 30 C over the course of the experiment to avoid condensation the flow through cell is usually filled with a dry inert gas and sealed The internal instrument temperatures are somewhat higher than the ambient temperature due to heating by the electronic circuits and source If this experiment is done with air in the optical path of an open path transmissometer i e in a temperature controlled chamber some method must be used and documented to avoid artifacts due to condensation on the windows 2 4 FIELD MEASUREMENT METHODS The procedures for measuring in situ profiles over depth z of c z X using constant output LED source transmissometers are straightforward The instrument is connected into a data acquisition system and mounted on a profiling cage following the manufacturer s instructions If the instrument has an analog output the user must 23 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV ensure that the external analog to digital converter used to digitize the readings is calibrated in absolute units of V since that is the basis on which the instrument has been calibrated The windows on the beam transmissometer must be cleaned with lens cleaner or a mild detergent solution and a soft cloth or tissue rinsed with distilled water then rinsed with isopropyl alcohol and wiped dry An approximate air calibration reading should be made before every cast t
165. er measurement over pathlength 7 the dark corrected detector output V A 7 is proportional to the flux reaching the detector window 7 0 If two transmissometer measurements are made using different path lengths 7 andr the transmittance over the pathlength difference between the two measurements is simply 2 7 0 V n T X h n A 7 0 AMAN 2 1 16 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV and c A may be calculated from 1 6 with r r r The assumptions implicit in this calculation are that the beam attenuation coefficient is constant over the time and space extents of the measurements and that the optical alignment and electronic properties of the instrument also are constant over time Barth et al 1997 describe the design and application of a variable pathlength instrument for use in coastal waters However they also note that the errors in alignment made their instrument unsuitable for clear water applications The requirement to exactly repeat the optical alignment at two distances is the most difficult aspect of building a variable pathlength instrument Small changes in the alignment of the reference detector or reflector will introduce large errors in the beam attenuation coefficient by causing the focal point of the beam to wander relative to the aperture in front of the detector If biofouling exists the spatial gradients in t
166. er should be mounted on the same underwater package as the water sampler ideally together with a CTD transmissometer and other inherent optical properties IOP sensors In some cases it may be desirable to also include a radiometer on this package if shading effects associated with the package and or ship are not significant In situ fluorometers produce nearly continuous profiles of artificially stimulated fluorescence Fluorometer data in volts should be corrected by subtracting an offset determined by shading the instrument on deck These unscaled fluorescence responses are adequate to provide guidance in K profile analysis and interpretation To produce vertical continuous profiles of pigment concentration HPLC derived pigment concentrations from water samples taken at discrete depths may be interpolated with the aid of in situ fluorescence profiles These fluorescence interpolated profiles should then be used with K z A profiles to compute the optically weighted average pigment concentration over the top attenuation length Gordon and Clark 1980 The A D channel used to acquire and record signal voltages from the in situ fluorometer must be calibrated and its temperature dependent response to known voltage inputs characterized The range dependent A D bias coefficients should be determined at approximately 5 C intervals over the range from 0 25 C to characterize the temperature sensitivity of the data acquisition system Zero fluoresc
167. erous individual filters using AN accurate measurement tool like a caliper that is accurate to at least 0 1 mm 52 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Scattering of light within the GF F filter increases the absorption pathlength The absorption coefficient of filtered particles must be corrected for pathlength amplification and the equivalent absorption coefficient in m in suspension is computed as 2 3034 a A V BY where OD A is the measured optical density of the sample filter OD 4 is the optical density of a fully hydrated blank filter and OD absorption is minimal See also detailed discussion of null point selection in Mitchell et al 2000 LOD 4 OD 4 OD out 4 5 nut is a null wavelength residual correction from the infrared where particle a Particle absorption blank spectra If a spectrophotometer with automatic reference baseline correction is used and the reference filter blank baseline is flat over the spectral range of interest OD 2 does not need to be subtracted Spectra of OD 4 must be determined recorded and provided with the sample data Properly prepared blanks generally have flat spectra relative to the reference baseline filters If the OD 4 is confirmed to be flat then it is recommended that only a null absorbance is subtracted from the OD A to compensate for baseline offsets Subtraction of a spectrally flat baseline t
168. ertainty of the methods used to correct for the integrated scattering error Zaneveld et al 1994 which will be briefly summarized below in Sect 3 4 The remaining sections of this chapter summarize protocols related to characterization measurement and data analysis using the ac 9 reflective tube absorption meter Determination of Absorption by Measuring Flux Reflected from a Diffuse Reflectance Surface Figure 3 2 illustrates an alternative proposed instrument concept for use in combination with a backscattering meter Chapter 5 to determine a A in situ A divergent source illuminates a diffusely reflecting target oriented parallel to the instrument s window at a fixed distance d An instrument of this type called the a Beta is commercially available through HOBILABS Inc Detector Source Window Diffuse Reflectance Plaque Figure 3 2 Conceptual schematic illustration of an instrument designed to determine the volume absorption coefficient by measuring diffuse reflectance from a plaque The VSF at one or more angles must be independently and concurrently measured in this approach See also Figure 5 1 and the related discussion of calibrating a VSF meter using a diffuse reflecting plaque in Section 5 3 in Chapter 5 of this Volume 29 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV For simplicity in this conceptual discussion we will assume 1 that the source beam and detecto
169. es Bogucki et al 1998 1 3 RADIANT FLUX TRANSMISSION MEASUREMENT CONCEPTS Geometry and Nomenclature In Fig 1 4 the origin of a local instrument coordinate system is placed at the exit aperture of a source of monochromatic radiant flux A 0 0 0 in uW nm directed as a collimated beam along the positive zm axis see also Fig 2 2 in Vol I Ch 2 The subscript m associated with the coordinate basis vectors 3 2 in The choice of these units rather than e g W m is customary in ocean color science and is used throughout these protocols Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Fig 1 4 indicate that the local measurement coordinate frame is associated with a particular instrument concept as distinguished from global coordinates defining positions and directions in the extended medium cf Figs 2 1 and 2 2 in Vol I Ch 2 The local instrument coordinate framework is related to global coordinates by a translation and rotations that are arbitrary and need not be considered in the present context The direction associated with an optical path vector intersecting the transmitted beam axis zm axis is described by the angle pair y Where Ox y x is measured from the z axis and 0 lt lt 2z is measured from the Xm axis counterclockwise in the xmym plane The variable r with various subscripts will denote geometric distance along any such optical path
170. es and all raw data files are kept on the lab manager s computer These are backed up weekly with the back up stored off site The computer is password protected and is only used by the lab manager Protocols and the sample database are also password protected Handwritten run sheets are stored in a filing cabinet in the lab Instrument run and maintenance logs are combined with the QC data to form one large Excel file where instrument performance can easily be compared to instrument repair and the number of analyses etc This file is also stored on the lab manager s computer and is password protected All information pertinent to a sample is stored in the sample database From this database we can easily determine the date of analysis and the location of the raw data file Page E 9 if further review is necessary The amount of information provided to sample originators is dependent on what is required by the project or funding agencies Page E 10 Table 1 List of standard operating procedures and description of analyses done at the Water Quality Analysis Laboratory Standard Analysis Instrument Description Protocol EPA Operating Used Latest method Procedure Revision or other reference Ion Anions Ion Anions via ion Anions Chromatography Chromatograph chromatography EPA Protocol for w suppressed 300 1 Anions and and conductivity June 11 Cations Protocol 2002 Cations Ion Cations via ion Chroma
171. esources pdf nhepmonitoringplan nhep 04 pdf NHEP 2006 State of the Estuaries New Hampshire Estuaries Project University of New Hampshire Durham NH Available at www nhep unh edu Short FT and Burdick DM 1996 Quantifying eelgrass habitat loss in relation to housing development and nitrogen loading in Waquoit Bay Massachusetts Estuaries 19 730 739
172. et tera ird Ae acca ane ea 14 Table 3 Special Personnel Training Requirements essere 15 Table 4 List of Parameters 5e emper ap inane rA ab Voas a ubi NES 17 Table 5 Sampling Station Summary for Activity 1 essere 18 Table 6 Sample Process Design for Field Measurements for Activity 1 esses 18 Table 7 Sampling Station Summary for Activity 4 esssssssssssseeeeeeeeeee nennen 19 Table 8 Sample Process Design for Field Measurements for Activity 23 sss 21 Table 9 Method Reference sesto rra ei AR quies ai rta teli da re arsenal Eee 25 Table 10 Quality Control Test Frequency 2 2 rri cit t rede aa Fe TEE Pe gu d iin retn sen Reed een 25 Table 11 Non Direct Data Sources for this Study sssssssssssseeeeeeeeene 30 Table 12 Project Assessment Table zs etis vto qoc reet eva code ceder see u D Deus 31 Table 13 List of Reports to Management u u sssseseeesereree reote ctt Mics eint rn dan ances 32 List of Figures Figure 1 Project organizational charts oigo oc et oe deu re ae INSCR a Sean es 6 Figure 2 Dissolved inorganic nitrogen concentrations in Great Bay NHEP 2006 8 Figure 3 Eelgrass cover and biomass in Great Bay NHEP 2006 sess 8 Figure 4 Study Aretan evo eae o gd ote tr anda vat se pire se el desea 9 Figure 5 Buoy and sampling locations within the Great Bay Estuary sssssss 1
173. ew should say IlI which corresponds to the underwater connector I2I corresponds to the air connector 7 Switch to view I2I take the cap off of the air sensor check the reading then cover the sensor with your hand to confirm the reading changes the reading should decrease with a decrease in light 8 Switch to view III take the protective covering off of the underwater sensor check the reading and then cover the sensor with your hand to confirm the reading changes again the reading should decrease Qu det At Each Station l Turn on the DataLogger Take out the respective data sheet for the site Record the time when the underwater sensor is put in the water Lower the sensor to 10cm Allow the reading to stabilize 1 2 seconds and then press ENTER This logs the data into the DataLogger Cross off 10cm and each subsequent depth for which you log data into the DataLogger on the data sheet Lower the sensor to the next depth In shallow areas record measurements every 25cm as marked on the cable In deep and or clearer water areas the sensor can be lowered every 50cm At least 6 8 depths should be recorded in the DataLogger for each station When If the sensor reaches bottom write the bottom depth approximate using the depth markers on the datasheet and press ENTER to log data into the DataLogger You do not need to go to the bottom if you have gt 10 good readings if the DataLogger is showin
174. f the problems cited above In 2001 we deployed our Biospherical Instruments PRR 800 system at approximately 80 stations combined between our AMLR and ACE Asia cruises We consider this our highest quality radiometric data set because of the free fall deployment the spectral range from 312 710 nm and because we acquired 4 5 separate free fall profiles at each station to improve the confidence in our final estimate In Figure 4 4 we show estimates of the mean cosine for spectral downwelling irradiance 4 4 of the upper ocean mixed layer open symbols Here we define 4 A as the ratio a 4 a 4 a A K For Figure 4 4 values for pure water are estimated from Pope and Fry 1997 for 380 700 nm Quickenden and Irvin 1980 for 300 320 and a linear interpolation between those values for 320 380 nm as recommended by Fry 2000 If the individual components are accurate this can be considered a reasonable estimate of the mean cosine near the ocean surface see Mobley 1994 for detailed discussion of the mean cosine Theoretically the values of 4 a 4 should be less than 1 0 and for typical radiance distributions of the upper ocean they should be in the range of 0 70 0 85 near the surface For both AMLR and ACE Asia all absorption data were determined fresh at sea with consistent methods between the two cruises We found that in the region 500 nm to 650 nm there is little difference between the estimates of 4 4 for the Southern Ocean and
175. f they were sample filters e Add5mL to 10 mL of 100 methanol to each filter by gently pouring it down the sides of the filter funnel to minimize resuspension of the sample particles and let stand for 1 min e Filter the methanol through the sample turn off the vacuum close the valves and add 10 15 mL of methanol e Allow the sample to stand in methanol for approximately 1 hr Do not allow the filter to go dry during the extraction period Time of extraction will vary depending on the filter load and phytoplankton species composition Place aluminum foil over the filtration cups to minimize contamination during extraction e After extraction is complete turn on the vacuum and draw the methanol and dissolved pigments through the filter Rinse the sides of the filter tower twice with small amounts of methanol Finally rinse the sides of the filter tower three times with 20 mL of 0 2 um FSW Also rinse the blanks with FSW after methanol extraction to minimize filter dehydration during spectrophotometric analysis 46 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV e Pigment extraction is complete when the 675 nm chlorophyll a absorption peak is not present in the OD 4 spectrum e Successive short extractions of 10 minutes can sometimes improve the pigment extraction e Phycobilins and some eukaryotic pigments will not be extracted efficiently by methanol b Sodium Hypochlorite oxidation
176. fer also from those published in Trees et al 2000a although care must be used in this comparison since the concentrations were 2 1 2355 P expressed there in ng L which accounts for the factor of 10 differences in the respective offset coefficients These results call into question the stability of the fluorometer It is also evident that the equations provided by the manufacturer must be verified with HPLC data and that these calibration relationships should be reviewed frequently It is interesting and noteworthy that the TD 700 fluorometer did not detect pheopigments in any of the samples analyzed 20 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 logHPLC 0 916LogFluor 0 365 12 0 888 n 179 10 p AMT 3 Cruise Atlantic Ocean b 30 N to 30 S oD amp S gt 5 5 o zx 0 1 Q Q 2 0 01 0 1 1 10 Fluorometric Chlorophyll a mg ni Figure 3 1 Comparisons between fluorometrically determined chlorophyll and HPLC determined total chlorophyll a chlorophyllide a chlorophyll a epimer chlorophyll a allomer monovinyl chlorophyll a and divinyl chlorophyll a from samples collected during Atlantic Meridional Transect 3 cruise 30 N to 30 S October 1996 y 0 432x 7255 logHPLC 0 856LogFluor 0 364 r 0 733 n 285 MOCE 4 Hawaiian Islands um HPLC Chlorophyll a mg m e o far 0 01 0 1 1 Fluorometric Chlorophyll a mg n d
177. ference RPD abs dup1 dup2 average of dupl and dup 2 A difference greater than 10 requires further investigation of the sample run A difference greater than 15 is failure unless the average of the two samples is less than 10X the MDL and results in re analysis of the entire sample queue unless there is a very reasonable and supported explanation for the inconsistency Long term averages for relative difference are included in Table 2 LFM must show 85 to 115 recovery A recovery lt 90 or gt 110 requires further investigation of the sample run A recovery lt 85 or gt 115 is failure unless the sample is less than 10X the MDL and results in re analysis of the entire sample queue Page E 7 unless there is a very reasonable and supported explanation for the inconsistency Long term averages for recovery are included in Table 2 Method Detection Limits are calculated at least twice per year or whenever major changes to instrumentation or methods occur Table 2 lists most recently measured MDL values VIII Schedule of Internal Audits Internal audits are not routinely performed however review of QC charts and tables are done at least quarterly by the lab manager IX Preventive maintenance procedures and schedules The laboratory manager Jeff Merriam has 10 years of experience and is highly experienced with all laboratory equipment used within the WQAL The laboratory manager conducts all maintenance and ins
178. ference should be maintained at the same temperature but in practice this is often difficult to do If strong temperature residuals are apparent in the spectra near 750 nm one must inspect the data to determine an appropriate wavelength range to use as a null point For the data in Figure 4 3 it appears that assuming a null point as the average from 590 600 nm is reasonable This assumption may not be reasonable in turbid lake bay and coastal waters however where large soluble absorption values may persist into the near IR Selection of wavelengths for null correction must be evaluated carefully for each data set following principles discussed at more length by Mitchell et al 2000 Particle Absorption Coefficients To compute particle absorption a A in suspension from spectrophotometric OD 2 measured with the particles concentrated on a GF F filter it is necessary to appropriately adjust the optical pathlength This includes substituting the geometric optical pathlength of the particles in suspension and a scaling factor J accounting for the increase in the optical measurement path by scattering within the filter sample The geometric absorption pathlength ofthe filtered material in suspension is given by l uM 4 4 a where Vr is the volume of water filtered and Af is the clearance area of the filter calculated from the diameter Df of the part of each filter that contains the particles Dr should be determined very carefully on num
179. filtered through a 0 2 um filter should be used to hydrate the filters Freshly filtered seawater should be used since water that is left standing in clear containers may grow considerable amounts of algae over relatively short periods of time if there are any nutrients in the filtered seawater For fresh inland water samples purified fresh water may be used Glass fiber cellulose acetate and other strongly diffusing filters have large scattering coefficients which increase the optical path length of photons in the measurement beam Filtration volume V should be adjusted so that the optical densities of the filter samples relative to the blank filter satisfy the criteria that 0 05 lt OD 675 x 0 25 and OD p 440 lt 0 4 OD Mitchell 1990 Optical density spectra of the sample filters should be measured as soon as possible following filtration because pigment decomposition may occur Stramski 1990 If filters must be stored immediately place the unfolded filters into flat tissue containers designed for liquid nitrogen storage Liquid nitrogen storage is recommended because alternative freezing methods were shown to have more artifacts in comparison tests Sosik 1999 a Sample Filter Preparation e Collect water samples and maintain them in the dark at or near in situ water temperature e Prepare 0 2 um filtered seawater FSW in sufficient volume for hydrating sample and blank filters e Set up and maintain the filter apparatus in di
180. filters should be pre soaked in 10 HCl rinsed with 75 100 mL of freshly purified water and rinsed again with a 75 100 mL of the sample before it is used Tests with purified water have shown that all filters leach contamination that resembles soluble absorption data not shown Using polycarbonate membrane filters an acid soak pure water rinse and sample rinse minimizes this contamination Still we have found the sample preparation procedure increases the apparent absorption spectra of purified water that is prepared as though it were a sample when referenced to purified water drawn directly into the measuring cuvette from the pure water system Therefore correction for this sample preparation blank is recommended Glass fiber filters should be avoided if possible because they have been shown to cause rather severe contamination of the filtrate in tests using purified water For samples collected from very turbid waters glass fiber filters have routinely been used as a pre filter to minimize clogging of the final filtration with a membrane filter Kowalczuk 1999 In such cases the investigator must develop a procedure to rinse the glass fiber filter to ensure that the contamination from this method is minimized Since situations requiring pre filtration often coincide with large soluble absorption coefficients the effects may be easily corrected but it is the responsibility of the investigator to demonstrate this Careful assessment of the contam
181. fluorometer window The fluorometers were purchased with the optional bio wiper assembly which is a copper and rubber wiper that is designed to keep the window clean by covering it when not in use and by wiping it clean each time the instrument is powered To further mitigate fouling the instrument housing is wrapped in copper tape prior to deployment Instrument Maintenance and Calibration The instrument is sent to WET Labs for maintenance and calibration after each deployment period Turbidity Antifouling The ECO fluorometers are equipped with copper plating surrounding the fluorometer window The fluorometers were purchased with the optional bio wiper assembly which is a copper and rubber wiper that is designed to keep the window clean by covering it when not in use and by wiping it clean each time the instrument is powered To further mitigate fouling the instrument housing is wrapped in copper tape prior to deployment Instrument Maintenance and Calibration The instrument is sent to WET Labs for maintenance and calibration after each deployment period Nitrate Antifouling The ISUS is equipped with a measurement probe housing consisting of copper mesh and 20 um Nitex screen Instrument Maintenance and Calibration The ISUS is sent to Satlantic for maintenance and calibration at the end of each deployment year usually in December The probe housing is removed and cleaned during regular maintenance dives A range of nitrate concent
182. fluorometric chlorophyll a and pheopigment concentrations are required measurements for which detailed protocols are described in Chapters 2 and 3 respectively Observation of chlorophyll a fluorescence intensity in situ 1s listed as highly desired and protocols for its measurement and data analysis are also included in Chapter 3 Six additional biogeochemical observations are listed as specialized measurements These include concentrations of Phycobiliprotein Phycoerythrin and suspended particulate measurements including Coccolith concentrations total Suspended Particulate Matter SPM Particulate Organic Carbon POC Particulate Organic Nitrogen PON and Particle Size Distribution PSD Methods of measurement and data analysis for these specialized observations most of which are related to applications of ocean color image data to ocean process studies are reviewed briefly in the present chapter 1 2 PHYTOPLANKTON PIGMENT CONCENTRATIONS High Performance Liquid Chromatography HPLC Measurements and Analysis Chapter 2 Mueller and Austin 1995 simply adopted the JGOFS HPLC protocols for measuring phytoplankton pigment concentrations by reference UNESCO 1994 and supplemented them with some brief instructions on sampling and sample handling procedures Although this approach embraced protocol documentation describing a complete methodology and represented a community consensus the lack of a comprehensive end to end protocol statement has
183. for HPLC pigment measurements it was decided that the protocols for fluorometric measurement of the concentrations of chlorophyll a and phaeopigments were too briefly abstracted in Mueller and Austin 1995 Therefore new detailed protocols for this measurement were added as Chapter 14 to Revision 2 Fargion and Mueller 2000 updated as Chapter 17 of Revision 3 Mueller and Fargion 2002 and reproduced here without significant change as Chapter 3 Chapter 3 provides complete protocols for obtaining water samples filtering them freezing the filtered samples in liquid nitrogen sample handling and storage extraction fluorometer calibrations and measurements data analysis and quality control Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 In addition Chapter 3 discusses geographic and temporal variability in the relationship between fluorometric chlorophyll concentrations and combined concentrations of total chlorophyll pigments determined by the HPLC methods Chapter 2 It is both easier and less expensive to measure chlorophyll a and pheopigment concentrations using the fluorometric method which has the added advantage of allowing shipboard analyses at sea during lengthy cruises When these data are used for remote sensing algorithm development or validation however regional and temporal i e cruise to cruise dispersions and or biases may be introduced unless the fluorometric data are first statisticall
184. from subsequent measurements of sample filter OD 4 s If using a single beam instrument or instruments run in the single beam mode the blank is not kept in the instrument so one does not need to rehydrate the blank reference filter regularly Most modern single beam spectrophotometers will also automatically use the blank reference stored in memory for estimates ofOD s 4 i Remove the blank filter from the quartz glass sample mount in the measurement beam and replace it with a sample filter ensuring proper hydration of the sample see above Measure the sample OD s 4 spectrum save it in a digital file and record all relevant information 45 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV e The blank reference filter will dry out over time and must be hydrated regularly If absorption signal deviates significantly from zero more than 0 02 OD in the infrared 750 800 nm this often indicates a dry reference or sample filter If using a quartz plate check the reference filter after every 5 6 scans and hydrate as needed If the filters are mounted in air hydrate the blank before every scan Sample Filter Preparation for De pigmented Particle Absorption After preparing an a 4 filter sample and determining its OD s 4 spectrum on the spectrophotometer the sample should be processed to remove its pigments and determine 4 The shape of the a A spectrum usually decreases mo
185. g an exponential function to the global mean after setting a null point as the average from 590 600 nm There can be small differences in blank spectra cruise to cruise but we do not find this to be significant relative to the overall statistics of all cruises or the variance within a single cruse For relatively weakly absorbing samples like open oceans observed during ACE Asia there is negligible apparent absorption gt 600 nm and there is clear evidence in 3A of uncompensated temperature effects 650 800 nm Therefore we chose to set the null value as the mean from 590 600 nm However if very strong soluble absorption is present the temperature effects 650 800 nm will be less significant and the absorption 590 600 nm may be important The investigator should evaluate their data to determine the best null point and report that assessment Figure 4 3C are optical density of spectra for a 10 cm cuvette after correcting for the null value and the blank spectrum The effort to carefully determine the purified water relative to air and blanks during each cruise will allow different investigators to inter compare their results better and will ensure better quality control of data collected over time We have also determined the time dependent change of our standard water data not shown and when we use that as a reference due to the failure of our purified water system at sea we subtract a different blank than the global fit shown in Figure 4 3B An alter
186. g light readings less than 0 5 or if the sensor begins to stream out in strong currents Raise the underwater sensor out of the water and put the protective cover on Put the cap on the air sensor also Turn the DataLogger OFF until reaching the next station At End of Sampling 1 Unplug the BNC connectors from the LI 1400 2 Rinse underwater sensor frame and cable with freshwater and let dry before storage Download Data to Excel in the Laboratory Tom pee CA After returning to the lab the data should be retrieved from the DataLogger Attach the DataLogger to the computer using the serial cable Open the LI 1400 program and then turn the DataLogger on Under the remote menu click on CONNECT Under the connect window type 2 next to com port number and click CONNECT Under the remote menu click RECEIVE DATA Save the data on the computer Open Microsoft Excel and then open the file you just saved The file is a delimited file and click FINISH Download LiCor Data into a new Excel file and Save As GBSWMP Raw Light Profile MMDDYY where the MMDDYY represents the sampling date Once you are certain that you have successfully downloaded and saved the data the data in the DataLogger should be cleared from memory This can be done 2 ways a On the DataLogger press the FCT key Arrow to the right twice till clear memory is in the window Arrow down to clear all down to date down to time
187. gery to USGS For each imagery dataset x MA DOCUIT DUSIIOR digital orthophoto quads Field replicate measurements with Each sampling date 5 stations A Precision grab samples collected along flow Activity 3 through transect Flow through Calibration check with known Yearly i DECAY standards measurements Complet Data completeness check by QA Once at the end of the project ompleteness Officer 6 30 08 oa Every 10 measurement Precision field Field replicate ivi i E 10 1 a eis Precision lab Laboratory replicates d TREE Grab samples for laboratory Independent calibration Yearly for spectrophotometers 2 les Accuracy lab analysis verification samples times per year for fluorometer C let Data completeness check by QA Once at the end of the project ompleteness Officer 6 30 08 The definitions of precision and accuracy are provided below Precision Precision is the degree of agreement among repeated measurements of the same characteristic parameter under the same or similar conditions Precision 1s calculated for field and laboratory measurements through measurement replicates instrumental variability and 1s calculated for each sampling day For field replicates the measure of precision will be a parameter specific relative percent difference RPD as derived from equation 1 below 1 Accuracy Accuracy is the extent of the agreement between an observed value sample result and the true
188. gly influences the bidirectional aspects of remote sensing reflectance Chapter 4 of Volume III and e g Morel and Gentili 1996 Particle size distributions have been measured for many years using Coulter Counters and related to IOP including c A e g Kitchen et al 1982 More recently several investigators have used the Spectrix Particle Size Analyzer to measure particle size distributions see e g Chapter 2 Vol VI Protocols for measurements and analyses of particle size distributions are not included in this version of the ocean optics protocols but should be written and added to a future revision of this protocol volume Coccolith Concentrations Concentrations of coccoliths calcium carbonate CaCO platelets detached from coccolithophorids sp are measured as cell counts number density per unit volume using a microscope with polarization optics Balch et al 1991 An epifluorescence microscope is used to count plated and naked intact cells before and after the coccoliths are dissolved by acidification Also measured before and after acidification are the Volume Scattering Function VSF values at three angles from which the volume specific backscattering coefficient for coccoliths is determined by subtraction Voss et al 1998 1 5 FUTURE DIRECTIONS Future additions to this volume include chapters providing detailed prototolc for Phycoerythrin measurement and data analysis measurements and analyses of coccolith concentra
189. h piece in half and using a fine point permanent marker write a short sample identifier e g first letter of the cruise and a sequential sample number on the foil Writing on the folded foil prior to placement of the filter both avoids puncturing the foil with the marking pen and improves the legibility of the sample identifier Place the folded filter in the aluminum foil Fold the three open sides to form an envelope that is only slightly larger than the folded filter 3cm x 1 5cm The use of foil containers minimizes the size requirement of the storage container It is also acceptable to use either cryogenic tubes or HistoPrep tissue capsules but they occupy more storage volume per sample and they are more expensive than aluminum foil If fluorometric analysis is to be done soon after collection it is still recommended to place the samples in liquid nitrogen to assist in pigment extraction and on removal from the liquid nitrogen toplace them immediately in chilled 90 acetone Recordkeeping Information regarding sample identification should be logged in a laboratory notebook with the analyst s initials For each filter sample record the sample identifier as written on the sample container station number for the cruise water volume filtered V r 1 in mL and depth of the water sample together with the date time latitude and longitude of the bottle cast during which the sample was acquired 3 3 LABORATORY METHODS FOR FLUOROMETRI
190. h that VW w c 1 5 10 As an example the weighting functions calculated for the WET Labs VSF 3 are illustrated in Fig 5 2 for nominal scattering angles V V 1009 1255 150 These particular triangular source functions were derived assuming that both the source beam and detector FOV are conical about the respective centerlines illustrated in Fig 5 1 Generalized Weighting Functions for Arbitrary Source Beam and Detector FOV Geometries In the above development of equations 5 1 through 5 7 it was assumed that the flux emitted by the source was uniformly distributed over a conical beam with its axis directed in direction sin 24 3 2 0 cos Z4 3 2 and that the detector flux responsivity was also uniformly distributed over a conical FOV having its axis aligned in direction sin E 0 2 amp 0 cos 2 L 2 We may generalize the vector solid angle associated with the source beam as Q which represents the angular solid mw Il angle domain measured relative to over which flux emitted by the source is non zero Similarly Q is the solid angle domain relative to over which the detector s responsivity is non zero There are no restrictions on either the patterns of angular limits associated with and Q or on the relative distributions of flux within Q or of flux responsivity within Q Real sources generally emit flux in a somewhat irregular beam pattern that typicall
191. hamber and additional purification filters Water for calibration is drawn through a 0 01 micron ultra filter at the point of delivery The circulating holding tank allows the highly reactive de ionized water to equilibrate with the ambient conditions and the ultra violet chamber prevents any biological contamination from entering the reservoir For field calibrations one approach is to either purchase HPLC grade pure water or produce it in the lab and transport it to the ship especially for short cruises On some research vessels a water deionization and purification system is permanently installed to support the scientific party If so care must be taken to insure that the filters are fresh and do not produce Colored Dissolved Organic Matter CDOM from decaying particles trapped in the filter Alternatively a portable system consisting of a commercial filtration unit such as the Barnstead E Pure or the Milli Q Q Pak treatment systems may be set up temporarily on the ship The input water should be pre filtered using a 1 5 um commercial filter cartridge and an activated charcoal filter to increase the lifetime of the primary unit Pure water should be produced in advance of the calibration and stored in a clean 20 liter polycarbonate carboy and be allowed to stand for approximately 12 hours to equilibrate with the ambient temperature and to remove bubbles To calibrate an ac 9 the carboy may be equipped with a cap having barb fittings to connect
192. hat varies only due to the instrument noise increases the noise of the result If the instrument baseline cannot be maintained within the recommendations summarized in Section 4 3 the investigator should consider using a different instrument since the errors in the methods caused by using unstable instruments are difficult to control for b Null point corrections to particle absorption spectra To correct for residual offsets in the sample filter relative to the reference and for scattering artifacts due to particle loading it is assumed that a null absorption wavelength in the infrared can be identified Historically many investigators used 750 nm as the null absorption wavelength but recent reports indicate that this wavelength is too short for some waters It is recommended that the null wavelength be set at 800 nm or longer and that the investigator must examine the spectra to evaluate residual absorption structure near the null wavelength Rather than use a single wavelength a mean OD 4 in a 10 nm interval e g 790 nm to 800 nm may be used as the null value to minimize the introduction of noise in the null correction procedure Mitchell et al 2000 discuss at more length factors affecting the choice of an appropriate wavelength for estimating OD In Case 2 waters the definition of the null absorption is more difficult and the investigator may consider the benefits of the transmission reflectance estimates of particle absorption Ta
193. he fouling will cause V A 5 to vary if the alignment is not perfect Additionally if the beam is not truly collimated but instead has a slight divergence the beam divergence will cause a different area of the detector window to be illuminated in each measurement and any spatial gradients in the optical properties of the window will translate into errors in c X Many laboratory benchtop spectrophotometers have a design very similar to a collimated beam transmissometer A complication that arises when using laboratory spectrophotometers to measure beam attenuation is that much of the scattered light is kept in the sample by the total internal reflection at the glass air interface This makes it more likely that multiply scattered light will be received at the detector This problem can be reduced by the addition of light baffles within the sample cuvette Source and Detector Characteristics o 4 7 0 9 The transmittance ratio o 0 0 e Le the ratio of the flux transmitted to the detector window divided by the flux entering the water at the source window must be known to compute c X from 1 6 A transmissometer does not actually measure either of these quantities A transmissometer s detector output signal V 2 represents its response in the presence of flux the part of 0 750 e that arrives at the detector after passing through the instrument s detector assembly window and other optical elements Fig 2 1
194. he investigator should use the standard water prepared prior to the cruise as the reference Spectra of OD 4 of the bottled standard water should be determined before and after a cruise for each lot of bottled standards that are prepared This precaution is important to assist in any corrections that might be required 1f standard water is used as a reference or if the purified water system degrades over time during a cruise There are still relatively few spectra of soluble absorption determined fresh at sea using the revised protocols recommended here Spectra of OD 4 and OD A collected during ACE Asia are shown in Figure 4 3 Raw optical density relative to Millipore Alpha Q water are shown in 3A We routinely find small positive offsets from 600 800 nm that we feel should be compensated by subtracting a null value Figure 4 3B illustrates OD 4 during ACE Asia prepared as recommended in section 4 5 but plotted at 10x smaller scale as Figure 4 3A The recommended procedure is to subtract a cruise or global mean of this blank solid line in Figure 4 3B from the raw sample OD values and then to adjust this difference to zero at a null reference Equation 4 3 The smoothed 55 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV global blank was determined by taking the mean of all blanks for each cruise we have completed since 1998 subsequently taking the mean of all cruises and lastly fittin
195. he quartz glass plate on the sample holder There should be a uniform layer of water between the filter and quartz glass mounting plate If bubbles are present which will be obvious pick up the filter with forceps and replace it on the plate with a slight dragging motion across a drop of filtered seawater Re inspect the back of the filter and repeat the foregoing procedure until no bubbles are present Adjust the amount of FSW as necessary to ensure proper hydration Alternative mounts that expose both sides of the filter to air may be used to avoid bubbles altogether Sample hydration is more difficult to maintain when using this type of filter mount so the investigator must develop a satisfactory procedure to ensure proper hydration of sample and reference Run the instrument baseline correction using the two blanks For most commercial units this baseline will be automatically used as the reference to calculate OD 4 Immediately after the baseline correction is finished and without touching the blank filters run the two blanks as a sample scan to confirm that baseline performance is within acceptable tolerance over the spectral range of determination Sect 4 3 above This spectrum should be flat spectrally Baseline noise less than 0 005 OD is recommended Save this scan for confirmation of instrument performance If a spectrally flat baseline cannot be achieved over the spectral range of interest the stored baseline must be subtracted
196. he total absorption coefficients in the ultraviolet UV and visible region of the spectrum The protocols presented here are based on the evolution starting with articles by Kalle 1938 and Yentsch 1962 of methods for analyzing the absorption by soluble and particulate material in natural waters Laboratory measurements and data analysis protocols are described for separating the total spectral absorption coefficient a A into its components by spectrophotometric measurements of samples prepared from filtration of discrete water samples The spectral absorbance of the filters and filtrate from these samples as measured in a spectrophotometer are expressed in units of Optical Density OD defined as OD A Log V 4 Log o V 4 V A is the spectrometer response for spectral flux transmitted through the reference material and V A is the response for spectral flux transmitted through the sample For the methods presented here the reference is either a properly hydrated GF F blank filter for particle absorption or a clean quartz glass optical cuvette filled directly from a 39 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV purified water source for soluble material absorption Note that OD is a dimensionless quantity The use of base 10 logarithms in this context is a carryover from common practice in chemical spectroscopy and is the typical output of commercial spectrophotometers r
197. his section should be followed However in the event of a non standard situation in which the methods cannot be followed the field sampling staff of any agency should contact the Project Manager for direction on how to proceed Great Bay Nutrient Criteria Study QAPP Figure 8 Flight lines for hyperspectral imagery collect Tapo USAR 60 Tate Ler si jert ta tits TGEA Del pera Tapa L8AOS N t M 2 wer deis mn core VN 15 8 1 Serene B3 Sample Handling and Custody Draft No 1 August 24 2007 Page 24 Field sampling crews will deliver grab samples to the Project Manager at Jackson Estuarine Laboratory The Project Manager will process the samples at JEL All the samples from each date for the UNH WQAL will be delivered to WQAL together to avoid confusion and lost samples The sample handling protocols are provided in Appendices A C and D Chain of custody forms will not be used Each sample will be clearly labeled with the station ID date and time of collection and the initials of the sampler Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 25 B4 Analytical Methods Grab samples for chlorophyll a CDOM TSS and absorption spectra will be analyzed in the UNH Jackson Estuarine Laboratory Durham NH Protocols for analysis are provided in Appendices C and D Grab samples for dissolved nutrients will be analyzed by the UNH Water Quality Analysis Laboratory Durham NH The Quality Assurance
198. hs in the water and one location in the air The buoy will be deployed in the middle of Great Bay at approximately 43 0715 degrees N latitude and 70 8677 degrees W longitude Figure 4 3 Obtain hyperspectral aerial imagery due by 10 31 07 SpecTIR will obtain hyperspectral band imagery for the study area on two different dates between 7 15 07 and 10 31 07 4 Collect water quality data from flow through surveys and grab samples due by 10 31 07 UNH Coastal Observing Center will measure water quality parameters along transects using a flow through sampling device on the same date as the hyperspectral aerial imagery UNH Marine Program will collect grab samples for water quality parameters at seven stations and operate six in situ datasondes on the same date as well Figure 4 These data will be used for ground truthing the aerial imagery 5 Present preliminary results to nutrient criteria work group due by 12 31 07 NHEP will present the preliminary results of the project to the nutrient criteria workgroup during the fall of 2007 The group will provide feedback on the results and guidance for additional analysis 6 Interim status report due 12 31 07 The NHEP will prepare a report to EPA on the status of the project The interim status report will summarize the field data collection activities that occurred in 2007 and will note any discrepancies from the QAPP 7 Final report due 6 30 08 The final report will conta
199. i 0 2 0 1 0 0 350 400 450 500 550 600 650 700 750 Wavelength nm c 1 0 0 9 0 8 esr cw F 06 am ay Chl 3 mg m 3 0 5 a a Chl 10 mgm H 0 4 amp 0 3 0 2 OSes ET SO NS a 350 400 450 500 550 600 650 700 750 Wavelength nm Fig 1 1 Spectral variations of absorption in seawater a Qualitative comparison of the shapes of absorption spectra of pure water Table 1 1 specific absorption by Chl Prieur and Sathyendranath 1981 and CDOM as implemented in the HYDROLIGHT radiative transfer model Mobley and Sundman 2000 described further by Morel and Maritorena 2001 b Comparisons between a A the absorption spectrum of pure water and a Chl the sum of absorption by suspended particles and CDOM for Chl concentrations of 1 3 and 10 mg m following Mobley and Sundman 2000 An absorption meter calibrated relative to pure water would measure a A Chl The sums of pure water and measured absorption spectra from panel b Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Table 1 1 Volume absorption and scattering coefficients for pure water a 4 and b A respectively Values for a X are those of Sogandares and Fry 1997 340 to 390 nm Pope and Fry 1997 400 to 700 nm and Van Zee et al 2002 as derived from Kou et al 1993 705 to 750 nm Alternative values of 5 X compared here are denoted B Buitveld et al 1994 and M Mor
200. ificantly revised in the future given the rapidly developing state of the art in IOP measurement instruments and methods Volume V The overview chapter Chapter 1 briefly reviews biogeochemical and bio optical measurements and points to literature covering methods for measuring these variables some of the material in this overview is drawn from Chapter 9 of Revision 3 Detailed protocols for HPLC measurement of phytoplankton pigment concentrations are given in Chapter 2 which differs from Chapter 16 of Revision 3 only by its specification of a new solvent program Chapter 3 gives protocols for Fluorometric measurement of chlorophyll a concentration and is not significantly changed from Chapter 17of Revision 3 New chapters covering protocols for measuring Phycoerythrin concentrations Particle Size Distribution PSD and Particulate Organic Carbon POC concentrations are likely future additions to this volume Volume VI This volume gathers chapters covering more specialized topics in the ocean optics protocols Chapter 1 introduces these special topics in the context of the overall protocols Chapter 2 is a reformatted but otherwise unchanged version of Chapter 11 in Revision 3 describing specialized protocols used for radiometric measurements associated with the Marine Optical Buoy MOBY ocean color vicarious calibration observatory The remaining chapters are new in Revision 4 and cover protocols for radiometric and bio optical measurements f
201. ility between 50 N and 50 S Progress in Oceanography 45 3 4 329 368 Glaser J A D L Foerst G D McKee S A Quave and W L Budde 1981 Trace analyses for wastewaters Environ Sci Technol 15 1426 1435 Goericke R and D J Repeta 1993 Chlorophylls a and 5 and divinyl chlorophylls a and b in the open subtropical North Atlantic Ocean Mar Ecol Prog Ser 101 307 313 Gordon H R and D K Clark 1980 Remote sensing optical properties of a stratified ocean an improved interpretation Appl Optics 19 3 428 3 430 Hoepffner N and S Sathyendranath 1992 Bio optical characteristics of coastal waters absorption spectra of phytoplankton and pigment distribution in the western North Atlantic Limnol Oceanogr 37 1660 1679 Holm Hansen O CJ Lorenzen R W Holmes and J D H Strickland 1965 Fluorometric determination of chlorophyll J du Cons Intl Pour l Expl de la Mer 30 3 15 Jeffrey S W and G F Humphrey 1975 New spectrophotometric equations for determining chlorophylls a b c and c in higher plants algae and natural phytoplankton Biochem Physiol Pflanzen 167 191 194 Jeffrey S W R F C Mantoura and S W Wright eds 1997 Phytoplankton Pigments in Oceanography Monographs on Oceanographic Methodology UNESCO 661 pp Kolber Z S C L Van Dover R A Niederman and P G Falkowski 2000 Bacterial photosynthesis in surface waters of the open ocean Nature 407 177 179 Kolbe
202. in the a 715 channel with depths of strong changes in water temperature these changes are linked because absorption by water is temperature dependent in the near infrared Sect 3 4 and the time lag between matched changes can be derived from the depth separation and the profiler s rate of descent A combination of unfiltered and filtered ac 9 measurements can be used to derive particle absorption and attenuation coefficients as well as absorption by CDOM There are several combinations that can be used e From measurements using a single ac 9 with the c side filtered and the a side unfiltered particle absorption can be obtained as a X a A a A le A c where the measurements have been corrected using the methods described in 3 6 below The subscript g is associated with CDOM based on historical use of the term gelbstoffe or yellow matter as a pseudonym of CDOM e From measurements with two ac 9 s one filtered and one unfiltered a X is derived directly from the filtered measurements after the corrections of Sect 3 6 and a X 2 a A a where a X is derived from the unfiltered instrument and the pure water terms cancel This approach may also be used with a single instrument by making successive casts one with the filter attached and the second with the filter removed e Another alternative approach is to make successive casts with one instrument filtering the a intake on one cast an
203. in the planned outputs for the project listed below conclusions and recommendations Planned Outputs A A single or multi variate model between the light attenuation coefficient and concentrations of CDOM turbidity suspended solids and chlorophyll a for the Great Bay system which can be used to develop numeric nutrient criteria B Maps of the distribution of CDOM turbidity and chlorophyll a and light attenuation using the model described above on at least two different days for the entire Great Bay system and C A calibrated light availability model for the Great Bay system 8 Present results to nutrient criteria work group due by 6 30 08 NHEP will present the results of the project to the nutrient criteria workgroup during the spring of 2008 9 Recommendation to the Water Quality Standards Advisory Committee due 12 31 08 The nutrient criteria workgroup staffed by DES will prepare a white paper to present its recommendations to the WQSAC Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 14 AT Quality Objectives and Criteria The specific data quality objectives that will be used to determine the quality of the measurements for the study are listed in Table 2 Table 2 Data quality objectives QC Sample and or Activity Used Parameter Condition to Assess Measurement Data Quality Objective Performance Field replicate measure
204. in the red and near infrared portions of the spectrum Limnol Oceanogr 38 1 188 192 Pegau W S J S Cleveland W Doss C D Kennedy R A Maffione J L Mueller R Stone C C Trees A D Weidemann W H Wells and J R V Zaneveld 1995 A comparison of methods for the measurement of the absorption coefficient in natural waters J Geophys Res 100 C7 13 201 13 220 Pegau W S D Gray and J R V Zaneveld 1997 Absorption and attenuation of visible and near infrared light in water dependence on temperature and salinity Appl Opt 36 24 6035 6046 Petzold T J 1972 Volume scattering functions for selected ocean waters Contract No N62269 71 C 0676 UCSD SIO Ref 72 78 Pope R M and E S Fry 1997 Absorption spectrum 380 700 nm of pure water II Integrating cavity measurements Appl Opt 36 8710 8723 Prieur L and S Sathyendranath 1981 An optical classification of coastal and oceanic waters based on the specific spectral absorption curves of phytoplankton pigments dissolved organic matter and other particulate materials Limnol Oceanogr 26 4 671 689 Smith R C and K S Baker 1981 Optical properties of the clearest natural waters 200 800 nm Appl Opt 20 2 177 184 Sogandares F M and E S Fry 1997 Absorption spectrum 340 640 nm of pure water I Photothermal measurements Appl Opt 36 33 8699 8709 Trees C C and K J Voss 1990 Optoacoustic spectroscopy and its application to mo
205. ination of any method and proper corrections must be carried out and reported Previously we recommended the use of amber colored borosilicate glass bottles e g Qorpak bottles that screen ambient light for sample preparation and to store laboratory prepared standard water However recent work details not shown indicate that the amber bottles may leach some colored material into the purified standard water that is prepared before cruises and used to assess the quality of purified water prepared at sea Therefore we now recommend use of clear borosilicate Qorpak M bottles or equivalent for sample preparations and for the preparation of the standard reference water Prior to each experiment all filtration apparatus and storage bottles should be thoroughly cleaned Purified water for soluble absorption measurements Purified water freshly drawn from a water purification system such as the Millipore Milli Q Millipore Alpha Q and Barnstead Nanopure units or their equivalent is strongly recommended for use at sea in preparing pure water for absorption reference blanks and for equipment rinses specified in these protocols Mitchell et al 2000 compared the water to air baseline reference of purified water prepared with these three water purification systems All three systems provided similar results in baseline tests relative to air at wavelengths between 300 nm and 900 nm while small differences were found below 300 nm It is also recomm
206. ing function W w c determined using 5 8 Strictly speaking near forward scattered light still enters AV x and can be scattered to the detector see also the discussion of transmissometer acceptance angles in Chapter 2 but we will neglect this complication in the present discussion The ratios of integrated weighting W yse sin way Wwe 0 sin yd VSF weighting functions illustrated in Fig 5 2 These functions are clearly log linear and should we choose to represent the weighting function exclusively using W w c 0 it would be a simple matter to adjust the results for functions are compared against increasing beam attenuation coefficient c for the three ECO c dependence This dependence may either be applied as a correction to the weighting function or by a 70 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV transmittance function of the form 1 W c B 2 W exp er v where B A W is the measured VSF using W w c 0 see below and ra V is an effective net pathlength for the particular scattering angle measurement Integrated Weighting Function 0 4 i 4 n 4 4 4 4 i 4 0 l 2 3 4 5 6 7 S8 9 10 Beam Attenuation Coefficient c A m l Fig 5 3 Dependence of the integrated weighting functions fw y c sinydy on the beam attenuation coefficient for the 3 ECO VSF weighting functions of Fig 5 2 Calibration with Polystyrene Spheres In this approach a s
207. ing mean diameters of 2 um solid line and 9 8 um dashed line and in both cases relatively small standard deviations The open and closed circles show the corresponding weighted phase functions B A V calculated by convolving each phase function with the ECO VSF weighting functions W w illustrated in Fig 5 2 The response calibration factor for a given bead concentration CO to CN is determined as bi X B X Von V V v V4 V where the polystrene sphere phase function P Q V is determined from 5 15 If necessary the coefficient for Fa YW 5 16 each Cn is adjusted for dependence on the beam attenuation coefficient and the sample is averaged to obtain the linear calibration coefficient F v Given VSF measurements V v in an unknown natural water mass the m weighted VSF for particles is calculated as B 2 9 2 F v V v V v V v 5 17 5 3 CHARACTERIZATION and CALIBRATION OF A VSF SENSOR USING A REFLECTING PLAQUE Maffione and Dana 1997 approach the calibration of a VSF sensor by inserting a horizontal plaque of assumed Lambertian reflectance into the position of the xy plane illustrated in Fig 5 1 Substituting this reflectance for n the VSF in 5 6 and integrating over x and y yields the equation W x c dxdy Ew z c 5 18 x amp amp 5h o Azc p xx 73 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV
208. ion filtration assembly is illustrated in Mitchell et al 2000 Pre soak each filter for at least 15 min in 10 HCl Rinse the filter thoroughly with purified water Mount the filter on a filtration funnel and filter 100 mL of purified water through it into a sample bottle Shake the bottle and discard the water pouring it over the inside of the cap to rinse it Cover the filtration funnel with aluminum foil until ready to filter the sample Collect 200 mL of seawater into a clean sample bottle For the blanks use purified water drawn directly from the purification unit into 2 clean sample bottles Filter 75 mL of the samples and 1 blank directly into clean bottles at low vacuum 120 mm Hg Do not allow filters to go dry during sample rinsing Shake the bottles and discard the water Filter 75 mL of the samples into bottles For the blank filter 75 mL of purified water When finished cap the bottles and store them until they are to be measured in the spectrophotometer If the samples will be measured within 4 hr store them in the dark at room temperature If the samples will be measured 4 hr to 24 hr later refrigerate them in the dark Longer storage is not recommended because artifacts of undocumented magnitude are known to occur Several researchers have reported results from measurements of frozen samples but no systematic evaluation of possible artifacts resulting from freezing has yet been reported Warm refrigerate
209. ion are possible in order to quantify relative proportions of each pigment in a co eluting pair Determination of Algal Chlorophyll and Carotenoid Pigments by HPLC Wright et al 1991 a Equipment and reagents 1 Reagents HPLC grade acetone for pigment extraction HPLC grade water methanol acetonitrile and ethyl acetate 0 5 M ammonium acetate aq pH 7 2 and BHT 2 6 di tert butyl p cresol Sigma Chemical Co 2 High pressure injector valve equipped with a 200uL sample loop 3 Guard column 50 mm x 4 6 mm ODS 2 Spherisorb Cig packing material 5 um particle size for extending the life of the primary column 4 Reverse phase HPLC column with end capping 250 mm x 4 6 mm 5 um particle size ODS 2 Spherisorb C g column 5 Variable wavelength or filter absorbance detector with low volume flow through cell Detection wavelengths are 436 nm and 450 nm 6 Data recording device a strip chart recorder or preferably an electronic integrator and computer equipped with hardware and software for chromatographic data analysis 7 Glass syringe 500 uL or HPLC autosampler 8 HPLC Solvents solvent A 80 20 by volume methanol 0 5 M ammonium acetate aq pH 7 2 0 01 BHT w v solvent B 87 5 12 5 by volume acetonitrile water 0 01 BHT w v and solvent C ethyl acetate Solvents A and B contain BHT to prevent the formation of chlorophyll a allomers Use HPLC grade solvents Measure volumes before mixing Filter solve
210. is batch generally 40 55 samples is reviewed by Jeffrey Merriam for QC compliance All users are trained by the lab manager and must demonstrate through close supervision and inspection proficiency with the analytical instrumentation used and required laboratory procedures II Standard Operating Procedures Standard Operating Procedures for all instruments and methods are kept in a 3 ring binder in the laboratory and are stored electronically on the Lab manager s computer The electronic versions are password protected SOPs are reviewed annually or as changes are required due to new instrumentation or method development Page E 1 III Field Sampling Protocols Sample collection procedures are generally left up to the sample originators however we recommend the guidelines described below and provide our field filtering protocol on request All samples are filtered in the field through 0 7 um precombusted 5 hours at 450 C glass fiber filters e g Whatman GF F Samples are collected in acid washed 60 mL HDPE bottles We prefer plastic to glass as our preservative technique is to freeze Sample containers are rinsed 3 times with filtered sample and the bottle is filled with filtered sample Samples are stored in the dark and as cool as possible until they can be frozen Samples must be frozen within 8 hours of sample collection Once frozen samples can be stored indefinitely Avanzino and Kennedy 1993 although they are typical
211. is not meant as a substitute for scientific literature Instead it will provide a ready and responsive vehicle for the multitude of technical reports issued by an operational Project The contributions are published as submitted after only minor editing to correct obvious grammatical or clerical errors Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Table of Contents CHAPTER 1 nie eee ete SUSER DEER ERE RES N o ER eese see Vero ee bass elee ERE e SEES SETE TRES SEES SS SENSE SES SER SEERE 1 OVERVIEW OF BIOGEOCHEMICAL MEASUREMENTS AND DATA ANALYSIS IN OCEAN COLOR RESEARCH 1 INIRODUCGCTION EL DE eee Rp a Foe it enone 1 1 2 PHYTOPLANKTON PIGMENT CONCENTRA TIONS sese 1 High Performance Liquid Chromatography HPLC Measurements and Analysis 1 Fluorometric Measurement of Chlorophyll a Concentration eee 1 Phycoerythrin and other Phycobiliproteins eene eren 2 1 3 IN SITU CHLOROPHYLL A FLUORESCENCE eere eene 2 I SUSPENDED PARTICLES 4 re nt E HEU ER te INE RU PEERS EHE R Ss 3 Suspended Particulate Matter eese ete eterne eret 3 Particulate Organic Carbon and Particulate Organic Nitrogen eee 3 Particle Size Distributions siete e te etie e e eti e ee ei deua 3 Goccolith Concentrations ti e eee e RR TEE ER EN DU Te RESTE aa 3 L5 F UTURE BDIRECTIONS 5 5 erede e ea e ITE ERU
212. ith the purified water that has been filtered as though it were a sample and record the blank spectrum OD 4 relative to the reference cuvette filled directly from the purified water source e Repeat the rinsing for each subsequent sample The first sample rinse for seawater samples is most important to eliminate all purified water especially for seawater samples due to refractive index differences between fresh and salt water Fill the cuvette with the next water sample e Prior to running each sample dry the exterior of the sample cuvette carefully and inspect it as described above to ensure a clean sample e Replace the sample cuvette in the spectrophotometer and measure the OD 4 spectrum relative to freshly purified water Store the digital data and record all necessary information 4 6 DATA PROCESSING AND ANALYSIS The protocols in this section should be followed to compute particle and soluble material absorption coefficients from the spectrophotometric OD measurements described above The following discussion assumes that all measured OD 4 spectra whether for samples or reference blanks have been corrected for the instrument baseline spectrum either automatically or by post measurement calculations appropriate to a particular spectrophotometer configuration see above in Section 4 3 and specific reference spectrum measurement checks in the protocols of Sections 4 4 and 4 5 Computations for absorption coeffici
213. itive Vol I Ch 2 Sect 2 4 the absorption and scattering properties of natural water consists of the sums of these IOP of pure water suspended particles dissolved substances and turbulence It is very difficult to experimentally determine the absorption of pure water in the laboratory due principally to the difficulty of making and maintaining pure water during the course of an experiment Nevertheless there have been several successful experiments several are cited below over the past few decades and the spectral absorption and scattering coefficients of pure water are reasonably well known Using this information several types of IOP instruments are calibrated by measuring their responses using pure water as an optical standard Thus the calibrated responses of these instruments in field measurements represent the IOP of particles and dissolved material independent of water IOP From another perspective the general characteristics of absorption and scattering properties vary spectrally and in the case of scattering angularly between the different optically important constituents of seawater The contrast in angular distribution characteristics of scattering by water and by particles can be an important element of instrument design concepts Absorption by Pure Water The spectral values recommended in Vol I Ch 2 Sect 2 4 for the volume absorption coefficients of pure water dy A m are those of Sogandares and Fry 1997 for w
214. izontal plane is shown passing through the the source beam a nearly transparent light shaded ellipse and detector FOV a dark shaded ellipse the intersection of the source beam and detector FOV is the intermediate gray shaded area The plane is divided into elemental volume elements AV AxAyAz and a particular volume element is denoted AV x The radiant flux amp emitted by the source is assumed to be evenly distributed over the solid angle so by definition the source radiant intensity is by definition 7 2 The flux transmitted in direction o 1 x X where the vector length x Vx x from the source to the elemental volume AV x is Ix F AQ AV x Ao AV x c 1 AQ AV x Jexp c s exp c x 5 1 os AvAy x eA where AO Av x is the solid angle subtended at the source by the horizontal elemental area XeX AxAy at position X and fi is the unit normal to the xy plane Fig 5 1 Thus the irradiance incident on AV x is AQ AV x Q o E xc as e z The radiant flux intensity scattered from AV x in direction x x toward the detector at x is exp cs 5 2 I5 w s P w 3 E s AV 53 where the scattering angle y x for the incremental volume element is 67 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV cos w x amp X 8
215. l be on file at the NHEP offices in Durham NH Interim Report The NHEP QA Officer will prepare a report to EPA on the status of the project by 12 31 07 The interim status report will summarize the field data collection activities that occurred in 2007 and will note any discrepancies from the QAPP Final Report The Project Manager will prepare a final report to EPA by 6 30 08 The final report will contain the planned outputs for the project listed below conclusions and recommendations Planned Outputs e A single or multi variate model between the light attenuation coefficient and concentrations of CDOM turbidity suspended solids and chlorophyll a for the Great Bay system which can be used to develop numeric nutrient criteria e Maps of the distribution of CDOM turbidity and chlorophyll a and light attenuation using the model described above on at least two different days for the entire Great Bay system and e A calibrated light availability model for the Great Bay system Archiving Water quality data from the study will be permanently archived in the DES Environmental Monitoring Database EMD with all relevant metadata Hyperspectral imagery data will be permanently archived in the NH GIS repository GRANIT with all relevant metadata The QAPP interim report and final report will be kept on file at the NHEP for a minimum of 10 years after the publication date of the final report All data from the project will be made availa
216. latively minor changes in e g cross referencing and to maintain self contained consistency in the protocol manual More critically as it grows bigger the book becomes more difficult to use by its intended audience A massive new protocol manual is difficult for a reader to peruse thoroughly enough to stay current with and apply important new material and revisions it may contain Many people simply find it too time consuming to keep up with changing protocols presented in this format which may explain why some relatively recent technical reports and journal articles cite Mueller and Austin 1995 rather than the then current more correct protocol document It is hoped that the new format will improve community access to current protocols by stabilizing those volumes and chapters that do not change significantly over periods of several years and introducing most new major revisions as new chapters to be added to an existing volume without revision of its previous contents The relationships between the Revision 4 chapters of each protocol volume and those of Revision 3 Mueller and Fargion 2002 and the topics new chapters are briefly summarized below Volume I This volume covers perspectives on ocean color research and validation Chapter 1 fundamental definitions terminology relationships and conventions used throughout the protocol document Chapter 2 requirements for specific in situ observations Chapter 3 and general protocols for fi
217. le intermediate save so as to not lose data eae Ff At this point the Diffuse Attenuation Coefficients Ka should have been calculated for each station at which you did the regression Ka 1 x coefficient from the regression For Great Bay values of Ka should range from 0 5 clear to 6 0 very turbid QA QC Examine the regression output data a Acceptable regressions must have an R gt 0 95 and for stations with an optimal number of sample depths gt 8 should have an R gt 0 98 b Examine the Quantum Raw Water data These data should show a continuous decrease with depth except for the odd cases where the Quantum Air data increased significantly from the preceding reading e g the passing of a cloud Highlight any questionable reading by applying an Orange fill to the cells in question In the event that the R 0 95 and there is a data point at the top or bottom of the profile that is clearly bad these are the most likely places for this to occur because of surface reflection or sediment resuspension you may choose to run the regression again omitting the suspect data In such cases it is imperative that you make a notation in Column I just below the KG calculation block Appendix F Standard Operating Procedure for EPA Water Quality Project 1 Navigate to station use attached maps and note station date time location and water depth below 2 Measure water temperature salinity and PAR and reco
218. lecular and particle absorption OCEAN OPTICS X SPIE 1302 149 156 13 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Voss K J 1989 Use of the radiance distribution to measure the optical absorption coefficient in the ocean Limnol Oceanogr 34 1614 1622 Van Zee H D Hankins and C deLespinasse 2002 ac 9 Protocol Document Revision F WET Labs Inc Philomath OR 41pp Wells W H 1983 Techniques for measuring radiance in sea and air Appl Opt 22 2313 2321 Zaneveld J R V E Boss and A Barnard 2001 Influence of surface waves on measured and modeled irradiance profiles Appl Opt 40 9 1442 1449 Zaneveld J R V J C Kitchen A Bricaud and C Moore 1992 Analysis of in situ spectral absorption meter data Ocean Optics XI G D Gilbert Ed SPIE 1750 187 200 Zaneveld J R V and H Pak 1972 Some aspects of the axially symmetric submarine daylight field J Geophys Res 77 15 2677 2680 14 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Chapter 2 Beam Transmission and Attenuation Coefficients Instruments Characterization Field Measurements and Data Analysis Protocols Scott Pegau J Ronald V Zaneveld and James L Mueller College of Oceanographic and Atmospheric Sciences Oregon State University Corvallis Center for Hydro Optics and Remote Sensing San Diego State University California
219. lidation Revision 4 Volume IV Scattering by Particles In many natural waters the volume scattering coefficient for particles b X is comparable to or larger than that of pure water Moreover the shape of a particle scattering phase function B v an example of which is illustrated as the solid curve in Fig 1 3 is strongly peaked by several orders of magnitude in the forward direction The extreme contrast between the angular probability distributions of particulate and molecular scattering the dashed curve in Fig 1 3 are important factors that must be considered when designing transmissometers and scattering meters for use in the sea 0 90 180 Scattering Angle y degrees Fig 1 3 The solid curve is an example of a measured scattering phase function for ocean water dominated by particle scattering Petzold 1972 San Diego Harbor Stn 2040 The dashed curve is the pure water phase function from Fig 1 2 shown here for comparison Scattering by Turbulence Random fluctuations in water density induced by turbulence act to steer photons through very small angles in the forward direction and therefore scattering by turbulence is also strongly peaked by orders of magnitude in the forward direction Because turbulent fluctuations are completely random in space and time the variance of photons scattered by turbulence at small angles is much greater than the variance associated with small angle scattering by particl
220. liquid nitrogen Liquid nitrogen is the best method for storing samples with minimum degradation for short as well as longer storage times e g 1 year Placing samples in liquid nitrogen also assists in pigment extraction by weakening the cell wall and membrane during this rapid temperature change Ultra cold freezers 90 C can be used for storage although they have not been tested for longer than 60 days Jeffrey et al 1997 Conventional deep freezers should not be used for storing samples more than 20 hours before transferring them to an ultra cold freezer or liquid nitrogen Again storage of samples in liquid nitrogen immediately after filtration is the preferred method Samples should be folded in half with the filtered halves facing in This eliminates problems of rubbing particles off the filter during placement in sample containers and storage It is strongly recommended to use aluminum foil wrappings for sample containers This simple but effective container is both inexpensive and easy to use Cut small pieces of heavy duty aluminum foil into approximately 4 cm squares Fold each piece in half and using a fine point permanent marker write a short sample identifier e g first letter of the cruise and a sequential sample number on the foil Writing on the folded foil prior to placement of the filter both avoids puncturing the foil with the marking pen and improves the legibility of the sample identifier Place the folded filter i
221. ll a are shown in Figures 3 1 3 2 and 3 3 for three cruises in different geographic areas In each example the regression slopes are significantly different from a one to one relationship although for the Gulf of California GoCAL November 1996 Figure 3 3 the slope is close to unity One to one ratios have also been found for other geographic areas but not necessarily during all seasons Therefore the relationship slope and offset between HPLC total chlorophyll a and fluorometric chlorophyll a must be determined for a selected number of samples for each cruise so that a cruise specific scaling factor can be applied to other fluorometric samples The protocols specified below for fluorometric chlorophyll a analyses follow closely those prescribed in the JGOFS Core Measurement Protocols UNESCO 1994 but they differ in one important respect Absorption of light in seawater or any other medium is a volumetric process even though the volume absorption coefficient may 15 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 vary with the density of the medium For ocean color and optical analyses therefore the concentration of chlorophyll a shall be expressed in units of mass per unit volume of seawater either in ug L or mg m This differs from the JGOFS protocols which specify that concentrations in seawater of chlorophyll a and pheopigments should be expressed in ug kg 3 2 SAMPLE ACQUISITION A
222. lor validation together with methods of analyzing the data Chapter 1 detailed measurement and data analysis protocols for in water radiometric profiles Chapter 2 above water measurements of remote sensing reflectance Chapter III 3 determinations of exact normalized water leaving radiance Chapter 4 and atmospheric radiometric measurements to determine aerosol optical thickness and sky radiance distributions Chapter 5 Chapter 1 is adapted from relevant portions of Chapter 9 in Revision 3 Chapter 2 of Volume III corresponds to Chapter 10 of Revision 3 and Chapters 3 through 5 to Revision 3 Chapters 12 through 14 respectively Aside from reorganization there are no changes in the protocols presented in this volume Volume IV This volume includes a chapter reviewing the scope of inherent optical properties IOP measurements Chapter 1 followed by 4 chapters giving detailed calibration measurement and analysis protocols for the beam attenuation coefficient Chapter 2 the volume absorption coefficient measured in situ Chapter 3 laboratory measurements of the volume absorption coefficients from discrete filtered seawater samples Chapter 4 and in situ measurements of the volume scattering function including determinations of the backscattering coefficient Chapter 5 Chapter 4 of Volume IV is a slightly revised version of Chapter 15 in Revision 3 while the remaining chapters of this volume are entirely new contributions to the ocean o
223. low for HPLC pigment analyses follow closely those prescribed in the JGOFS Core Measurement Protocols UNESCO 1994 Both sets of protocols include 1 Use of Whatman GF F glass fiber filters approximately 0 7 um pore size 2 Extraction in aqueous acetone and 3 Calibration with standards The present protocols differ from the JGOFS protocols in one critical respect Absorption of light in seawater or any other medium is a volumetric process even though the volume absorption coefficient may vary with the density of the medium For ocean color and optical analyses therefore the concentrations in seawater of all phytoplankton pigments shall be expressed in units of mass per unit volume of seawater ug L or mg m This differs from the JGOFS protocols which specify that concentrations in seawater of all phytoplankton pigments should be expressed in ng Kg In addition to HPLC analyses it is recommended that the standard fluorometric methodology used for measuring chlorophylls and pheopigments Holm Hansen et al 1965 Strickland and Parson 1972 also be applied to the same extracted pigment samples used for HPLC analysis Protocols for fluorometric measurements of chlorophyll a and pheopigments are given here in Chapter 3 of the present volume For a more in depth review of guidelines for measuring phytoplankton pigments in oceanography see Jeffrey et al 1997 2 2 SAMPLING PROTOCOLS FOR PHYTOPLANKTON PIGMENTS Water Samples Water sam
224. ly analyzed within a few months After collection and freezing samples are either hand delivered to the lab or are shipped via an over night carrier Samples arriving in the lab are inspected for frozen contents broken caps cracked bottles illegible labels etc Any pertinent information is entered into a password protected database MS Access We do not require chain of custody paperwork unless a specific project requires it If a project requires chain of custody forms are provided by the specific project s manager IV Laboratory Sample Handling Procedures Samples are given a unique 5 digit code This code and sample information including name collection date time if applicable project name collector logger the Page E 2 date received at the WQAL sample type e g groundwater surface water soil solution and any other miscellaneous information are entered into a password protected database From this point through the completion of all analyses we use the log number to track samples Log numbers are used on sample run queues spreadsheets and when importing concentrations and run information into the database After samples are logged into the WQAL they are stored frozen in dedicated sample freezers located in the laboratory Samples from different projects are kept separated in cardboard box tops or in plastic bags Samples that may pose a contamination threat based on the source or presumed concentration range are
225. m and detector FOV the shaded conical region in Fig 3 2 is negligibly small compared to the flux reflected from the plaque At this point it may be appropriate for the reader to compare the similarities between the instrument concept illustrated Fig 2 2 Chapter 2 and the calibration geometry for determining the weighting function of a VSF as illustrated in Fig 5 1 and as described for a plaque reflectance measurement geometry at a fixed distance z as part of the VSF calibration described in Sect 5 2 Chapter 5 of this volume and in Maffione and Dana 1997 Following the approach used to determine the backscattering coefficient from a measurement B y of the VSF at a single angle w in the backward direction Chapter 5 Sect 5 4 Dana Maffione and Coenen HOBILabs Inc personal comm circa 2000 originally assumed that b b xB w 3 6 where y is an unknown constant The a Beta instrument designed and manufactured by HOBILabs combines a VSF meter Chapter 5 to measure B 140 with a device conceptually similar to that illustrated in Fig 3 2 mounted at opposite ends of a small cylinder If the source is regulated to emit constant flux the system constants of the diffuse reflectance device may be collected as k Ek Pk o 3 7 Tt where F is the detector assembly s signal responsivity to flux received at the instrument window in water i e dark y Vj EF V and V are the detector flux response a
226. m light to minimize photodegradation of the samples e For each sample place a GF F filter onto the filtration rig Also prepare two blank GF F filters by soaking them in 25 ml of 0 2 um filtered water while mounted on the filtration funnel with valves closed during the sample filtration e Filter the samples on GF F filters under low vacuum 125 mm Hg e Filter a sufficient volume of water Vf to yield sample optical density relative to the blank filter in the range specified above For field samples collected in the upper 100 150 m and filtered onto 25 mm GF F filters Veis typically in the range 0 5 L to 5 L depending on the in situ density concentration of particles e Do not let the preparations run dry during filtration Turn off the vacuum to each sample as it completes filtering Immediately place samples on a drop of 0 2 um FSW in the appropriate container depending on how they will be stored e Record the filter and filtration funnel type the diameter Dr of the area on the filter that contains the concentrated particles and the volume of water filtered V y e Measure the absorption spectra in a spectrophotometer or store the filters in liquid nitrogen as soon as possible 43 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV b Sample Filter Storage e If the filter samples will be analyzed immediately store each filter in a labeled petri dish e g Gelman snap top dishes
227. mall angle scattering acceptance J Atmos and Oceanic Tech 19 1 113 121 Wattenberg H 1938 Untersuchungen uber Durchsichtigkeit und Farbe des Seewassers I Kieler Meeresforsch 2 26 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Chapter 3 Volume Absorption Coefficients Instruments Characterization Field Measurements and Data Analysis Protocols Scott Pegau J Ronald V Zaneveld and James L Mueller College of Oceanographic and Atmospheric Sciences Oregon State University Corvallis Center for Hydro Optics and Remote Sensing San Diego State University California 3 1 INTRODUCTION Concepts and methods for measuring the absorption coefficient a X of seawater are briefly reviewed in Chapter 1 Sect 1 4 of this Volume Chapter 4 of this Volume is devoted to laboratory spectrophotometric methods of measuring absorption of particles and dissolved materials in filtered water samples The present chapter focuses on commercially available instruments that may be used from ships and moored platforms to practically measure a X in support of satellite validation activities This first version of absorption protocols is particularly focused on instruments that fall under the reflective tube design concept briefly introduced in Sect 1 4 However the conceptual basis for determining absorption by measuring flux reflected from a diffuse target is also described later in this s
228. many of the Volumes and Chapters of this protocol document The chapters of this volume Vol IV describe the conceptual background instrument characteristics and methods of calibration field measurements and data analysis for determining the IOP of seawater The scope of this protocol volume is limited to practical methods for using commercially available instruments to determine the IOP identified in Vol I Chapter 3 Table 3 1 of Ocean Optics Protocols for Satellite Ocean Color Sensor Validation Rev 4 The scope of the present volume does not include applications of measured IOP to aspects of ocean color sensor validation that are described elsewhere in the document The role of IOP in the determination of Exact Normalized Water Leaving Radiance Lyn X as a function of wavelength A for example is discussed in Vol III Chapter 4 In this chapter we extend the IOP definitions and relationships of Vol I Ch 2 to develop the theoretical and mathematical bases for practical instrument concepts and methods for measuring IOP in seawater Instruments will be described to measure in situ at depth z the beam attenuation coefficient c z X the volume absorption coefficient a z X and the volume scattering function VSF B z A w at one or more scattering angles v Spectrophotometric laboratory methods are also described in detail for determining absorption coefficients from filtered discrete water samples Methods of data analysis are desc
229. measurement of photosynthetic pigments in freshwaters and standardization of methods conclusion and recommendations Arch Hydrobiol Beih Ergebn Limnol 14 91 106 Phinney D A C S Yentsch 1985 A novel phytoplankton chlorophyll technique Toward automated analysis J Plankton Res 77 633 642 Smith R C R R Bidigare B B Prezelin K S Baker and J M Brooks 1987 Optical characterization of primary productivity across a coastal front Mar Biol 96 575 591 Snyder L R and Kirkland J J 1979 Quantitative and trace analysis In Introduction to modern liquid chromatography John Wiley and Sons New York 541 574 Strickland J D H and T R Parsons 1972 A Practical Handbook of Sea Water Analysis Fisheries Research Board of Canada 310 pp Tester P A M E Geesey C Guo H W Paerl and D F Millie 1995 Evaluating phytoplankton dynamics in the Newport River estuary North Caroline USA by HPLC derived pigment profiles Mar Ecol Prog Ser 124 237 245 Trees C C M C Kennicutt II and J M Brooks 1985 Errors associated with the standard fluorometric determination of chlorophylls and pheopigments Mar Chem 17 1 12 Trees C C D C Clark R R Bidigare M E Ondrusek and J L Mueller 2000 Accessory pigments versus chlorophyll a concentrations within he euphotic zone a ubiquitous relationship Limnol Oceanogr 45 5 1130 1143 UNESCO 1994 Protocols for the Joint Global Ocean Flux Stud
230. ment were introduced in Chapter 2 and will not be repeated here Moreover the manufacturer provides extremely detailed 31 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV protocols for calibrating and using this instrument and for analyzing its data both in the ac 9 User Manual and in a detailed protocol manual Van Zee et al 2002 both of which are available online www wetlabs com Additional background information related to characterization calibration and data analysis methods for this instrument may be found in Moore et al 1992 Zaneveld et al 1992 and Twardowski et al 1999 Here we will briefly highlight critical aspects of the protocols that must be carefully followed to obtain accurate a X measurements using this or a similar instrument in the field Many of these topics as they relate to the beam transmissometer side of the instrument have been discussed in Chapter 2 of this volume Bulkhead Pressure sensor connector AL Optional mum Reflecting Tube Absorption Beam Transmissometer Components Meter Components Chapter 3 EM Chapter 2 Upper can Large Area Detector Collimated Detector a Detector c Receiver LEE v Sleeve w Lip Sleeve No Lip O ring Black Plastic Reflecting Quartz Flow Flow Tube Liner Non Reflecting Tube Ee Liner c Flow Tube Flow Tube a Flow Tube O ring A Stainless Sleeve w Lip Nozzles em
231. ments with RPD x 30 Precision an independently calibrated meter Activity 1 or grab samples 2s Buoy sensor Accuracy Calibration check with known Calibrations are performed on measurements standards schedule Commies Data completeness check by QA 80 of planned measurements Officer must be collected M Accuracy Calibration with a NIST traceable RPD lt 5 e E 1 irradiance spectral radiance nr i Accuracy position Comparison of imagery to USGS MEDIE imagery collected digital orthophoto quads from 3 800 m altitude Field replicate measurements with RPD lt 30 van Precision grab samples collected along flow Activity 3 through transect Flow through Calibration check with known Calibrations are performed on SUEVEY Accuracy standards schedule Mi do Companies Data completeness check by QA 80 of planned measurements Officer must be collected 0 Precision field Field replicate Sere LIS 0 Activity 4 Precision lab Laboratory replicates TRENA Grab samples for laboratory A Independent calibration Calibrations are performed on analysis setae lap verification samples schedule Completeness Data completeness check by QA 80 of planned measurements Officer must be collected The sampling stations will be situated within the study area Grab samples and hyperspectral imagery will be collected during the index Representativeness period of 7 1 07 to 10 31 07 Grab samples will be collected within 1 Al hour of the flight time Flow through transec
232. merican Public Health Association American Water Works Association Water Environment Federation Clesceri L S A E Greenberg and A D Eaton eds 1998b Part 10000 Biological Examination Section 10200 B in Standard Methods for the Examination of Water and Wastewater 20th ed Baltimore MD American Public Health Association American Water Works Association Water Environment Federation Dickson M L and P A Weeller 1993 Chlorophyll a concentrations in the North Pacific Does a latitudinal gradient exist Limnol Oceanogr 38 1813 1818 Gordon H R and D K Clark 1980 Remote sensing optical properties of a stratified ocean an improved interpretation Appl Optics 19 3 428 3 430 Hoepffner N and S Sathyendranath 1992 Bio optical characteristics of coastal waters absorption spectra of phytoplankton and pigment distribution in the western North Atlantic Limnol Oceanogr 37 1660 1679 24 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Holm Hansen O C J Lorenzen R W Holmes and J D H Strickland 1965 Fluorometric determination of chlorophyll J du Cons Intl Pour l Expl de la Mer 30 3 15 Jeffrey S W R F C Mantoura and S W Wright eds 1997 Phytoplankton Pigments in Oceanography Monographs on Oceanographic Methodology UNESCO 661 pp Lorenzen C J and S W Jeffrey 1980 Determination of Chlorophyll in Seawater UNESCO Technical Papers in Marine S
233. n Revision 4 Volume 5 detailed measurement and data analysis protocols for in water radiometric profiles Chapter 2 above water measurements of remote sensing reflectance Chapter III 3 determinations of exact normalized water leaving radiance Chapter 4 and atmospheric radiometric measurements to determine aerosol optical thickness and sky radiance distributions Chapter 5 Chapter 1 is adapted from relevant portions of Chapter 9 in Revision 3 Chapter 2 of Volume III corresponds to Chapter 10 of Revision 3 and Chapters 3 through 5 to Revision 3 Chapters 12 through 14 respectively Aside from reorganization there are no changes in the protocols presented in this volume Volume IV This volume includes a chapter reviewing the scope of inherent optical properties IOP measurements Chapter 1 followed by 4 chapters giving detailed calibration measurement and analysis protocols for the beam attenuation coefficient Chapter 2 the volume absorption coefficient measured in situ Chapter 3 laboratory measurements of the volume absorption coefficients from discrete filtered seawater samples Chapter 4 and in situ measurements of the volume scattering function including determinations of the backscattering coefficient Chapter 5 Chapter 4 of Volume IV is a slightly revised version of Chapter 15 in Revision 3 while the remaining chapters of this volume are entirely new contributions to the ocean optics protocols These new chapters may be sign
234. n are too high The very reasonable or slightly high by about 10 15 values for the mean cosine of downwelling irradiance shown in Figure 4 4 for 400 600 nm indicates that the absorption methods recommended here are rather robust compared to simple estimates of diffuse attenuation coefficients Reynolds et al 2001 and Stramska et al 2000 have reported reasonable closure between estimates of absorption using these methods radiometric observations and modeling We have used pure water absorption for our estimate of a 4 and salts should in fact be added if important in the comparison of absorption to diffuse attenuation in Figure 4 4 Our estimate of a 4 relative to purified water will include absorption by salts if they are significant Salts in seawater are significant absorbers at short wavelengths Lenoble 1956 see also Shiffrin 1988 reported values for pure salts dissolved in purified water that indicate absorption coefficients near 300 nm comparable to the sample optical density of filtered samples relative to purified water that we routinely determine at sea in this spectral region This UV absorption lt 320 nm relative to purified water is generally assumed to be caused by colored dissolved organic matter but this may be inaccurate at these short wavelengths Therefore one must be very cautious interpreting the apparent optical density of seawater filtrates relative to purified water for wavelengths less than 320nm We r
235. n at least two different days for the entire Great Bay system and C A calibrated light availability model for the Great Bay system All three of the outputs will support the expected outcome of developing numeric nutrient criteria for water clarity and therefore the protection of eelgrass beds Eelgrass is a critical estuarine habitat The protection of this habitat would benefit all users of the estuary fish waterfowl and humans Presentations of the plans for the studies and the results of the research will be made to the NHEP Technical Advisory Committee which is serving as the advisory group to DES on the process of developing nutrient criteria Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 8 Progress toward achieving these outputs will be documented in one interim and one final report to EPA The desired outcome will be achieved when NHEP makes a recommendation to the Water Quality Standards Advisory Committee for a water clarity based water quality criterion for NH s estuaries The project will be completed in the Great Bay estuarine system of NH and Maine This area encompasses the Great Bay Little Bay Piscataqua River and some or all of the tidal portions of the Winnicut Squamscott Lamprey Oyster Bellamy Cocheco and Salmon Falls Rivers Figure 4 Approximately 40 square kilometers of estuarine waters will be part of the study area Figure 2 Dissolved inorganic nitrogen concentrations in Grea
236. n of the general form of 5 7 is straightforward The more difficult aspect of obtaining generalized weighting functions is the experimental determination of the functions A e9 and h 8e The detector FOV responsivity distribution function may be measured by mounting the detector in a rotating stage with its entrance aperture centered on the intersection of the axis of rotation and the optical axis of a stable collimated source The stage is rotated in small angular increments and the detector response is recorded at each angle to measure the relative variations in response in one plane containing The instrument is then rotated in increments about and the process is repeated to map the distribution of responses in a sequence of planes adequate to resolve the full function A eo This is essentially the same procedure used to characterize the angular FOV of field radiometers Vol II Ch 3 The inverse of the above setup may be used to map the flux distribution of the source beam The instrument is mounted with the source aligned with the optical and rotation axes and a narrow FOV detector is substituted for the collimated source The stage is rotated through a suitable angular range to map out flux variations in a plane through and the instrument is rotated about and the process repeated to measure flux distributions in a sequence of planes If the temporal stability of flux output by the source is in questi
237. n the aluminum foil Fold the three open sides to form an envelope that is only slightly larger than the folded filter 3 cm x 1 5 cm The use of foil containers minimizes the size requirement of the storage container It is also acceptable to use either cryogenic tubes or HistoPrep tissue capsules but they occupy more storage volume per sample and they are more expensive than aluminum foil If fluorometric analysis is to be done soon after collection it is still recommended to place the samples in liquid nitrogen to assist in pigment extraction and on removal from the liquid nitrogen to place them immediately in chilled 90 acetone Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Recordkeeping Information regarding sample identification should be logged in a laboratory notebook with the analyst s initials For each filter sample record the sample identifier as written on the sample container station number for the cruise water volume filtered Vs 1 in mL and depth of the water sample together with the date time latitude and longitude of the bottle cast during which the sample was acquired 2 3 LABORATORY METHODS FOR HPLC PHYTOPLANKTON PIGMENT ANALYSIS Internal Standard and Solvent Preparation In addition to daily calibration of the HPLC system with external standards an internal standard e g canthaxanthin should be used to determine the extraction volume It is important to verify th
238. n the injector valve overfilling the 200 uL sample loop 2 5 fold To check for possible interferences in the extraction solvent and or filter prepare a blank by extracting a glass fiber filter in 90 acetone mixing 1000 uL of the 90 acetone filter extract and 300 uL distilled water and injecting the mixture onto the HPLC system For each pigment i plot absorbance peak areas arbitrary system units against working standard pigment masses concentrations multiplied by injection volume The HPLC system response factor F area ug for pigment i is calculated as the slope of the regression of the peak areas of the parent pigment plus areas of peaks for structurally related isomers if present against the pigment masses of the injected working standards ug Structurally related isomers e g chlorophyll a allomer contribute to the absorption signal of the standards and disregarding them will result in the over estimation of analytes in sample extracts Bidigare 1991 Prepare pigment samples for injection by mixing a 1000 uL portion of the aqueous acetone pigment extract and 300 uL distilled water shake and equilibrate for 5 min prior to injection Inject the sample onto the HPLC column Samples that are pre mixed with distilled water or other injection buffer should not be allowed to reside in autosampler compartments for extended durations because hydrophobic pigments will precipitate out of solution Mantoura eft al 1997 10 Ocean O
239. nal choice of p is difficult to assess because the de pigmented particles are created operationally from the treatment and the relationships between their absorption on filters compared to suspensions may differ from those derived empirically for the original particles The spectral absorption coefficient for phytoplankton pigments can be computed as the difference between particulate and de pigmented estimates dj 4 a 4 a4 4 4 7 4 7 DATA REPORTING For purposes of data reporting and archiving the absorption coefficients will be reported in m and computed using the equations summarized above Uncorrected optical density spectra for the filter samples blank filter referenced to a blank filter pure water referenced to air pure water referenced to pure water and soluble absorption blank spectra must be recorded and provided so alternative algorithms could be applied to the original data The pathlength amplification factor a description of or reference to the method and the procedure for assignment of the null absorption and any blank or spectral scattering corrections for the soluble absorption calculations must be reported 4 9 PROTOCOL STATUS AND FUTURE DIRECTIONS Absorption spectra for particles filtered on GF F filters Details of various issues related to this frequently used method for estimating particle absorption for filtered samples are not significantly changed since the summary of the NASA sponsored Workshops foun
240. nate method for preparing samples for soluble absorption allows multiple use of Sterivex sealed filtration cartridges Use of these cartridges has been described by D Sa et al 1999 who used the method to prepare samples delivered to a capillary light guide spectrophotometer for estimating absorption by soluble material The procedure provides high sensitivity and can be adapted to continuous flow determinations This new method may prove useful in various applications but has not been applied extensively at this time Evaluation of the performance of the Sterivex cartridges for sample preparation and of light guides for spectroscopy warrant further research Constraints on the estimate of soluble and particle absorption To constrain our water sample estimates of particle and soluble absorption we have compared them to spectral estimates of the diffuse attenuation coefficient for downwelling irradiance K z 4 determined using a free fall radiometer during a Southern Ocean cruise AMLR and a western Pacific Ocean cruise ACE Asia It is well known that accurate estimate of K z A in the upper ocean is difficult Problems include heave of the ship foam bubbles shadow tilt sky conditions and other influences on this apparent optical property see more detailed discussions in other chapters of these protocols Waters et al 1990 described advantages of free fall systems and many investigators have adopted this procedure to minimize some o
241. nce has been widely used to describe shapes of BO y in natural waters Mobley et al 2001 compared measured and modeled nadir viewing remote sensing reflectances using measured c X and a 4 with BO v of different assumed shapes including that of Petzold 1972 and the VSF measured using a general angle scattering meter of a new design Lee et al 2003 best agreement was achieved using the measured VSF Their results showed that large systematic offsets can result 1f one arbitrarily assumes a scattering phase function having an incorrect backward scattering fraction The results of Mobley er al 2001 also indicated that nadir viewing radiance reflectance is less sensitive to the detailed shape of the forward scattering lobe of BO v Details of scattering at intermediate forward angles might however be more important for off nadir viewing geometry Vol IIL Ch 4 At present commercially available VSF sensors are designed with detector beam spread and detector acceptance angles ranging from 10 to 20 Full Width Half Maximum FWHM These instruments measure the VSF weighted as in 1 19 at one or a few scattering angle s and are typically used to determine the backscattering coefficient using the methods described below in Sect 5 4 Although these methods depend on assumptions concerning BO wv determinations of b from VSF profile measurements with these instruments when combined with absorption and beam attenuati
242. nd dark response signals respectively d Substituting 3 6 and 3 7 allows 3 5 to be rewritten in terms of the dark corrected detector response V yp as 30 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV V VE F kexp 2a xB y Z and taking the natural logarithm of both sides and rearranging yields 1 arl a In k In V v 2 xp w 3 8 Equation 3 7 contains one unknown variable a two measured variables V v and B y and three unknown coefficients z the mean effective pathlength between the source or detector and reflectance target k an overall system optical characteristics constant and y the scaling factor relating the VSF at one angle to the combined sum of backscattering plus forward scattering beyond y for the two optical paths The constant coefficients in 3 8 may be determined by placing the a feta or a similar instrument in pure water and sequentially adding scattering and absorbing materials to increase a b and B y in n 1 2 N increments spanning a suitable range of each variable At each n incremental step the reflectance detector response V and VSF measurement p v are recorded together with the absorption coefficient a 4 measured In k 1 using a WET Labs ac 9 It is convenient to define two new constants y S and 9 e and express 3 8 in Z Z matrix form for the N sets of measurements as a Xy 3 9
243. nformances C2 Reports to Management The reports to management for this project are listed in Table 13 Table 13 List of Reports to Management Type of Report Preparer Recipient Schedule Interim Project Project Manager QAPP distribution list 12 31 07 Status Report Data Quality Audit NHEP QA QAPP distribution list 6 30 08 Officer Final Report Project Manager QAPP Distribution List 6 30 08 NHEP Technical Advisory Committee Public via NHEP website D1 Data Review Verification and Validation The Project Manager will review all monitoring results and evaluate QC requirements for usability in obtaining the objectives of the project based on the criteria established in Section A7 There are no project specific algorithms or calculations required to generate definitive water quality data D2 Verification and Validation Procedures The NHEP QA Officer will be responsible for ensuring that data meet the QC requirements in Section A7 The NHEP QA Officer will prepare a memo for the Project Manager which describes the data submittal any non conformances with the QAPP and any data that did not pass the QC requirements The Project Manager will undertake any of the following corrective actions as necessary if unacceptable results exist 1 Incomplete data Omissions from logs notebooks and worksheets place the entire analysis in question The Project Manager will consult with the field crews and the NH
244. ng locations within the Great Bay Estuary lab cT 2 0 2 4 6 8 10 Kilometers For the second task of the project the NHEP will arrange for at least two overflights to collect hyperspectral imagery of the entire Great Bay system The overflights will be conducted by SpecTIR www SpecTIR com SpecTIR proposes an airborne data collection with the VNIR sensor with a spatial resolution of 2 5 meters for the area of interest Figure 6 in red and a nominal spectral resolution of 10nm or 64 spectral channels from approximately 430 nm to 1000 nm The delivered product will consist of calibrated radiance and geographic lookup tables with navigation Navigation will be performed with high speed airborne DGPS integrated with a laser ring gyro Personnel in the company have more than 10 years in the planning of hyperspectral flights and the collection processing of airborne hyperspectral data Specifications for the SpecTIR VNIR sensor are appended to this workplan Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 11 Figure 6 Area for hyperspectral imagery collection shown in red 2 0 2 4 6 8 10 Kilometers The overflights will be coordinated with times of buoy operation grab sample collection and flow through surveys to ground truth the imagery Field sampling and buoy operation will be completed by the UNH Coastal Observing Center and the UNH Marine Program The flow through transects will
245. nly indirectly linked to first principles through debatable assumptions and its use is not recommended Although these measurements have been shown to contain errors as compared to HPLC determinations Trees et al 1985 Smith et al 1987 Hoepffner and Sathyendranath 1992 Bianchi et al 1995 Tester et al 1995 the CZCS phytoplankton pigment concentration algorithms were based on them entirely The SeaWiFS protocols for this analysis will be those given in Strickland and Parsons 1972 as updated by this chapter Pigment databases generally show a log normal distribution which is consistent with that proposed by Campbell 1995 for bio optical properties Therefore it is appropriate to perform log linear regressions on HPLC determined total chlorophyll a chlorophyllide a chlorophyll a epimer chlorophyll a allomer monovinyl chlorophyll a and divinyl chlorophyll a and fluorometrically determined chlorophyll a using model I regressions Standard Model I regressions were selected because HPLC determined total chlorophyll a concentrations are to be predicted from fluorometrically determined chlorophyll Model I regressions are appropriate for both predictions and determining functional relationships whereas Model II regressions should not be used to predict values of y given x page 543 Sokal and Rohlf 1995 Examples of regression models predicting log HPLC total chlorophyll a following Chapter 2 HPLC protocols from log fluorometric chlorophy
246. notonically with wavelength following exponential form that is flatter than the shape of the soluble absorption spectrum Since the goal is generally to get an estimate of phytoplankton absorption if there is a residual chlorophyll a absorption peak in the red near 675 nm the extraction process should be repeated to remove it Variations of this method include use of hot or boiling methanol and varying extraction times Use of hot methanol has risks due to flammability and volatility If this process is used extra precautions must be taken Bleaching of the organic pigments can also be accomplished for situations with difficult to extract pigments including phycobilins or other chemically polar pigments that do not extract well in methanol Pigment extraction in a chemical solvent such as methanol is a fundamentally different chemical process than bleaching the pigments using sodium hypochlorite NaClO Bleaching involves placing a small amount of 0 1 active chlorine solution onto the filter then rinsing it off with FSW The NaClO oxidizes the pigment molecules making their light absorption negligible FSW rinses then remove the excess NaClO which absorbs negligibly at wavelengths gt 400 nm but absorbs strongly at shorter wavelengths The bleaching method of pigment removal has been shown to be effective in situations where methanol cannot be used as on cellulose membranes such as the 0 22 um Millipore filter or when phycobilins are present Ta
247. ns of the purified water relative to air 1 is the apparent residual optical density at a long visible or near infrared wavelength where null e g OD 4 Figure 4 2 and also evaluate the sample preparation methods by determining the blanks routinely e g daily when at sea Figure 3B 51 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV a Filtered pure water blank spectra There are generally small spectral effects of the filtration and preparation procedure that cause blanks prepared from purified water to have a higher OD bs 4 at short wavelengths compared to the reference cuvette containing purified water drawn directly from the purification system Examples of filtered blank spectra OD bs 4 for ACE Asia where Millipore Alpha Q water was used as the purified water source in the reference cuvette are illustrated in Figures 4 3B and 4 3D c f Mitchell et al 2000 The OD bs 4 spectrum should be determined recorded and included with the data for each sample It is recommended that the investigator carefully determine these blanks for each station or at least once per day during a field program and evaluate the stability of this blank for quality control purposes If the purified water system is performing well and the preparation procedures are carefully implemented the OD bs 4 sample blank offsets will generally be very consistent Figure 4 3B In such cases the recommended proce
248. nstrument cage following directions provided by the manufacturer Van Zee et al 2002 It is strongly recommended to mount a CTD data the same profiling package as an ac 9 and to develop a method for accurately merging the measurements from both instruments combining the data streams from the two instruments in real time as part of the data acquisition system is the preferred approach with a second choice being to time tag both data records and merge the data on that basis The basis of these recommendations is that water temperature and salinity data are essential for the corrections described below in Sect 3 4 To begin a cast place the instrument package in the water before they are powered up Then hold the package underwater near the surface allow approximately 5 min for the instruments to warm up stabilize the electronics and reduce the possibility that thermal shock may adversely affect the measurements Monitor the instrument outputs and wait to begin profiling until the instrument stabilizes at the surface If an absorption meter will not stabilize its readings after 5 10 minutes under these conditions it is recommended that it be returned to the manufacturer for characterization of the problem and necessary repairs If possible place the instrument 10 to 20 meters below the surface to help purge bubbles Purging bubbles is more difficult when making filtered measurements see below If you are not making filtered measurements the instrume
249. nts through a solvent resistant 0 4 um filter before use and degas with helium or an in line vacuum degassing system during analysis 10 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Calibration standards Chlorophylls a and b and p and B carotene can be purchased from Sigma Chemical Co St Louis MO 63178 USA Other pigment standards can be purchased from the International Agency for C Determination VKI Water Quality Institute Agern All 11 DK 2970 H rsholm Denmark The concentrations of all standards in the appropriate solvents should be determined using a monochromator based spectrophotometer prior to calibration of the HPLC system Latasa et al 1999 Spectrophotometric readings should be made at a bandwidth 2 nm and the optical density OD of the pigment standards should range between 0 2 to 0 8 OD units at Amax Marker et al 1980 The recommended extinction coefficients for the various phytoplankton pigments can be found in Appendix E of Jeffrey et al 1997 Absorbance is measured in a 1 cm cuvette at the peak wavelength Amax and at 750 nm to correct for light scattering Concentrations of the standards are calculated as B 10 A OA ax A 750 bE lem Ciro 2 1 where Ci is the concentration ug L of the standard for pigment i A a and 4 750 are absorbances at 2 and 750 nm respectively b is the pathlength of the cuvette cm and E Ei lem
250. nts will generally purge at the surface but purging them below 10 m is still a good idea The reader is referred to Van Zee et al 2002 for detailed recommendations concerning rates of descent during profiles using an ac 9 After the instruments are brought on deck following a cast they should be immediately rinsed and the flow tubes flushed with fresh water to mitigate corrosion If the instrument will be on deck for more than 30 min between casts the optics and flow tubes should be cleaned with Nannopure water and dried At least once per day while at sea the optics and flow tubes should be cleaned with methanol cleaned again using a mild detergent dissolved in Nannopure water rinsed with Nannopure water cleaned again with methanol and finally dried Use soft tissues such as KimWipes to gently clean and dry the optical surface and be extremely careful to wipe them in a constant direction and to not scrub the optical surfaces When the instrument package is be stored on deck for a prolonged period between casts cover it with a tarpaulin to protect the absorption meter from direct exposure to the sun Excessive solar heating of the instrument may exceed the practical limits 5 C to 30 C of internal temperature corrections for an ac 9 and thus invalidate its measurements until it has cooled sufficiently to restore normal operations Filtering the Water Intake Port of an ac 9 for Measurements of Absorption by CDOM and Particles Th
251. o 0 0 T A n E ee is the fraction of radiant flux transmitted over the path distance r Equation 1 6 is the 2 fundamental equation by which the beam attenuation coefficient is determined from a measurement made with a transmissometer Chapter 2 of this volume The attenuation of radiant flux transmitted over a short optical pathlength r in seawater may be determined using the Beer Lambert Bouguer Law equation 2 41 Vol I Ch 2 which here follows directly from 1 6 as D A 7 0 0 0 0 0 e 1 7 1 4 ABSORPTION MEASUREMENT CONCEPTS Reflecting Tube Absorption Meters To determine the volume absorption coefficient a X with a source and detector pair arranged on a common axis e g the source and Detector 1 in Fig 1 4 the flux reaching the detector window must include the sum of directly transmitted and scattered fluxes i e b If the source and collector are equal in area and the water path between them the shaded transmission path volume in Fig 1 4 were enclosed in a perfectly reflecting tube then all forward scattered photons would be redirected into the beam and reach the detector For the present we will postpone consideration of the flux loss due to backscattered photons and treat it as being negligible Under this construct and assumption equation 1 3 may be rewritten as bd XA 4 6 XA 6 X A X TO Oak OO ai EO 1 8 Ar0 A Ar ar gt 0 Ar exp
252. o verify that the windows are clean A transmissometer dark voltage should also be measured at this time These on deck air calibrations should be logged and compared to the more careful air calibrations done under dry laboratory conditions before and after each cruise Section 2 3 If pre and post cruise air calibrations are significantly different the time history should indicate whether the change occurred suddenly e g a scratch in the window or as a drift over time Each time an open path transmissometer is placed into the water care must be taken to assure that bubbles do not collect on the windows particularly if the instrument is mounted in a vertical orientation Protocols covering methods for making field measurements with the ac 9 instrument are described in detail in Zee et al 2002 Some critical aspects of these protocols are briefly reviewed in Chapter 3 to emphasize their importance 2 5 DATA ANALYSIS METHODS There are several generic steps needed to process and analyze a vertical profile of measured transmissometer data 1 Merge the transmissometer data with externally measured depth and temperature data Assuming that the transmissometer does not have an internal high quality depth transducer it is usually mounted together with a CTD to provide the depth and water temperature fields If the transmissometer output data record does not include the internal instrument temperature measured by a built in thermistor external
253. of time Clesceri et a 1998 These quality control graphs should be retained with the data analysis logbooks to document the quality of each data set A selected number of samples should be analyzed in duplicate or triplicate to assess representativeness and uncertainty in the method and instrumentation In multi ship investigator studies replicate samples should be collected and archived for future intercalibration checks Fortified samples should be analyzed as part of the quality assurance effort Fortified samples are prepared in duplicate by spiking a sample with known quantities of the analytes of interest at concentrations within the range 11 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 expected in the samples Fortified samples are used to assess the method s uncertainty in the presence of a typical sample matrix The method detection limit MDL for the analytes of interest can be determined by measuring seven replicate standard injections Glaser et al 1981 The standard deviation S of the seven replicate measurements is calculated and the MDL is computed as MDL t 6 0 99 S 2 4 where 1 6 0 99 is the Student s t value for a one tailed test at the 99 confidence level with N 1 6 degrees of freedom For this particular sample size N 7 and the 99 confidence level 6 0 99 3 707 Abramowitz and Segun 1968 Table 26 10 System and spiked blanks should be routinely an
254. ogy and Oceanography 24 664 672 Kiefer D A and J B SooHoo 1982 Spectral absorption by marine particles of coastal waters of Baja California Limnology and Oceanography 27 492 499 Kishino M N Okami M Takahashi and S Ichimura 1986 Light utilization efficiency and quantum yield of phytoplankton in a thermally stratified sea Limnology and Oceanography 31 557 566 Kishino M N Takahashi N Okami and S Ichimura 1985 Estimation of the spectral absorption coefficients of phytoplankton in the sea Bulletin of Marine Science 37 634 642 Kou L D Labrie and P Chylek 1993 Refractive indices of water and ice in the 0 65 to 2 5 um spectral range Appl Opt 32 3531 3540 Lenoble J 1956 L absorption du rayonment ultraviolet par les ions presents dans la Mer Revue d Optique 35 10 526 531 Mitchell B G and D A Kiefer 1988a Chlorophyll a specific absorption and fluorescence excitation spectra for light limited phytoplankton Deep Sea Research I 35 639 663 Mitchell B G and D A Kiefer 1988b Variability in pigment specific particulate fluorescence and absorption spectra in the northeastern Pacific Ocean Deep Sea Research I 35 665 689 Mitchell B G A Bricaud and others 2000 Determination of spectral absorption coefficients of particles dissolved material and phytoplankton for discrete water samples In Fargion G S and J L Mueller Eds Ocean Optics Protocols for Satellite Ocean Color Senso
255. ohren and Huffman 1983 other coding implementations are also available at various web sites The Mie scattering intensity functions should be calculated at angle intervals Aw matching those at which the weighting functions W y c were resolved equations 5 8 and 5 9 It is important that the selected angle increment adequately resolves variations in p wv D for the narrow size distributions typically used in this application an interval Ay lt 0 5 is recommended Determine the phase function for the sample polydispersion by numerical quadrature of the convolution integral B Qv B 4 w D p D aD S wb wi D nAD p D nAD AD 5 14 n 250 where w are the weighting coefficients of the selected numerical quadrature algorithm e g the composite Simpson formula To obtain the weighted phase function to be measured by the sensor divide both sides of 1 19 by b and numerically approximate the integral equation as N 2 x B Q u gt wB 2 0 ndAwW y 9 n y c sinvAv 5 15 Nay Ug where again w are the quadrature weighting coefficients E n Measure and record the instrument s dark offset response V V by pointing the source and detector at a black velvet cloth at a distance of approximately 2 m in a completely dark room Prepare a volume of filtered optically pure water using the procedures described in Chapter 3 Using an ac 9 calibrate it using the freshly prepared pure wate
256. ols for Satellite Ocean Color Sensor Validation Revision 4 Volume I Introduction Background and Conventions Volume II Instrument Specifications Characterization and Calibration Volume III Radiometric Measurements and Data Analysis Methods Volume IV Inherent Optical Properties Instruments Characterization Field Measurements and Data Analysis Protocols Volume V Biogeochemical and Bio Optical Measurements and Data Analysis Methods Volume VI Special Topics in Ocean Optics Protocols The earlier version of Ocean Optics Protocols for Satellite Ocean Color Sensor Validation Revision 3 Mueller and Fargion 2002 Volumes 1 and 2 is entirely superseded by the seven Volumes of Revision 4 listed above The new multi volume format for publishing the ocean optics protocols is intended to allow timely future revisions to be made reflecting important evolution of instruments and methods in some areas without reissuing the entire document Over the years as existing protocols were revised or expanded for clarification and new protocol topics were added the ocean optics protocol document has grown from 45pp Mueller and Austin 1992 to 308pp in Revision 3 Mueller and Fargion 2002 This rate of growth continues in Revision 4 The writing and editorial tasks needed to publish each revised version of the protocol manual as a single document has become progressively more difficult as its size increases Chapters that change but little must neverthele
257. oments of an axially symmetric radiance distribution in the asymptotic regime Zaneveld and Pak 1972 Wells 1983 Other examples include the determination a X using an integrating cavity Pope and Fry 1997 photothermal methods Sogandares and Fry 1997 and differential optoacoustic spectroscopy Voss and Trees 1987 Optoacoustic spectroscopy was also used to measure a in phytoplankton cultures Trees and Voss 1990 Absorption may also be determined from measurements of irradiance divergence from a submerged isotropic 7 It would be advantageous were this situation to change in the future as such camera systems are potentially even more useful for determining the Bidirectional Reflectance Distribution Function BRDF and Exact Normalized Water Leaving Radiance Vol III Ch 4 10 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV source Maffione et al 1993 and earlier references cited there The present version of this volume does not address any of these methods 1 5 SCATTERING MEASUREMENT CONCEPTS Scattering Coefficient Determinations There is no practical way to directly measure the volume scattering coefficient b Given measurements of absorption and beam attenuation coefficients however the volume scattering coefficient may computed from 1 1 as b A4 2 c A a A m In practice it s not quite that simple and several interrelated scattering and absorption corrections m
258. on a second detector may be mounted to monitor the source output from a fixed off axis direction relative to i e by mounting it on an extension to the rotational stage Whether one must go to the trouble to determine the beam and FOV weighting functions more accurately than can be modeled from simple geometric elements of the optical design depends on the shape of the VSF in the region to be measured The detailed behaviour of the outer edges of the two distribution functions are not important factors in determing the weighting functions for measurements of the VSF of pure water or of a particulate VSF at scattering angles near or greater than 90 Figs 1 2 and 1 3 Therefore relatively simple approximations to h e9 and h e 9 should be completely adequate for the commercial backscattering instruments mentioned above Conversely the angular breadth and details of the beam and FOV distribution functions both become increasingly more critical when one wishes to measure the VSF at decreasing angles in the forward direction Dependence of the Weighting Functions on the Beam Attenuation Coefficient c The effect of the beam attenuation coefficient on the weighting function W x c for each volume element is explicitly represented in 5 7 by the transmittance over the combined pathlength from the source to the volume element at x and from there to the source location The transmittance term is integrated into each angular weight
259. on A800 US Federal Aviation Administration Dangerous Good Bulletin DGAB 98 03 August 25 1998 That approval notwithstanding many investigators have experienced difficulties in clearing customs and in transport of liquid nitrogen dry shippers via commercial airfreight or as checked baggage The investigator should contact the carriers in advance and provide the IATA approval and FAA bulletins pertaining to liquid nitrogen dry shipper transport If the dry shipper is to be transported as checked baggage advanced coordination with the airline is strongly recommended to avoid confiscation of samples and delays in return shipment When samples are shipped as checked baggage or freight the IATA memo DOT memo and manufacturer s certificate should be affixed to the dry shipper to minimize potential delays e Temporary storage of filter samples on dry ice can be considered during transport But maximum duration of dry ice in insulated shipping boxes is several days so the use of liquid nitrogen dry shippers is strongly recommended Determination of spectral optical density of sample filters After preparation the optical density spectrum of each sample filter is measured using a laboratory spectrophotometer The performance characteristics and calibration requirements of the spectrophotometer used for these measurements are described above in Section 4 3 a Reference Blank Spectra With a dual beam spectrophotometer two reference filter blanks s
260. on coefficients radiometric profiles and pigment concentration measurements have provide useful information about relationships between IOP AOP and optically important material constituents of the water column e g Stramska et al 2000 Lh hk A AR G o ED E AE he am v he Lk E AE E ARI hak zouk D SZ D ur a ANT AY AU A AR ABT Am dvo amm nme MY n NN D a LITE AAA LLL eda DZ z FSS ZZ E PEAS et MP MIA A e LII LEAR JERE EAA Fig 5 1 Schematic illustration of a VSF sensor geometry used for numerical integration over the volume intersected by a source beam and detector FOV of incremental elements of the scattered radiant flux received by the detector 12 Certain commercial equipment instruments or materials are identified in this chapter to foster understanding Such identification does not imply recommendation or endorsement by the National Aeronautics and Space Administration nor does it imply that the materials or equipment identified are necessarily the best available for the purpose 66 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV An example of a generalized source and detector arrangement to measure the VSF B A w at a scattering angle y z is illustrated schematically in Fig 5 1 To determine a calibration factor relating the detector response to flux scattered from the source beam into the field of view FOV of the detector we mu
261. or Validation NASA TM 2000 209966 NASA Goddard Space Flight Center Greenbelt MD pp 162 169 Trees C C D K Clark R R Bidigare M E Ondrusek and J L Mueller 2000 Accessory pigments versus chlorophyll a concentrations within the euphotic zone a ubiquitous relationship Limnol Oceanogr 45 5 1130 1143 Trees C C M C Kennicutt II and J M Brooks 1985 Errors associated with the standard fluorometric determination of chlorophylls and pheopigments Mar Chem 17 1 12 UNESCO 1994 Protocols for the Joint Global Ocean Flux Study JGOFS Core Measurements Manual and Guides 29 170pp Vernet M and C J Lorenzen 1987 The presence of chlorophyll b and the estimation of pheopigments in marine phytoplankton J Plankton Res 9 255 265 Yentsch C S and D W Menzel 1963 A method for the determination of phytoplankton chlorophyll and phaeophytin by fluorescence Deep Sea Res 10 221 231 25 Appendix E LI 1400 DataLogger PAR Measurements Standard Operating Procedures Overview The LI 1400 DataLogger and calibrated quantum sensors provide the capability to quantify Photosynthetically Active Radiation PAR both above and below the water surface The fair sensor remains above the water and quantifies downwelling radiance from the sun each time a discrete measurement is taken this is most often used to normalize readings taken over several minutes to a constant downwelling value The underwater sensor i
262. ore the NHEP sought and received funding from the Environmental Protection Agency to support an instrumented buoy in Great Bay which will be managed by the University of New Hampshire UNH Coastal Observing Center to gather sufficient data to resolve uncertainties in relationships between parameters Funding will also support coordinated collection of spatial data from aerial imagery and flow through surveys to characterize spatial heterogeneity in water quality parameters The goal of the research is to develop a scientifically defensible conceptual model of the relationships between water clarity and water quality parameters The conceptual model will be the basis of nutrient criteria for NH s estuaries A secondary goal of the project is to demonstrate the value of integrating buoy based measurements with aerial imagery and flow through surveys to map heterogeneity in water quality parameters within estuarine and near coastal systems The expected outputs for this project are results of research which supports development of environmental results based nutrient criteria for estuaries specifically A A single or multi variate model between the light attenuation coefficient and concentrations of CDOM turbidity suspended solids and chlorophyll a for the Great Bay system which can be used to develop numeric nutrient criteria B Maps of the distribution of CDOM turbidity and chlorophyll a and light attenuation using the model described above o
263. orporated into the beam In most ocean waters multiply scattered light is not in general a problem for the commercially available transmissometers If scattered light leaves the beam then it will take two additional scattering events to get the light back into the beam and redirected towards the detector The addition of baffles along the light path can nearly eliminate any possibility of multiply scattered light being detected in ordinary circumstance In extremely turbid waters however the single scattering albedo is very large and the volume scattering phase function B V is extremely biased in the near forward direction Fig 1 3 Ch 1 Under such conditions if r 3c A m there is a significant probability that some fraction of scattered photons will undergo 3 or more successive small angle scattering events re enter the transmission path and join the flux reaching the detector The apparent beam attenuation coefficient will be artificially reduced if this occurs There are also engineering concerns associated with the optical pathlength The path must be short enough that light reaches the detector it would do no good to have an instrument with a pathlength r 10c A m because the transmitted signal would not be detectable On the other hand the pathlength must be long enough for attenuation to reduce the transmitted flux enough that the difference in incident and transmitted fluxes are large enough to be measurable Longer pa
264. outinely used for these methods Therefore it is necessary to convert the OD measurements described in this chapter to the base e representation of absorbance i e to multiply OD by 2 303 to conform to the convention used throughout the ocean optics protocols In general these protocols are written assuming that the instrument that is used directly computes the optical density of the sample relative to the appropriate reference sample There has been considerable research to develop robust protocols that provide the most accurate estimates of absorption for various material fractions in natural waters NASA sponsored workshops were held at Scripps Institution of Oceanography and Bigelow Laboratory for Ocean Sciences to review absorption protocols evaluate instrumentation and define areas of consensus as well as areas of uncertainty that warrant further research Mitchell et al 2000 The most widely used approach for estimating absorption by particulate matter in water samples involves analysis of the particles concentrated on filters Yentsch 1957 Absorption of phytoplankton suspensions determined using procedures that capture most of the forward scattered light Shibata 1958 can be related to the absorption measured on the filters to make quantitative corrections for the pathlength amplification effect B caused by the highly scattering filter medium Duntley 1942 Butler 1962 The pathlength amplification parameter was symbolized as B by
265. owever we recommend here that preference be given to the b scales of Buiteveld et al 1994 Both scales are listed in Table 1 1 for comparison The difference between the two scales is lt 0 0001 m at wavelengths gt 475 nm increases to lt 0 0005 m as wavelength decreases to 400 nm and increases further to lt 0 0014 m at 340 nm In no instance does the difference closely approach the 0 005 m measurement uncertainty of beam attenuation and absorption meters that are commercially available to date The angular distribution of the molecular scattering phase function B v as approximated with equation 2 29 Vol I Ch 2 is illustrated in Fig 1 2 The magnitude of B v represents the probability that a photon scattering interaction with a water molecule will redirect the photon path direction by an angle y measured from its original path The shape of B v is sometimes referred to as isotropic in the literature a characterization that is true only in that the function is axially symmetric and the probabilities of forward and backward scattering are equal 0 11 0 10 B 0 09 0 08 0 07 0 06 0 90 180 Scattering Angle y degrees Fig 1 2 The dashed curve represent the angular distribution of the scattering phase function for pure water calculated using the approximate Rayleigh scattering model equation 2 29 of Vol I Ch 2 Ocean Optics Protocols For Satellite Ocean Color Sensor Va
266. p II A reflectance model for remote sensing Limnol Oceanogr 44 618 627 UNESCO 1994 Protocols for the Joint Global Ocean Flux Study JGOFS Core Measurements Manuals and Guides 29 170pp Vernet M B G Mitchell and O Holm Hansen 1990 Adaptation of Synechococcus in situ determined by variability in intracellular phycoerythrin 543 at a coastal station off the Southern California coast USA Mar Ecol Prog Ser 63 9 16 Voss K J W M Balch and K A Kilpatrick 1998 Scattering and attenuation properties of Emiliania huxleyi cells and their detached coccoliths Limnol Oceangr 43 5 870 876 Wood A M P K Horan K Muirhead D Phinney C M Yentsch and J M Waterbury 1985 Discrimination between types of pigments in marine Synechococcus by scanning spectroscopy epifluorescence microscopy and flow cytometry Limnol and Oceanogr 30 1303 1315 Wood A M M Lipsen and P Coble 1999 Fluorescence based characterization of phycoerythrin containing cyanobacterial communities in the Arabian Sea during the Notheast and early Southwest Monsoon 1994 1995 Deep Sea Res II 46 1769 1790 Wyman M 1992 An in vivo method for the estimation of phycoerythrin concentrations in marine cyanobacteria Synechococcus spp Limnol Oceangr 37 1300 1306 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Chapter 2 HPLC Phytoplankton Pigments Sampling Laboratory Methods and
267. pection of equipment based on manufacturer requirements and specifications Each day an instrument is used it receives a general inspection for obvious problems e g worn tubing syringe plunger tips leaks The instruments are used frequently and data is inspected within a few days of sample analysis This allows instrument or user malfunctions to be caught quickly and corrected as needed Each day s run is recorded in the instrument s run log with the date the user the number of injections standards samples and QC samples the project and other notes of interests Maintenance routine or otherwise is recorded in the instrument run log and Page E 8 includes the date the person doing the maintenance what was fixed and any other notes of interest X Corrective Action Contingencies Jeffrey Merriam is responsible for all QC checks and performs or supervises all maintenance and troubleshooting When unacceptable results are obtained based on within sample analysis batch QC checks the data from the run are NOT imported into the database The cause of the problem is determined and corrected and the samples are re analyzed Problems are recorded in the sample queue s data spreadsheet or on the handwritten runsheet associated with the run Corrective actions instrument maintenance and troubleshooting are documented in each instrument s run log XI Record Keeping Procedures Protocols Instrument Logs QC charts databas
268. pectrophotometer Absorption maxima for the various phytoplankton pigments can be found in Part IV of Jeffrey et al 1997 Calculate individual pigment concentrations as Ai V A Cantha Ci Sample Extracted STD Sample i Cantha F V ected V sample sample is the individual pigment concentration ug L A 2 3 where C Is the area of individual Sample ample pigment peak for a sample injection V is the volume extracted mL to nearest 0 1 mL xtractet Via 1 the volume injected mL measured to the nearest 0 001 mL V is the sample ample volume filtered L measured to the nearest 0 001 L and the other coefficients are defined above This method is designed for the separation of chlorophyll and carotenoid pigments but it is also capable of separating the major chlorophyll breakdown products The uncertainty of the HPLC method was assessed by performing triplicate injections of a mixture of phytoplankton and plant extracts coefficients of variation standard deviation mean x 100 94 ranged from 0 6 to 6 0 The use of an appropriate internal standard such as canthaxanthin will decrease the uncertainty 2 4 QUALITY ASSURANCE PROCEDURES Quality assurance procedures outlined here should be routinely employed to insure accurate precise and representative results As a means of monitoring an instrument s performance individual pigment response factors F should be charted as functions
269. performance is assessed based upon USGS 1m DOQQ imagery The Project Manager will be responsible for maintaining spare parts and supplies for the field sensors and dataloggers for this project B7 Instrument Equipment Calibration and Frequency Instrument calibration frequency is described in section B6 B8 Inspection Acceptance Requirements for Supplies and Consumables The sample bottles will be visually inspected immediately prior to the collection of the sample to determine the presence of damage e g cracks or contamination e g dirt or other particulate matter within the container The sample bottles will be accepted for use 1f damage and contamination are not visible or otherwise apparent Similarly the calibration reagents will be visually inspected for Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 30 discoloration or other indicator of poor quality or contamination The reagents will be accepted for use if discoloration or other indicator is not observed The Project Manager is responsible for the inspections B9 Non direct Measurements UNH will use data from the following non direct sources as part of this study Table 11 Non Direct Data Sources for this Study Type of Data Original Use Relevance Acceptance Criteria Limitations Physico chemical observations from The Great Bay National Estuarine Research Reserve Physico chemical observations may Th
270. ples should be taken using e g Niskin bottles at the site of and simultaneously with the surface in water upwelled radiance and reflectance measurements and at depth increments sufficient to resolve variability within at least the top optical depth The K z A profiles over this layer will be used to compute optically weighted near surface pigment concentration for bio optical algorithm development Gordon and Clark 1980 When possible samples should be acquired at several depths distributed throughout the upper 200 m of the water column or in turbid water up to seven diffuse attenuation depths i e In E z A E z A 7 to provide a basis for relating fluorescence signals to pigment mass concentrations Samples should be filtered as soon as possible after collection If processing must be delayed for more than an hour hold the samples on ice or in a freezer at 4 C and protect them from exposure to light For delays longer than several hours the samples should be stored in liquid nitrogen Use opaque sample bottles because even brief exposure to light during sampling and or storage might alter pigment values Filtration Whatman GF F glass fiber filters with approximately 0 7 um pore size are preferred for removing phytoplankton from water The glass fibers assist in breaking the cells during grinding accommodate larger sample volumes and do not form precipitates after acidification Twenty five mm diameter GF F glass fiber filters
271. pply a multi spectral radiative transfer model Hydrolight Sequoia Inc to the Great Bay to predict light availability to eelgrass under different water quality conditions The model will be customized to Great Bay conditions using the information from the first part of the study By comparing the model output to the measured light availability UNH will be able to verify consistency with optical theory Output C Finally this project has been designed to meet many of the aims and goals of the Integrated Ocean Observing System IOOS by facilitating the use of observing system measurements by those involved in managing the state s coastal water Funding for the initial development and deployment of the Great Bay Coastal Buoy was derived from an IOOS pilot project from the NOAA Coastal Services Center to the Coastal Observing Center at UNH Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 13 The specific tasks and schedule for this project are listed below 1 Prepare quality assurance project plan due one month after receipt of award This report will document the methods to be used for the study and the quality assurance procedures The plan will be approved by project partners and EPA Region I 2 Purchase sensor equipment and deploy buoy due by 7 15 07 UNH Coastal Observing Center will purchase with separate funds a junction box and other equipment needed to measure hyperspectral light intensity at two dept
272. ptics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 For additional information regarding HPLC method implementation and injection conditions see Wright and Mantoura 1997 Following injection of the sample onto the HPLC system use the following solvent system program to separate the chlorophyll and carotenoid pigments 0 0 90 A 10 B 1 0 100 B 11 0 78 B 22 C 27 5 10 B 90 C 29 0 100 B and 30 0 100 B Degas solvents with helium or an in line vacuum degassing system during analysis It should be noted that method performance varies significantly between HPLC systems because of differences in dwell volume equilibration time and injection conditions It is therefore recommended that analysts validate that desired peak separations are attained for pigment pairs of interest by calculating the peak resolution indices R as as 2 tes hi 2 2 s Wgi Wo where f and f are the retention times min of peaks 1 and 2 and wy and Wp are the widths min of peaks 1 and 2 at their respective bases Wright 1997 Peak separation values R 1 0 are insufficient for accurate quantification of peak areas Wright 1997 Peak identities are routinely determined by comparing the retention times of sample peaks with those of pure standards Peak identities can be confirmed spectrophotometrically by collecting eluting peaks from the column outlet or directly with an on line diode array s
273. ptics protocols These new chapters may be significantly revised in the future given the rapidly developing state of the art in IOP measurement instruments and methods Volume V The overview chapter Chapter 1 briefly reviews biogeochemical and bio optical measurements and points to literature covering methods for measuring these variables some of the material in this overview is drawn from Chapter 9 of Revision 3 Detailed protocols for HPLC measurement of phytoplankton pigment concentrations are given in Chapter 2 which differs from Chapter 16 of Revision 3 only by its specification of a new solvent program Chapter 3 gives protocols for Fluorometric measurement of chlorophyll a concentration and is not significantly changed from Chapter 17of Revision 3 New chapters covering protocols for measuring Phycoerythrin concentrations Particle Size Distribution PSD and Particulate Organic Carbon POC concentrations are likely future additions to this volume Volume VI This volume gathers chapters covering more specialized topics in the ocean optics protocols Chapter 1 introduces these special topics in the context of the overall protocols Chapter 2 is a reformatted but otherwise unchanged version of Chapter 11 in Revision 3 describing specialized protocols used for radiometric measurements associated with the Marine Optical Buoy MOBY ocean color vicarious calibration observatory The remaining chapters are new in Revision 4 and cover protocols
274. r Chapters 2 and 3 Immerse the VSF sensor in the pure water volume and record its response V V V4 V Add a sufficient amount of the polystyrene microsphere bead sample to increase the instrument s response to approximately the maximum level desired for the calibration run a Label this bead concentration as CO and record the VSF sensor response Vo V b Measure aco X and cq relative to the pure water calibration offsets using the ac 9 for bead concentration CO Determine 52 A co A aco including scattering and temperature corrections to the ac 9 measurements Chapter 3 Add pure water to dilute the sequence to bead concentration C1 and record the VSF response signal Va V and repeat this step several times to obtain N 1 VSF response signal Voo V V s V corresponding to N 1 bead concentrations It is not necessary to determine either the absolute or relative bead concentrations so dilution volumes of pure water need not be measured At each dilution concentration Cn repeat steps 10a and 10b 72 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV 9 8 1 6 um bead Bly 0 02 r Y 0 018 AW100Y9 3 Wuos 9y 3 Wisoly 3_ Bly W w 80 90 100 110 120 130 140 150 160 170 180 2 040 022 um bead Bly Figure 5 4 Examples of phase functions Bs A W calculated using Mie theory for polydispersions of polystyrene microsphere beads hav
275. r Z S F G Plumley A S Lang J T Beatty R E Blankenship C L VanDover C Vetriani M Koblizek C Rathgeber and P G Falkowski 2001 Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean Science 292 2492 2495 Latasa M R R Bidigare M E Ondrusek and M C Kennicutt II 1996 HPLC analysis of algal pigments A comparison exercise among laboratories and recommendations for improved analytical performance Mar Chem 51 315 324 Latasa M R R Bidigare M E Ondrusek and M C Kennicutt II 1999 On the measurement of pigment concentrations by monochromator and diode array spectrophotometers Mar Chem 66 253 254 Letelier R M R R Bidigare D V Hebel M E Ondrusek C D Winn and D M Karl 1993 Temporal variability of phytoplankton community structure at the U S JGOFS time series Station ALOHA 22 45 N 158 W based on HPLC pigment analysis Limnol Oceanogr 38 1 420 1 437 Mantoura R F C R G Barlow and E J H Head 1997 Simple isocratic HPLC methods for chlorophylls and their degradation products Ch 11 in Jeffrey S W R F C Mantoura and S W Wright editors Phytoplankton pigment in oceanography guidelines to modern methods Vol 10 Monographs on oceanographic methodology UNESCO Publishing 661 pp 13 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Marker A F H E A Nusch H Rai and B Riemann 1980 The
276. r FOV geometries are identical 2 that the central viewing angles of each are equal i e 0 0 Fig 3 2 and 3 that the plaque s Bidirectional Reflectance Distribution Function BRDF is a constant P The flux reaching the plaque n from the source including flux scattered in the near forward direction up to 15 or so as well as direct transmission may be expressed as k exp a b Z 3 4 where k is a constant representing the optical characteristics reflection and transmission losses effective detector area etc of the source z is the mean effective pathlength for flux transmitted from the source window to the Vr plaque b b 2 B y sin wd is flux scattered beyond a forward scattering angle w 15 comparable to the 0 beam geometric width For typical particle phase functions a very large fraction of singly scattered flux is confined within the forward 15 cone By similar reasoning the flux reflected diffusely from the plaque and reaching the detector may be written as k ro exp a b z k Ek exp Qa b b Z 3 5 where ka is a constant accounting for the optical characteristics of the detector assembly and b represents scattering losses at angles too large to be detected in a single scattering approximation i e the counterpart for b for a diffuse source and the detector FOV Equation 3 5 assumes further that the flux backscattered from the intersection volume of the source bea
277. r Validation Revision 2 NASA TM 2000 209966 NASA Goddard Space Flight Center Greenbelt MD Chapter 12 pp125 153 Mitchell B G 1990 Algorithms for determining the absorption coefficient of aquatic particulates using the quantitative filter technique QFT Ocean Optics X 137 148 58 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Mitchell B G M Kahru and P J Flatau 1998 Estimation of spectral values for the mean cosine of the upper ocean SPIE Ocean Optics XIV CD ROM Mitchell B G and D A Kiefer 1984 Determination of absorption and fluorescence excitation spectra for phytoplankton Marine phytoplankton and productivity 8 157 169 Moore L R R Goericke and S W Chisholm 1995 Comparative physiology of Synechococcus and Prochlorococcus influence of light and temperature on growth pigments fluorescence and absorptive properties Marine Ecology Progress Series 116 259 275 Nelson N B D A Siegel and A F Michaels 1998 Seasonal dynamics of colored dissolved material in the Sargasso Sea Deep Sea Research 45 931 957 Pegau W S and J R V Zaneveld 1993 Temperature dependent absorption of water in the red and near infrared portions of the spectrum Limnology and Oceanography 38 188 192 Pope R M and E S Fry 1997 Absorption Spectrum 380 700 nm of Pure Water II Integrating Cavity Measurements Applied Optics 36 8 710 8 723 Preisendorfer R W 1976
278. r and place them in petri dishes on FSW to ensure hydration Allow the samples to thaw for approximately 5 min and then refrigerate them in the dark until each filter is ready for analysis An instrument specific sample mounting device is recommended to hold filters against a quartz glass mounting plate These mounts should be secure when placed in the sample compartment and hold the sample perpendicular to the illumination beam so only the filter and the quartz plate are in the beam Usually these mounts must be custom fabricated specifically for each different instrument Clean the quartz faceplates of the mounting device with purified water and detergent if needed Rinse them with purified water and ethanol and dry them thoroughly using lint free laboratory tissues Set the appropriate instrument parameters according to the manufacturer s instructions Mount two pre soaked and water saturated blank filters one for the sample beam and one for the reference beam To test for proper filter hydration confirm that there 1s a drop of FSW left on the mounting plate when the filter is lifted With the filter on the mounting plate there should be a slight sheen on the top surface of the filter and a very narrow 1 mm border of water around the edges of the filter Be careful not to use too much water or the sample may wash away Examine the back of the filter on the mounting plate to be sure that no bubbles are trapped between the filter and t
279. raphy 36 910 921 Sosik H M and B G Mitchell 1995 Light absorption by phytoplankton photosynthetic pigments and detritus in the California Current System Deep Sea Research I 42 1 717 1 748 Stramska M D Stramski B G Mitchell and C D Mobley 2000 Estimation of the absorption and backscattering coefficients from in water radiometric measurements Limnology and Oceanography 45 3 628 641 Stramski D 1990 Artifacts in measuring absorption spectra of phytoplankton collected on a filter Limnology and Oceanography 35 1 804 1 809 Tassan S and G M Ferrari 1995a An alternative approach to absorption measurements of aquatic particles retained on filters Limnology and Oceanography 40 1 358 1 368 Tassan S 1995b Proposal for the measurement of backward and total scattering by mineral particles suspended in water Applied Optics 34 8 345 8 353 Tassan S 1998 Measurement of the light absorption by aquatic particulates retained on filters determination of the optical pathlength amplification by the Transmittance Reflectance method Journal of Plankton Research 20 1 699 1 709 59 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Tassan S G M Ferrari A Bricaud and M Babin 2000 Variability of the amplification factor of light absorption by filter retained aquatic particles in the coastal environment Journal of Plankton Research 22 659 668 Vodacek A N V
280. rations is analyzed in the laboratory before and after each deployment period Instrument response slope and offset blank are checked by this method Sensors for hyperspectral imagery collection will be calibrated and serviced as follows Radiometric and Spectral Calibration Radiometric calibration is achieved through the use of a Labsphere USS 2000 V uniform source This 20 inch diameter integrating sphere 1s equipped with three internal 45 watt and one 75 watt externally mounted halogen light sources Each lamp is powered by separate DC regulated constant current power supplies and the addition of a variable attenuator provides even more precise control of light levels Luminance output is variable from 0 to 4000 foot lamberts and measured uniformity is gt 98 over the entire 8 inch exit port This sphere carries a NIST traceable spectral radiance calibration from 400nm to 2500nm at a sampling interval of 10nm Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 29 The resultant calibration allows SpecTIR to provide data that is within 5 of absolute radiance Wavelength calibration is generated and monitored through a characterized Mercury Argon HgAr emmision lamp source HgAr lamps are a common spectral calibration source for spectrometers and provides several fine distinct emission lines in both the VNIR and SWIR spectral domain allowing for accurate wavelength mapping During processing flight data
281. rd on field sheet below 3 Sample collection Plunge inverted bottle below surface at approximately 0 5 m Care must be taken to avoid sampling the very surface layer Right sample bottle underwater and allow bottle to partially fill and cap underwater Remove from water shake and empty Repeat for three rinses total Completely fill bottle with same protocol above 4 Store on ice in dark until delivered to processing team at JEL Contact cell numbers Ru Morrison 603 957 0998 Tom Gregory 808 294 0265 Mike Novak 603 828 5240 Your Name and affiliation Station Date Time Lat Lon Temp Salinity Water Depth local C psu Comments PAR Measurements Station Start Time local End Time Depth m Surface PAR PAR at depth units units Station Start Time local End Time Depth m Surface PAR PAR at depth units units Station Start Time local End Time Depth m Surface PAR PAR at depth units units Station Start Time local End Time Depth m
282. re 8 Sampling Methods for Activity 3 Near Continuous Flow Through Surveys Continuous along track measurements of a number of physical and bio optical properties are logged on the same computer with the geolocation and time information from a GPS unit Conductivity and temperature is measured with a Seabird SBE45 thermosalinograph http www seabird com products spec_sheets 45data htm CDOM and chlorophyll a are measured using two WetLABS WETStar fluorometers http www wetlabs com products pub specsheets wsxssg pdf Beam attenuation is measured with a WetLABS C Star transmissometer Turbidity http www wetlabs com products pub specsheets cstarssi pdf Light absorption and attenuation is measured at 9 wavelengths with a WetLABS ac 9 http www wetlabs com products pub specsheets ac9sse pdf Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 23 Optical backscattering is measured at three visible wavelengths with a WetLABS ECO bb3 http www wetlabs com products pub specsheets triplestsse pdf Sampling Methods for Activity 4 Point measurements with field sensors and grab samples Grab samples for chlorophyll a TSS CDOM and absorption spectra will be collected handled and stored according the Ocean Optics Protocols Appendix C and D Grab samples for nutrients nitrate nitrite orthophosphate will be collected handled and stored according the WQAL QAPP Appendix A Section III Fi
283. re f P decet eer tien pb dit 20 Ambient Light Rejection in Open and Enclosed Path Transmissometers sss 21 2 3 CHARACTERIZATION AND CALIBRATION OF BEAM TRANSMISSOMETERS 21 Calibration With Pure Water de eee eir niea tein eder tendre 21 Aint Calibrations i c aas ettet tkt iate ete beet ee sen 23 Instrument Temperature Dependence eese eene eene 23 2 4 FIELD MEASUREMENT METHODS esee enne teen sense even enes see enes es 23 2 5 DATA ANALYSIS METHODS ss endelser vant sladderen nete nete ennt iaiia teen enne 24 CHAPTER 3 ederet clit eel te e ett aote l iners SS e eodd SENESTE SEERE epos eva De coal Dose eo EEN ET ESS 27 VOLUME ABSORPTION COEFFICIENTS INSTRUMENTS CHARACTERIZATION FIELD MEASUREMENTS AND DATA ANALYSIS PROTOCOLS S INTRODUCTION cienie niao ER IRR Te EHE t ter a le sender e O cc i E A 27 Reflective Tube Absorption Meter Concepts esses nee 27 Determination of Absorption by Measuring Flux Reflected from a Diffuse Reflectance Surface 29 3 2 CHARACTERIZATION AND CALIBRATION OF REFLECTIVE TUBE SPECTRAL ABSORPTION METERS risene anus hah eh E aceite Dik e d s bier aet eee i 31 iii Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Pure WalterGalibration 2 ui c A p t M bt te 32 Pure Water Preparation nroa s A e Ato uet n edo ER AS as eel tae De aca tbe 32 Air Calibrations a i sla ete o tette elio b ERA e E eM EE 33 3 3 MEAS
284. re of the instrument and determine the how the constants change with temperature The first technique is used in many single wavelength transmissometers such as the Sea Tech and WET Labs transmissometers The second approach is used in the WET Labs ac 9 spectral absorption and beam attenuation meter Spectral Characteristics Many areas of research in ocean optics require knowledge of the spectral beam attenuation coefficient c X at more than one wavelength A Several c meters have been built to provide this spectral information Matlack 1974 used an instrument with a grating monochromator to measure c X in the wavelength range from 385 nm to 565 nm Using a pair of circular wedge interference filters Lundgren 1975 was able to measure the beam attenuation coefficient at wavelengths between 340 nm and 730 nm More recent transmissometers that use a monochromator as the detector include the one described by Barth et al 1997 and the WET Labs Histar Another design for obtaining the spectral beam attenuation coefficient utilizes several interference filters mounted in a wheel that rotates them through the beam Examples of filter wheel c meter designs include the VLST Petzold and Austin 1968 and the WET Labs ac 9 Moore et al 1992 Van Zee et al 2002 Beam Geometry Detector Acceptance Angle and Scattered Light Real transmissometers do not have perfectly collimated sources or detectors Unlike the idealized detector concept of Fig 1 4 Ch
285. ressed in differential form as de A r a A dr 1 9 apa LAG d and integrated over the path from 0 to r to obtain a n In A 0 0 In A 7 0 di Qn zu 1 10 Tr The reflecting tube method has been used to measure spectral absorption in the laboratory for many decades James and Birge 1938 In recent years this method has been adapted for use in the ocean Zaneveld et al 1992 Suitable instruments are now commercially available and are coming into general use within the oceanographic community The best known commercially available example of this type of instrument is the ac 9 manufactured by WET Labs Inc of Philomath OR Protocols for calibrating and using reflecting tube absorption meters and methods of data analysis are described in Chapter 3 of this volume and in more specific detail for the ac 9 by Van Zee et al 2002 which is available at www wetlabs com Ti Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Laboratory Methods for Determining Absorption Coefficients Protocols in Chapter 4 by Mitchell et al describe methods for filtering seawater to capture suspended particles on GF F filters and for measuring the absorption spectra of the particle laden filters with a laboratory spectrophotometer Methods are also described for extracting phytoplankton pigments from the filters and measuring the residual absorption spectrum of particulate materi
286. ribed to determine from combinations of these measurements the volume scattering coefficient b z and backscattering coefficient b z A We do not consider instrument concepts or methods for measuring either fluorescence or Raman scattering in Vol IV Even though the Raman and fluorescence cross sections of water suspended particles and dissolved materials are also IOP of seawater only elastic scattering processes are considered in this volume In the remainder of Vol IV we will ordinarily omit the explicit notation identifying IOP variables as functions of depth z in the water column This is partly a desire for simplifying the notation but the more important motive is to avoid confusing global coordinates geographic location and vertical depth in the water column with local coordinates optical axes and normal planes used to describe photon matter interactions and measurement concepts Certain commercial equipment instruments or materials are identified in this chapter to foster understanding Such identification does not imply recommendation or endorsement by the National Aeronautics and Space Administration nor does it imply that the materials or equipment identified are necessarily the best available for the purpose Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV 1 2 ABSORPTION AND SCATTERING PROPERTIES OF WATER PARTICLES AND DISSOLVED SUBSTANCES Because the IOP are add
287. rica 32 61 70 Ferrari G M and S Tassan 1996 Use of the 0 22 um Millipore membrane for light transmission measurements of aquatic particles Journal of Plankton Research 18 1 261 1 267 Ferrari G M 1999 A method for removal of light absorption by phytoplankton pigments using chemical oxidation Journal of Phycology 35 1 090 1 098 Fry E S 2000 Visible and near ultraviolet absorption spectrum of liquid water comments Applied Optics 39 2 743 2 744 Hewes C D and O Holm Hansen 1983 A method for recovering nanoplankton from filters for identification with the microscope The filter transfer freeze FTF technique Limnology and Oceanography 28 389 394 Hoge F E A Vodacek and N V Blough 1993 Inherent optical properties of the ocean retrieval of the absorption coefficient of chromophoric dissolved organic matter from fluorescence measurements Limnology and Oceanography 38 1394 1402 JGOFS 1991 JGOFS Core Measurements Protocol JGOFS Report 6 Scientific Committee on Oceanic Research 40 Kahru M and B G Mitchell 1998 Spectral reflectance and absorption of a massive red tide off Southern California Journal of Geophysical Research 103 21 601 21 609 Kalle K 1938 Zum problem der meerwasserfarbe Ann Hydr u martim Meterol 66 1 S 55 Kiefer D A R J Olson and W H Wilson 1979 Reflectance spectroscopy of marine phytoplankton Part 1 Optical properties as related to age and growth rate Limnol
288. rom moored and drifting buoys Chapter 3 ocean color measurements from aircraft Chapter 4 and methods and results using LASER sources for stray light characterization and correction of the MOBY spectrographs Chapter 5 In the next few years it is likely that most new additions to the protocols will appear as chapters added to this volume Volume VII This volume collects appendices of useful information Appendix A is an updated version of Appendix A in Revision 3 summarizing characteristics of past present and future satellite ocean color missions Appendix B is the List of Acronyms used in the report and is an updated version of Appenix C in Revision 3 Similarly Appendix C the list of Frequently Used Symbols is an updated version of Appendix D from Rev 3 The SeaBASS file format information given in Appendix B of Revision 3 has been removed from the protocols and is promulgated separately by the SIMBIOS Project In the Revision 4 multi volume format of the ocean optics protocols Volumes I II and III are unlikely to require significant changes for several years The chapters of Volume IV may require near term revisions to reflect the rapidly evolving state of the art in measurements of inherent optical properties particularly concerning instruments and methods for measuring the Volume Scattering Function of seawater It is anticipated that new chapters will be also be added to Volumes V and VI in Revision 5 2003 This technical report
289. rometers 17 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Fluorometer Calibrations Bench fluorometers used to measure concentrations of extracted chlorophyll and pheopigments should be calibrated using authentic chlorophyll a standards as prescribed also in the HPLC Protocols Chapter 2 Chlorophyll a standards can be purchased from Sigma Chemical Co St Louis MO 63178 USA If a fluorometer has been shipped for a cruise or if it has been unused for several weeks it is strongly recommended that it be recalibrated with an authentic chlorophyll a standard The use of solid standards like those provided by Turner Designs and other manufacturers can only provide a check for instrumental drift They cannot be used as primary pigment standards However the solid standard should be used at frequent intervals during each day s analyses to monitor instrument drift The concentration of the chlorophyll a standard in the appropriate solvent must be determined using a monochromator based spectrophotometer prior to calibrating the fluorometer The recommended extinction coefficients for chlorophyll a in several solvents can be found in Appendix E of Jeffrey et al 1997 Absorbance is measured in a 1 cm cuvette at the peak wavelength Ax and at 750 nm to correct for light scattering The bandwidth of the spectrophotometer should be between 0 5 and 2 um with the standard concentration being such that the
290. s 30 B10 TIC BUEYIEPIDUID IU 30 C1 Assessments and Response Actions eeeeeeee eee eee eese eese ee seen stt senses sns en netu netu setas tas tas etse tassa sens enses sense snae 31 C2 Reports to Management n Y 32 D1 Data Review Verification and Validation sccssssscssssssscssssscscsscsecsssssessesssccsessceccscssceesessccessssessesssseees 32 D2 Verification and Validation Procedures ssssscescesscssssssssssssssscssessessssssssessnsesessnessssssessecssonsssnsecnsesseees 32 D3 Reconciliation with User Requirements ssscscscssscssscsssscssssccssesssssssssssesessesesssesssesssessossssnsssnsesnsesssees 33 I angi p M 33 List of Appendices A Quality Assurance Plan for UNH Water Quality Analysis Laboratory B Specifications of the SpecTIR VNIR Sensor C Ocean Optics Protocols for Satellite Ocean Color Sensor Validation Revision 4 Volume IV D Ocean Optics Protocols for Satellite Ocean Color Sensor Validation Revision 4 Volume V E Standard Operating Procedures for LI 1400 Datalogger PAR Measurements F Field data sheet for station visits Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 3 List of Tables Table 1 QAPP Distribution Listrier cae rear reen ada td o eta pi duces dent 4 Table 2 Dat quality objectives ois a uere borane TRY pet
291. s Joyce SpecTIR is a small privately owned business with headquarters in Reno NV and another facility in Easton MD The company was founded in 1993 and has advanced from the design and production of hyperspectral instruments to full remote sensing collection and exploitation services SpecTIR s staff consists of spectral scientists project managers field and data collection personnel and a data exploitation group The Water Quality Analysis Laboratory at UNH will conduct laboratory analyses of water samples Jeff Merriam will be the UNH WQAL Laboratory QA Officer and will be responsible for reviewing and revising laboratory related elements of the QAPP Funding for the project will be provided by EPA Region I through a competitive 104 b 3 grant The EPA Project Officer will be Al Basile who will be responsible for managing contract deliverables Art Clark will be the EPA Project QA Officer The EPA QA Project Officer will provide technical reviews of the QAPP and any QAPP addenda throughout the duration of the study and will be responsible for approving this Quality Assurance Project Plan Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 6 Figure 1 Project organizational chart Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 7 AS Problem Definition Background Problem Definition Increasing nitrogen concentrations Figure 2 and declining eelgrass beds in Great Bay
292. s deployed on a frame that is lowered into the water This sensor is generally used to measure a profile of in water irradiance versus depth so as to estimate the diffuse attenuation coefficient K4 a measure of the rate at which photosynthetically active radiation is attenuated as it passes down through the water column In general the attenuation of light is exponential versus depth To obtain Ka from a series of light readings with depth a series of measurements at at least 8 depths is desired in shallow waters this may not be possible One obtains KG by making a linear regression of sample depth versus In PAR and calculating 1 slope of the regression Additional information of interest includes the percent of surface radiation reaching the bottom Estimates of Kg are considered robust if the r of the regression is 70 95 generally 70 98 The precision of the method is estimated by taking 3 complete profiles sequentially and calculating the standard error SE of the measurement The SE should be less than 10 Before First Sampling of the Day 1 Insure that the sensors are securely attached to their frames and confirm that the calibrations factors stored in the DataLogger are correct for the sensors in use Hook up the Underwater BNC connector to Channel I1 labeled underwater Hook up the Air BNC connector to Channel I2 labeled air Turn the DataLogger ON Under View press ENTER to view new data The first vi
293. s the investigator can confirm the stability of the instrument that 1s used these calibration procedures should be repeated each time the spectrophotometer is turned on As a minimum they should be performed at any time there is a change of lamp source blocking filter or other instrument setup characteristic that affects the optical response and on a regular basis during routine work The present version of these protocols is written assuming the use of a commercial dual beam spectrophotometer with the sample and reference targets illuminated by the collimated output of a grating monochromator The protocols also apply with minimal modifications to measurements using a single beam monochromator or otherwise similar optical configuration Mitchell et al 2000 report comparisons between OD measurements of a common set of GF F filtered particle samples using several spectrophotometers of these types as well as spectrophotometers based on very different optical configurations For a diatom culture measured during the Scripps workshop several commercial dual beam spectrophotometers estimated sample filter OD spectra consistently within 5 Figure 4 1 Some of the differently configured instruments were within 10 96 of the selected reference dual beam instrument but in some cases had limited spectral range either in the UV or the near infrared or both data not shown The largest divergence was found for a grating spectrograph instrument that illumina
294. salinity chlorophyll a turbidity CDOM light absorption and attenuation and backscatter and from sensors deployed on a moving boat Water is brought through the hull and flows through all the instruments which are on deck The sensor measurements are recorded every at variable sampling rates most commonly on the order of 1 Hz and are georeferenced using dGPS The result is a spatial dataset of water quality measurements along a transect The transects in Great Bay and Little Bay will be criss crossed to make a matrix of water quality measurements covering a majority of the estuarine area Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 19 Sample Process Design for Activity 4 Point measurements with field sensors and grab samples During the two days of aerial data collection point measurements of water quality will be collected at stations throughout the study area Table 7 Figure 7 Grab samples will be analyzed for physico chemical parameters dissolved nutrients chlorophyll a total suspended solids CDOM and water clarity At some of the stations a custom profiling package will measure the vertical distribution of the IOPs with a hyperspectral attenuation absorption meter and nine channel backscattering meter ACS and BB 9 WetLABS Inc Laboratory based measurements of absorption spectra for the optically important constituents from discrete water samples will help with the interpretation and validation
295. should be used with vacuum 7 8 inches of mercury or positive pressure 1 2 psi Positive pressure filtration is recommended because it filters larger volumes of water at reduced filtration times The only problem with vacuum filtration 1s that unobservable air leaks may occur around the filtration holder and as a result the pressure gradient across the filter is much less than what is indicated on the vacuum gauge When positive filtration is used any leakage around the filter holder results in observable dripping water Inert membrane filters such as polyester filters may be used when size fraction filtration is required When this Is done it is recommended to also filter a replicate sample through a GF F to determine the total concentration Summing the various size fractionated concentrations may not produce an accurate estimate of the total because of the potential for cell disruption during filtration There has been an ongoing discussion of filter types and retention efficiencies for natural samples Phinney and Yentsch 1985 showed the inadequacy of GF F filters for retaining chlorophyll a in oligotrophic waters as did Dickson and Wheeler 1993 for samples from the North Pacific In response to Dickson and Wheeler 1993 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Chavez et al 1995 compared samples collected in the Pacific Ocean using GF F and 0 2 um membrane filters with small filtered
296. sibility status MODIS ATBD document 27 Kitchen J C J R V Zaneveld and H Pak 1982 Effect of particle size distribution and chloropyll content on beam attenuation spectra Appl Opt 21 3913 3918 Morel A 1997 Consequences of a Synechococcus bloom upon the optical properties of oceanic case 1 waters Limnol Oceanogr 42 1746 1754 Morel A Y H Ahn F Partensky D Vaulot and H Claustre 1993 Prochlorococcus and Synechococcus A comparative study of their optical properties in relation to their size and pigmentation J Mar Res 51 617 647 Mueller J L and R W Austin 1995 Ocean Optics Protocols for SeaWiFS Validation Revision 1 NASA Tech Memo 104566 Vol 25 S B Hooker E R Firestone and J G Acker Eds NASA Goddard Space Flight Center Greenbelt Maryland 67 pp Mueller J L and G S Fargion 2002 Ocean Optics Protocols for Satellite Ocean Color Sensor Validation Revision 3 NASA TM 2002 210004 NASA Goddard Space Flight Center Greenbelt Maryland 184 pp Stewart D E and F H Farmer 1984 Extraction identification and quantification of phycobiliprotein pigments from phototrophic plankton Limnol Oceanogr 29 392 397 Strickland J D H and T R Parsons 1972 A Practical Handbook of Sea Water Analysis Fisheries Research Board of Canada 310 pp Subramaniam A E J Carpenter and P G Falkowski 1999 Bio optical properties of the marine diazotrophic cyanobacteria Trichodesmium sp
297. sing The folded pathlength design Fig 2 1 bottom panel uses one or more reflectors to create a longer pathlength The basic idea for this design can be attributed to Petterson 1934 Initial designs used plane mirrors to expand the pathlength Wattenberg 1938 Timofeeva 1960 The introduction of prisms to separate the incident and reflected beam Nikolayev and Zhil tsov 1968 Petzold and Austin 1968 and of concave mirrors as the reflectors have led to improved versions of this general design An optical pathlength of 10 m was achieved by Jerlov 1957 by using multiple reflections between three concave mirrors A currently available commercial instrument with a folded path is the HOBILabs c meter water path lens detector source window window folding mirrors water path detector Fig 2 1 Schematic illustrations of direct path top panel and folded path bottom panel beam transmissometers designs Other Types of Transmissometers A variable pathlength transmissometer is probably the most desirable and elusive c meter design concept One desirable factor would be such an instrument s ability to adjust the pathlength to make it optimal for the measuring conditions see Pathlength Considerations below More importantly the variable pathlength instrument is self calibrating To understand this property of such an instrument examine the basic equation 1 6 for transmissometer measurements For any transmissomet
298. sion 5 2003 This technical report is not meant as a substitute for scientific literature Instead it will provide a ready and responsive vehicle for the multitude of technical reports issued by an operational Project The contributions are published as submitted after only minor editing to correct obvious grammatical or clerical errors Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Table of Contents CHAP TER 1 BESES JERES SESSE SER SEES SE SE SER ENES SE SES SEES SSSE nsaneese soasonse scansue seaseuseasandesas EUST KE RE RR TERESE BESES 1 INHERENT OPTICAL PROPERTY MEASUREMENT CONCEPTS PHYSICAL PRINCIPLES AND INSTRUMENTS TEL INTRODUCTION ertet ee i e tere tet p ER ERE RAI ee vo e ele RES 1 1 2 ABSORPTION AND SCATTERING PROPERTIES OF WATER PARTICLES AND DISSOLVED SUBSTANCES gp btosttadiec eodem nennen Bette edoi iteratis 2 Absorption by Pure Walter 4e deett eden r e ted t t dendi dede 2 Absorption by Suspended Particulates and Colored Dissolved Organic Material CDOM 2 Scattering Dy Pure Walters ideis eee arre tede ito ete ete 5 Scattering by Pariclesu ach ds aet vete eiie fen ete pb ee vere eed 6 Scattering by Turbulente aet eee ee eee aee toc e peers be deed to bebe deed 6 1 3 RADIANT FLUX TRANSMISSION MEASUREMENT CONCEPTS eee 6 Geometry and Nomenclature ee esee esee a tren enne eterne trennen 6 Transmittance and Beam Attenuation
299. ss be rewritten for each revision to reflect relatively minor changes in e g cross referencing and to maintain self contained consistency in the protocol manual More critically as it grows bigger the book becomes more difficult to use by its intended audience A massive new protocol manual is difficult for a reader to peruse thoroughly enough to stay current with and apply important new material and revisions it may contain Many people simply find it too time consuming to keep up with changing protocols presented in this format which may explain why some relatively recent technical reports and journal articles cite Mueller and Austin 1995 rather than the then current more correct protocol document It is hoped that the new format will improve community access to current protocols by stabilizing those volumes and chapters that do not change significantly over periods of several years and introducing most new major revisions as new chapters to be added to an existing volume without revision of its previous contents The relationships between the Revision 4 chapters of each protocol volume and those of Revision 3 Mueller and Fargion 2002 and the topics new chapters are briefly summarized below Volume I This volume covers perspectives on ocean color research and validation Chapter 1 fundamental definitions terminology relationships and conventions used throughout the protocol document Chapter 2 requirements for specific in situ observ
300. ssan and Ferrari 19952 c Pathlength amplification corrections To correct for the pathlength increases due to multiple scattering in the filter the prevalent current practice 1s to estimate D empirically through either a quadratic or power function that may be expressed in the form p la C OD 4 OD ru E 4 62 or C 8 6 G OD 4 0D u 4 4 6b for quadratic equation or power function fits respectively Co C and C are coefficients of least squares regression fits of measured data Recommended coefficients have been reported in the literature Table 1 The investigator should either choose published coefficients consistent with the species composition equipment and measurement conditions for a given data set consider the discussion in Mitchell et al 2000 or independently determine 53 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV pathlength amplification factors by comparing absorption in suspension and on filters following procedures described previously Mitchell 1990 Mitchell et al 2000 d De pigmented Particle and Phytoplankton Absorption Coefficients The de pigmented particle absorption coefficients a 4 may be calculated using Equation 4 5 by substituting OD 4 for OD A At present it is recommended to use the same pathlength correction factor for the de pigmented samples as for the particle absorption sample The validity of this operatio
301. ssan and Ferrari 1995a Mitchell et al 2000 This procedure can also be adapted for use with particulate suspensions Neither methanol extraction nor NaClO oxidation provides an ideal means of separating particulate absorption into algal and detrital components In each case the action of the chemical agent is not well understood and in many situations the two methods will yield very different results The decision to apply either the bleaching or methanol extraction method will depend on the situation For example in inland waters where either cyanobacteria or chlorophytes are dominant the bleaching technique is preferred because of the presence of phycobilins and of extraction resistant algae e g Porra 1990 In coastal oceanic waters on the other hand the methanol technique is preferred because the results will be comparable to previously published results and there is no particular advantage to using bleach In open ocean samples e g the Sargasso Sea however absorption by phycobilins is small but present in some particulate absorption samples and in methanol extracted filters N B Nelson unpublished data The methanol technique will provide results which are comparable to earlier studies but with errors due to incomplete extraction and wavelength shifts in the phycobilin absorption bands a Methanol Extraction method e Replace the sample and blank filters on the filtration system Treat blank filters exactly as i
302. ssary for measuring the absorption by the dissolved component For measurement of the absorption by dissolved materials only one side needs to be filtered because scattering by particles less than 0 2 um in size is not detectable by an ac 9 and hence the filtered a and c measurements are equal On the other hand measurements with filters on intakes of both sides are useful for quality control tests Sect 3 5 34 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV If possible replace the filter daily If you choose to replace a filter less frequently soak it in DI water during long breaks between profile measurements during a deployment Record the date of each filter change in the cruise log Mixing of water within the filter cartridge will smear measurements of a vertical gradient in the absorption by dissolved materials and an unfiltered instrument will detect a gradient in total absorption with better vertical resolution In addition the reduced flow rate through the filter will increase the time lag to approximately 4 to 6 sec compared to 1 2 to 1 8 sec for unfiltered measurements Moreover the lag rate will gradually increase as a filter accumulates particles during its use The preferred means of determining flow rate and lag corrections is to attach a flow meter in line into the supply or exhaust tubing An indirect technique for estimating flow rate related lag times is to match depths of changes
303. ssible after collection and the filters stored immediately in liquid nitrogen Liquid nitrogen is the best method for storing filter samples with minimum degradation for short as well as longer storage times e g 1 year Placing samples in liquid nitrogen also assists in pigment extraction by weakening the cell wall and membrane during this rapid temperature change Ultra cold freezers 90 C can be used for storage although they have not been tested for longer than 60 days Jeffrey et al 1997 Conventional deep freezers should not be used for storing samples more than 20 hours before transferring them to an ultra cold freezer or liquid nitrogen Again storage of samples in liquid nitrogen immediately after filtration is the preferred method The addition of MgCO at the end of the filtration process to stabilize chlorophyll has not been used for many years as a routine oceanographic method because of the uncertainty in pigment absorption by MgCO3 If samples are to be stored for any length of time prior to fluorometric analysis they should be folded in half with the filtered halves facing in This eliminates problems of rubbing particles off the filter during placement in sample containers and storage It is strongly recommended to use aluminum foil wrappings for sample containers This simple but effective container is both inexpensive and easy to use Cut small pieces of heavy duty aluminum foil into approximately 4 cm squares Fold eac
304. st determine the sensor s response weighting function W A y c equation 1 19 either explicitly or implicitly The explicit approach to this problem is to determine W ww 9c from geometry and first principles and then calibrate the instrument s response signals in a medium having a known VSF A v the detailed steps in this approach are described below in Sect 5 2 The implicit approach Maffione and Dana 1997 is to insert a plaque of known near Lambertian reflectance in the position of the horizontal xy plane at distance z from the source detector axis illustrated Fig 5 1 and record the instrument s responses as the plaque is moved vertically in small increments through the volume defined by the intersection of the source beam and detector FOV this approach is briefly outlined in Sect 5 3 below but the reader is referred to Maffione and Dana 1997 for the detailed derivation and method of implementation For brevity we will henceforth omit the explicit wavelength dependence of variables 52 CHARACTERIZATION AND CALIBRATION OF A VSF SENSOR FROM ITS GEOMETRY AND RESPONSE TO SCATTERING BY POLYSTYRENE BEADS Geometric Determination of W w Figure 5 1 illustrates a source located at the origin x 0 0 0 and a detector located on the y axis at position X 0 y 0 As illustrated the source beam and detector FOV are assumed to be cones with divergence angles o and o respectively At a distance z above the xy plane a hor
305. sured scattering coefficient and subtract it from the measured absorption at each wavelength i e a 4 a A 2 a2 s c a5 A 3 15 Based on analyses of field measurements laboratory experiments using an ac 9 and theoretical calculations Kirk 1992 the fraction varies from approximately 0 14 for predominately biological particles in the open ocean Case 1 waters and increases to approximately 0 18 in waters were scattering 1s dominated by suspended sediments Case 2 waters Note that although the scattering correction using 3 15 is not sensitive to temperature and salinity corrections at wavelengths 650 nm it is nevertheless strongly recommended that the temperature and salinity corrected values be used here as well if for no other reason than facilitating quality control comparisons between corrections made by different methods Combine methods 1 and 2 and the assumptions underlying both methods to use the ac 9 measurements at the reference wavelength to determine e so that 3 15 becomes TS a a A3 a 3 an Anr 7 3 a AYN 1 a a dm ce un 5 Anr 5 s 3 6 The ac 9 instrument design constrains the scattering error fraction to 2 0 07 Kirk 1992 and although it is theoretically possible for amp to reach values exceeding 0 5 the authors have not encountered values greater than 0 35 The choice of which method should be used to correct scattering errors in ac 9 absorption me
306. t Bay NHEP 2006 0 6 gt 0 5 0 4 0 3 DIN mg N L 0 2 0 1 0 0 1974 1981 1997 2004 Period Figure 3 Eelgrass cover and biomass in Great Bay NHEP 2006 3 000 2 500 2 000 1 500 1 000 Eelgrass Habitat 500 0 1985 1990 1995 2000 2005 e Cover acres m Biomass metric tons Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 9 Figure 4 Study Area 2 0 2 4 6 8 10 Kilometers d aa A6 Project Task Description The project will consist of three parts For the first task of the project UNH Coastal Observing Center will redeploy a moored buoy in Great Bay Figure 5 with appropriate sensors for measuring the hyperspectral light field including attenuation coefficients and the remote sensing reflectance as well as CDOM turbidity chlorophyll a nitrate and other physico chemical parameters http www cooa unh edu buoydata buoy jsp These parameters will be measured in situ on a 30 minute time step The large volume of data on all the parameters related to light attenuation collected over a broad range of environmental and optical conditions will make it possible to derive a statistically significant relationship to predict water clarity from water quality parameters Output A Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 10 Figure 5 Buoy and sampli
307. tant to know the transmittance effects due to very near forward scattering independent of the sources that may dominate the scattering process From another perspective the angular resolution of radiative transfer models tends to be larger than one degree so fine angular resolution of the volume scattering coefficient and related beam attenuation coefficient is not needed for accurate model calculations Mobley et al 1993 For many such calculations it is preferable to smooth the highly forward peaked phase function Fig 1 3 Ch 2 and decrease the beam attenuation coefficient accordingly Gordon 1993 indicates that for irradiance level radiative transfer 1t 1s possible to completely disregard scattering in the first 15 an angle much larger than the acceptance angles of transmissometers Finally from an engineering perspective it is more difficult to build a stable transmissometer with a very small acceptance angle Based on these considerations most transmissometers are designed with an acceptance angle lt 1 The second question has been addressed by several investigators over the years Gumprecht and Sliepcevich 1953 Jones and Wills 1956 Jerlov 1957 Duntley 1963 Voss and Austin 1993 Voss and Austin 1993 examined the scattering error for both collimated beam and cylindrically limited instruments designs They found that the percent error increases with increasing acceptance angle and with increasing c X The average error for a
308. ted to select the waveband of the measurement and the light is passed into the water through a window At the other end of the optical path the light enters the detector assembly through another window and is focused by a lens An aperture at the focal point removes off axis scattered light and the transmitted light falls on the detector Although this instrument is conceptually simple it is difficult to build The alignment of components is critical and something as simple as the filament in the source sagging as the instrument 1s moved can create significant apparent changes in the derived beam attenuation coefficient Several commercial transmissometers including some laboratory Cylindrically limited beam as opposed to collimated beam transmissometers will be discussed later in this section Certain commercial equipment instruments or materials are identified in this chapter to foster understanding Such identification does not imply recommendation or endorsement by the National Aeronautics and Space Administration nor does it imply that the materials or equipment identified are necessarily the best available for the purpose 15 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV spectrophotometers and the former SeaTech and WET Labs field instruments use this basic design Design variations include the addition of a reference detector and placing the wavelength filter in the detector hou
309. tered out of the beam into direction w 4 The directionally scattered flux A 0 y is subsequently transmitted a distance 7 in that direction with further losses due to scattering and absorption and the reduced scattered flux rs y is measured by Detector 2 at position X See text for further explanations The beam attenuation coefficient is defined in equations 2 16 through 2 18 of Vol I Chapter 2 Sect 2 4 as c X 2 a X b X m 1 1 where the volume absorption and scattering coefficients a X and b X are defined in terms of absorptance A X and scatterance B X in the limit of the optical pathlength Ar approaching zero as a A lim an and b A fim O m 1 2 Ar gt 0 Ar respectively Equation 2 16 Vol I Chapter 2 may be rearranged as im SIDI 2 im suem 13 Ar gt 0 o A Ar Ar0 Ar where and are incident and transmitted radiant fluxes respectively Equation 1 3 may be expressed in differential form as d0 X A r Integrating 1 4 over an optical pathlength r as c A dr 1 4 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV r d a c 4 dr 1 5 I 7156 7 we obtain the solution for the beam attenuation coefficient In A 0 0 e In A 7 0 e InT quo uoo SEU CIEN icu 1 6 Tr I where we adopt the conventions and notations described above and in Fig 1 4 In 1 6 transmittance
310. tes the filter with diffuse white light Figure 4 1 This unit yielded OD values that were significantly higher than albeit linearly related to with a slope of approximately 0 7 the OD measurements made with conventional dual beam spectrophotometers Mitchell et al 2000 This result indicates that the pathlength amplification D factor associated with this instrument is significantly different from previously published values Table 4 1 which were derived using conventional dual beam spectrophotometers An investigator using this type of spectrophotometer or another design with yet a different optical configuration must either compare filter OD spectra measurements to reference measurements on the same filters with a conventional spectrophotometer to derive an OD scaling function or otherwise determine pathlength amplification factors for the instrument configuration using methods discussed in Mitchell et al 2000 and references cited therein 4 4 PARTICLE ABSORPTION SAMPLE FILTER PREPARATION AND ANALYSIS The procedures described in this section are recommended for determining the spectral absorption coefficients of particles in discrete samples of natural waters These laboratory measurements are complementary to methods for measuring in situ profiles of absorption as described in Chapter 3 of this volume and provide additional information on the partition of particle absorption by phytoplankton and other particles Water samples ar
311. the sample was acquired 4 3 SPECTROPHOTOMETER CHARACTERISTICS AND CALIBRATION A spectrophotometer used for absorption measurements following the protocols presented in this chapter must meet the following minimum performance specifications 1 The units monochromator or spectrograph must yield a Full Width at Half Maximum FWHM bandwidth lt 4nm A larger FWHM bandwidth will not adequately resolve the red chlorophyll a absorption band 2 The instrument s baseline spectrum characteristics specified below must be maintained over the range from 300 nm to 850 nm for measuring absorption by particles concentrated on filters and from 250 nm to 850 nm for measuring absorption by dissolved materials 3 For measuring absorption by particles concentrated on filters baseline noise must be 0 01 OD and noise 0 005 OD is strongly recommended 4 For measuring absorption by dissolved materials baseline noise must be 0 001 OD units and noise 0 0005 OD is strongly recommended 5 The instrument s baseline spectrum must be relatively flat over the wavelength range of interest and its shape and magnitude must be stable over time Any tendencies for the spectral shape and magnitude of an instrument s baseline to drift must be well behaved and slow enough that the rate of baseline drift may be characterized with an uncertainty less than the noise levels specified above It is recommended to check the instrument baseline at intervals of 1 hr to
312. thlengths also reduce the relative uncertainty in the measurement of the pathlength r A pathlength in the range e a lt rn lt 3c A is generally considered close to optimal As electronics and sources have improved however instruments with pathlengths r lt e a m have been shown to work well over a wide range of oceanic conditions 20 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV Ambient Light Rejection in Open and Enclosed Path Transmissometers The basic transmissometer designs Fig 2 1 do not physically reject all ambient sunlight which could add to the measured flux Enclosed path designs that place the optical path within a cell through which the water is pumped such as the ac 9 have more physical blocking of ambient light but are not totally immune to its effects Some scheme must be developed to remove ambient light artifacts A simple approach is to measure the signal with the source on and with the source off The ambient signal with the source off is used as the dark reference for relating output signal to transmitted flux The current generation of instruments use a more sophisticated but similar approach The light source is rapidly modulated chopped and the detector output is phase locked to the modulation frequency so that the transmitted flux 1s proportional to the amplitude of the alternating component of detector output The key underlying assumption is that th
313. tion Maintenance Sensors on deployed dataloggers will be inspected for possible debris or fouling and cleaned as necessary prior to calibration and re deployment The following anti fouling maintenance and calibration measures will be used for the sensors Temperature and Salinity Antifouling The conductivity cell in the SBE37 SIP is equipped with two plugs containing tributyl tin TBT which are designed to eliminate or retard biological activity Previous deployments have demonstrated the effectiveness of this system for at least several months Instrument Maintenance and Calibration The instrument is sent to Sea Bird for maintenance and calibration after each deployment period CDOM Antifouling The ECO fluorometers are equipped with copper plating surrounding the fluorometer window The fluorometers were purchased with the optional bio wiper assembly which is a copper and rubber wiper that is designed to keep the window clean by covering it when not in use and by wiping it clean each time the instrument is powered To further mitigate fouling the instrument housing is wrapped in copper tape prior to deployment Instrument Maintenance and Calibration Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 28 The instrument is sent to WET Labs for maintenance and calibration after each deployment period Chlorophyll a Antifouling The ECO fluorometers are equipped with copper plating surrounding the
314. tion coefficient and not including it in the VSF We may rerwrite 1 1 c X a X b X as c X 2 a X 2n B A w sinydy 2n B w sinydy ig FOV c A e A 2s BO w sin ydy a A 2n f B A w sin ydy a b 2 where c X and 5 X are the measured beam attenuation and volume scattering coefficients respectively In another design variant the beam is cylindrically limited rather than collimated In the cylindrically limited light arrangement the pinhole at the source is imaged on the receiver lens and the receiver aperture is focused on the source lens This design illuminates a large volume of water and uses more of the source light No currently available commercial instruments use the cylindrically limited design although at one point in history transmissometers of this type were manufactured by Martek The Visibility Laboratory Spectral Transmissometer VLST was a laboratory built instrument using a cylindrically limited beam in a folded path configuration Petzold and Austin 1968 Several copies of the VLST built in the late 1970 s continued in use to measure c A until circa 1990 Pathlength Considerations One issue that must be addressed when designing a transmissometer is what the in water pathlength should be Scientifically it is important to keep the pathlength long enough that the sample volume presents a statistical average of the surrounding water and short enough that multiply scattered light is not inc
315. tion has been determined have been reported by Sosik and Mitchell 1995 Soluble absorption observations were described by Bricaud er al 1981 for diverse ocean environments including oligotrophic and eutrophic regions Other field reports can be found in the references listed in more recent articles Carder et al 1989a 1989b Blough et al 1993 Vodacek et al 1996 Hoge et al 1993 Nelson et al 1998 D Sa et al 1999 Spectrophotometric measurement of absorption by dissolved materials is straightforward 40 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV but has limits due to the very small signal for short pathlengths routinely employed usually 10 cm and to difficulties in maintaining quality control of purified water used as a reference This chapter defines protocols for the operational determinations of absorption coefficients for particulate and soluble matter in water samples Methods are specified for separating particulate and soluble material by filtration partitioning total particulate absorption into contributions by phytoplankton and de pigmented particles detritus and corrections for pathlength amplification due to semi diffuse transmittance of the filters Recommendations are made based on widely accepted methods and processing procedures NASA sponsored workshops have confirmed various aspects of previously reported methods Mitchell et al 2000 4 2 SAMPLE ACQUIS
316. tion take place the refracted portion is transmitted to the outer quartz air interface where another refraction and reflection interaction occurs For simplicity in this conceptual discussion we do not consider multiple reflection and refractive transmittance interactions within the thin quartz layer Ray paths containing a scattering angle less than the critical angle w associated with total internal reflection at the outer quartz air interface are totally reflected on each encounter with the tube wall and are transmitted to the detector over a slightly elongated path for a quartz reflective tube y 42 and thus the total internal reflectance represents a very large fraction of all flux scattered by particles Fig 1 3 Flux transmitted along ray paths with a scattering angle in the range y y us undergoes partial transmittance losses 1 v at each encounter with the reflectance tube with the reflected portion continuing over a zig zag path until either reaching the detector or disappearing due to attenuation by absorption and transmission losses in multiple encounters with the tube wall Flux along ray paths containing a scattering angle T i i i y 2 i e backscattered flux is lost from the forward transmittance altogether Backscattering accounts for only a few percent of scattering by marine particulates Fig 1 3 Large Area Detector I I i I 1 Collimated I Source I I I 1 Quartz or Glass
317. tions and methods for measurement and analyses of SPM PSD and the organic suspended particulate fractions POC and PON REFERENCES Balch W M P M Holligan S G Ackleson and K J Voss 1991 Biological and optical properties of mesoscale coccolithophore blooms in the Gulf of Maine Limnol Oceanogr 36 629 643 In some previous versions of the Ocean Optics Protocols Mueller and Austin 1992 1995 Fargion and Mueller 2000 it was incorrectly stated that suitable protocols were part of the JGOFS core measurements protocols UNESCO 1994 The JGOFS protocols do not include SPM measurements of the type specified here Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Bidegare R R L Van Heukelem and C C Trees 2002 HPLC phytoplankton pigments sampling laboratory methods and quality assurance procedures Chapter 17 in Ocean Optics Protocols for Satellite Ocean Color Sensor Validation Revision 3 Mueller J L and G S Fargion Eds NASA TM 2002 210004 NASA Goddard Space Flight Center Greenbelt Maryland pp258 268 Fargion G S and J L Mueller 2000 Ocean Optics Protocols for Satellite Ocean Color Sensor Validation Revision 2 NASA TM 2001 209955 NASA Goddard Space Flight Center Greenbelt Maryland 184 pp Hoge F E C W Wright P E Lyon R N Swift and J Yungel 1999 Satellite retrival of the absorption coefficient of phytoplankton phycoerythrin pigment Theory and fea
318. tively canthaxanthin spiked HPLC grade acetone solvent may be prepared in advance in a batch large enough for all samples and 3 mL is added to each tube in a single step Since GF F filters retain a significant amount of seawater following filtration ca 0 2 mL per 25 mm filter the final acetone concentration in the pigment extracts is 94 9o acetone water by volume by measuring the canthaxanthin peak area A for each sample the ratio Ac du may be used to adjust for sample to sample variations in the extraction volume Samples are disrupted by sonication placed in a freezer and allowed to extract at 0 C for 24h Alternatively the cells can be mechanically disrupted using a glass Teflon tissue grinder and allowed to extract at 0 C for 24h If after disrupting the cells it is necessary to rinse the tissue grinder or mortar and pestle then a known volume of 90 acetone measured using a Class A volumetric pipette should be used The ease with which the pigments are removed from the cells varies considerably with different phytoplankton In all cases freezing the sample filters in liquid nitrogen improves extraction efficiency Prior to analysis pigment extracts are vortexed and centrifuged to minimize cellular debris To remove fine glass fiber and cellular debris from the extract as well as enhance the life expectancy of the HPLC column filter the extract through 13 mm PTFE polytetrafluoroethylene membrane syringe filters
319. tograph chromatography and conductivity Dissolved DOC Shimadzu TOC High June 25 EPA Organic Carbon 5000 with Temperature 2002 415 1 Protocol autosampler Catalytic Oxidation HTCO Total Dissolved TDN Shimadzu TOC HTCO with June 25 Merriam Nitrogen 5000 coupled chemiluminescent 2002 et al Protocol with an Antek N detection 1996 720 N detector DOC and TDN DOC and Shimadzu HTCO with June 25 EPA combined TDN TOC V with chemiluminescent 2002 415 1 Protocol TNM nitrogen N detection and module Merriam et al 1996 Lachat Nitrate Nitrite Lachat Automated Cd June 25 EPA QuikChem AE colorimetric QuikChem AE Cu reduction 2002 353 2 Protocol NO NO2 Ammonium Lachat Automated June 25 EPA colorimetric QuikChem AE Phenate 2002 350 1 NH Soluble Lachat Automated June 25 EPA 365 reactive QuikChem AE Ascorbic acid 2002 Phosphorous colorimetric PO Acid Washing Glass and 10 HCI rinse June 25 Protocol plastic ware and 6 rinses with 2002 cleaning DDW Field Filtering Sample prep 3 times rinse with June 25 Protocol filtered sample 2002 Page E 11 Table 2 Detection limits acceptable ranges and recent historical averages for QC samples at the Water Quality Analysis Lab Detection limit based on user experience and previous analysis not statistically calculated Method Detection Limit MDL is the minimum concentration of a substance that can be measured and reported with
320. tracking is primarily intended to be used to monitor offsets in the instrument s output due to changes in the optical system caused by shipping or mounting of the instrument to a cage or other deployment package Air tracking can also be used to monitor instrument drift over extended periods of time Historically before the advent of pure water field calibrations the air calibration was the only stability tracking method available Air tracking data is best obtained in the laboratory where the environment is consistently clean and dry preferably before and after each transmissometer deployment Although air calibrations can be performed while in the field it is at best difficult to do them on a ship due to the moist environment Readings in air may be significantly offset by small amounts of moisture either condensed on or adsorbed in the windows Detailed protocols for carrying out air calibrations are provided for particular instruments by the manufacturer In general terms the protocols include instructions and methods for careful cleaning of optical surfaces allowing time for exposed optical surfaces to dehydrate in a dry environment and procedures to avoid or compensate for temperature increases when the instrument is operated in air User air calibration values can be used to adjust the pure water calibration and responses to correct for instrument drift as adjusted Voir a Ve f dark f Vow yi a poke Pow e Vow 2 13 D air D
321. ts will be completed within pua 2 hours of the flight time Cotiparabiliy Data comparability will be achieved primarily through the use of standardized methods from past studies and the scientific literature Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 15 A8 Special Training Certification Data will be collected by trained professional staff at UNH and SpecTIR Each agency will be responsible for training staff working under the supervision of the Project Officers before any field work is conducted Table 3 Special Personnel Training Requirements Project Description of Training Training Deadline for Location of function Training Provided by Provided to Training Training Records Study design Sampling process Project Manager UNH Research 8 24 07 Documentation design from section Staff and will be on file at Bl SpecTIR Project NHEP Officers Water quality Field measurement Project Manager Field crews 8 24 07 Documentation field procedures in will be on file at procedures sections B2 through NHEP B9 and related appendices Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 16 A9 Documents and Records QA Project Plan The NHEP QA Officer will be responsible for maintaining the approved QA Project Plan and for distributing the latest version of the plan to all parties on the distribution list Table 1 A copy of the approved plan wil
322. ttenuation meters from HOBILabs WET Labs or Sea Tech for example each instrument model would yield a slightly different c because of its different acceptance angle These differences also depend on the shape of VSF These considerations lead to two questions What is the best detector acceptance angle choice for a transmissometer design What method should be used to correct the beam attenuation measurements for scattered light acceptance The first question appears to have a simple answer The above discussion and equation 2 8 would seem to imply that the smaller the acceptance angle the better the measurement That may not be correct One must further consider what is being measured when choosing the acceptance angle Pegau et al 1995 and particularly at very small angles in the presence of near forward scattering Density fluctuations due to natural or instrument related turbulence steer the beam into random fluctuations and increase the apparent beam attenuation coefficient Bogucki et al 1998 independently from ordinary molecular and particle scattering processes Ch 1 Sect 1 5 How might this phenomenon affect a particular application of the measurement Were a person interested in inverting the spectral beam attenuation coefficient to determine particle properties they wouldn t want a beam attenuation meter that is very sensitive to scattering by turbulence For active LIDAR imaging systems on the other hand it may be impor
323. tubing to a pressurization unit that pushes water to the instrument Fig 3 4 The carboy is pressurized to approximately 10 psi using an oil free air pump or a tank of dry nitrogen gas The air supply tube inside the carboy should be kept above the water level to prevent the creation of bubbles when pressurizing the carboy and the outlet tube should extend nearly to the bottom of the carboy To connect the carboy to the ac 9 Teflon tubing is recommended rather than Tygon tubing which may contain plasticizers that can contaminate the water The tubing from the carboy is connected to the bottom nozzle on the ac 9 flow tube The tubing near the ac 9 inlet and outlet should be covered with black tape to avoid ambient light leaks into the optical path A short piece of tubing with a valve is connected to the top nozzle on the flow tube both to control water flow through the system and to provide backpressure which helps to keep gases in solution and prevents the formation of micro bubbles An optional 0 2 micron filter may be placed at the point of delivery Fig 3 4 Schematic illustration of a pure water supply system for field calibrations of an ac 9 Air Calibrations This procedure is discussed adequately in Chapter 2 33 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV 3 3 MEASURING SPECTRAL ABSORPTION COEFFICIENTS WITH REFLECTIVE TUBE METERS The ac 9 should be mounted in a profiling i
324. umented buoy in Great Bay in 2005 2006 and 2007 This group also conducts periodic cruises throughout the Great Bay system with flow through instrument array to document spatial heterogeneity of water quality parameters Field crews from the UNH Marine Program will be used to collect water quality samples in the estuary The NHEP will provide administrative and technical oversight for this project The NHEP is part of EPA s National Estuary Program and is coordinating the nutrient criteria development process through its Technical Advisory Committee with the NHEP Coastal Scientist leading the work The NHEP s latest State of the Estuaries report highlighted declines in eelgrass beds and increases in nitrogen concentrations in Great Bay available at www nhep unh edu Jennifer Hunter the NHEP Director will be responsible for the contractual and fiscal aspects of the project Phil Trowbridge the NHEP Coastal Scientist will act as the QA Project Officer and will ensure the quality of the data products produced Chris Nash of the NH Department of Environmental Services DES will also assist with field sampling activities Several subcontractors will assist UNH in the data collection efforts Each subcontractor is listed below Hyperspectral imagery for the project will be provided by SpecTIR AJ Markow will be the Project Manager for SpecTIR with program oversight provided by Willam Bernard and assistance from Oliver Weatherbee and Chri
325. use the upcast water intake is taken in the wake of the rising package and turbulence may also cause apparent hysteresis symptoms to appear in the measurements Pressure effects should not have hysteresis If more than one ac 9 is available it is useful to plumb both instruments in identical configurations both with or without an intake filter on the same instrument and measure a quick sequence of comparative profiles to intercalibrate the instruments The profile data from the two instruments should be compared only after each has been fully processed and corrected for temperature salinity and scattering errors Sect 3 4 Discrepancies in this type of comparison cannot indicate which instrument is incorrect but does provide a clear indication that the calibration of one or both is not correct REFERENCES James H R and E A Birge 1938 A laboratory study of the absorption of light by lake waters Trans Wis Acad Sci 31 1 154 Kirk J T O 1992 Monte Carlo modeling of the performance of a reflective tube absorption meter Appl Opt 31 30 6463 6468 Moore C J R V Zaneveld and J C Kitchen 1992 Preliminary results from an in situ spectral absorption meter Ocean Optics XI Proc SPIE 1750 330 337 Maffione R A and D R Dana 1997 Instruments and methods for measuring the backward scattering coefficient of ocean waters Appl Opt 36 6057 6067 Pegau W S and J R V Zaneveld 1993 Temperature dependent absorption
326. ust be applied Chapters 3 and 5 in this Volume Alternatively attempts have been made to calculate b by integrating measurements of the VSF e g by Petzold 1972 Volume Scattering Function Measurements In Fig 1 4 the combination of the source at x directional scattering at X and Detector 2 at location Xj schematically illustrate the conceptual elements of a scattering meter designed to measure the VSF B A y o Collimated flux A 0 0 e is transmitted in a beam of cross sectional area A from the source to X as D A 7 0 0 D 4 0 0 e 5 1 12 The irradiance incident normal to the optical transmission axis at X is p Pr on 0 9 D 0 0 e e 5 i A A At position X some of the incident radiant flux is scattered in direction v c into the solid angle field of view 1 13 Oo of Detector 1 from the volume V y defined by the intersection of the beam and detector field of view The radiant intensity of the scattered flux is o 2 0 v nagg A aa 1 14 FOV and scattered flux reaching the detector is o Am v 9 0 4 0 v o e gt 1 15 From equation 2 30 we may determine the VSF averaged over the working volume and solid angle FOV approximately as z I 4 0 y B X v o 2 1 16 EV v or by substituting from 1 12 through 1 13 directly in terms of source and detector fluxes as n o 20172 A c Bh BO v e se guten 1 17 2 0 0 0 V
327. ution and estuarine ecology Phil Trowbridge P E NHEP DES Data synthesis and nutrient criteria development What Maps of eelgrass and nuisance macroalgae cover in the Great Bay Estuary from hyper spectral imagery collected in August 2007 and October 2007 Nuisance macroalgal cover multiple Ulva species Gracilaria e g G tikvahiae epiphytic red algae e g ceramialean red algae and detached entangled Chaetomorpha populations has not been quantified throughout the estuary using a standard synoptic method The hyper spectral imagery collected in August 2007 and October 2007 provides an opportunity to map the nuisance macroalgae and eelgrass cover in the estuary using standardized methods GIS software will be used to summarize the total coverage of eelgrass and the different species of nuisance macroalgae in different zones of the estuary The results will be compared to maps of areas where historic eelgrass beds have been lost to determine whether nuisance macroalgae correlates with eelgrass loss in the Great Bay Estuary The data will also be useful to compare the dominant macroalgae species in the Great Bay which has large intertidal areas and the lower estuary which does not Where The project will be completed in the Great Bay Estuary system of NH and Maine Figure 3 The hyper spectral imagery covers most of the Great Bay Estuary Great Bay Little Bay Upper Piscataqua River Lower Piscataqua River to the 1 95 bridge Salmon F
328. value of the parameter being measured Accuracy limits of laboratory analyses are defined through independent heb ze urges AE PT 0 X X 2 where x is the original sample concentration x is the replicate sample concentration Great Bay Nutrient Criteria Study QAPP Draft No 1 August 24 2007 Page 27 calibration verifications and continuing calibration verifications of laboratory control samples The measurement of accuracy will be the percent recovery of spiked compound from a matrix spiked duplicate sample using the following equation R mo m where R is the percent recovery 96 x is the lab fortified sample concentration X is the original sample concentration m is the amount of chloride added to the fortified sample Accuracy measurements using standard reference materials will be evaluated using relative percent difference which was discussed in the preceding paragraph Boresight Calibration In order to ensure the optimal translation of the INS positional data to the image the INS and camera must be boresighted To achieve this SpecTIR has established a boresight calibration site south of the Stead NV airport As control 6 inch orthophotography and matching 2 foot contour data was obtained from Washoe County The positional accuracy of the orthophotography is 9 inches Completeness Data completeness is the percent of planned samples that were actually collected B6 Instrument Equipment Testing Inspec
329. veloping nutrient criteria for NH s estuaries DES in collaboration with the New Hampshire Estuaries Project NHEP began this process with the formation of a workgroup in 2005 The NHEP Coastal Scientist a DES employee is coordinating the work to undertake this process with input from the workgroup Information from the workgroup meetings is available at www nhep unh edu programs nutrient htm This workgroup adopted eelgrass survival as the water quality target for nutrient criteria development for NH s estuaries In 2007 the New Hampshire Estuaries Project NHEP received a 104 b 3 grant from the U S Environmental Protection Agency to collect water quality information including that from hyper spectral imagery data of the Great Bay Estuary EPA Grant Award X7 97167001 The expected outcome of this research will support the development of numeric nutrient criteria for NH s estuaries The NHEP has successfully collected the data and will prepare the final report by the deadline of June 30 2008 Recommendations for numeric nutrient criteria are planned for December 31 2008 Preliminary analysis of the data revealed an opportunity to contribute to the development numeric nutrient criteria Analysis of the data showed that phytoplankton as measured by suspended chlorophyll a only accounts for 896 of the light attenuation in the estuary This finding does not support a hypothesis that nitrogen enrichment is causing phytoplankton blooms which r
330. verted data is combined averaged for each 10 minute activity period and combined with appropriate metadata providing an initial dataset for each deployment After each deployment a final QA step involving ancillary measurements made at the buoy such as grab samples allows the data to be finalized This information data and metadata from the buoy will be permanently archived in the NH EMD Data from the flow through system is initially stored on a laptop computer on board the boat At the end of each day this is uploaded to a server in Morse Hall on the UNH Durham campus Where appropriate raw count data is converted to calibrated engineering units and both raw and converted data are archived Typically flow through data undergoes QA checks and is averaged within a 20 second timestep This data with appropriate metadata will be permanently archived at the NH DES EMD All data from the project will be made available to the public through the EMD and GRANIT which are publicly accessible Great Bay Nutrient Criteria Study QAPP C1 Assessments and Response Actions Draft No 1 August 24 2007 Page 31 In order to determine that field sampling field analysis and laboratory activities are occurring as planned field staff and laboratory personnel shall meet after the first sampling event to discuss the methods being employed and to review the quality assurance samples At this time all concerns regarding the sampling protocols and analysis te
331. y JGOFS Core Measurements Manual and Guides 29 170pp Van Heukelem L and C S Thomas 2001 Computer assisted high performance liquid chromatography method development with applications to the isolation and analysis of phytoplankton pigments J Crom A 910 31 49 Wright S W S W Jeffrey R F C Mantoura C A Llewellyn T Bjornland D Repeta and N Welschmeyer 1991 Improved HPLC method for the analysis of chlorophylls and carotenoids from marine phytoplankton Mar Ecol Prog Ser 77 183 196 Wright S W 1997 Summary of terms and equations used to evaluate HPLC chromatograms Appendix H in Jeffrey S W R F C Mantoura and S W Wright editors Phytoplankton pigment in oceanography guidelines to modern methods Vol 10 Monographs on oceanographic methodology UNESCO Publishing 661 pp Wright S W and R F C Mantoura 1997 Guidelines for selecting and setting up an HPLC system and laboratory Ch 15 in Jeffrey S W R F C Mantoura and S W Wright editors Phytoplankton pigment in oceanography guidelines to modern methods Vol 10 Monographs on oceanographic methodology UNESCO Publishing 661 pp 14 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume 5 Chapter 3 Fluorometric Chlorophyll a Sampling Laboratory Methods and Data Analysis Protocols Charles C Trees Robert R Bidigare David M Karl Laurie Van Heukelem and John Dore Center for Hydro Opti
332. y adjusted on a local basis to agree with HPLC determinations of the concentration of total chlorophylls A cost effective strategy is to acquire on each cruise a majority of filtered pigment samples for fluorometric chlorophyll a and pheopigment analysis supplemented by a smaller number of replicate samples for HPLC pigment analysis The HPLC replicates should provide a representative distribution over geographic location depth and time during a cruise and will be used to determine a local regression relationship between the two measurements This approach is now required for pigment data submitted for SeaBASS archival and SIMBIOS validation analysis Phycoerythrin and other Phycobiliproteins Res A may be enhanced by fluorescence by phycoerythrin PE in a band near 565 nm e g Hoge et al 1998 Wood et al 1999 The detection from aircraft of laser induced phycoerythrin fluorescence is already well established Hoge et al 1998 It is more difficult to detect and quantify solar induced phycoerythrin fluorescence but some work has been done in that area as well Morel et al 1993 Morel 1997 Hoge et al 1999 Subramaniam et al 1999 Various phycoerythrins differ from one another in chromophore composition All phycoerythrins contain phycoerythrobilin chromophores PEB maximum a A near X 550 nm many others also contain phycourobilin chromophores PUB maximum a A near X 500 nm which extends the range of wavelengths absorbed by the
333. y peaks in the vicinity of 8 may be relatively flat for much of its FWHM beam width and then tends to fall sharply near the edges of the beam and gradually decay beyond the nominal FWHM limits Detector angular responsivity FOV patterns generally exhibit similar geometric characteristics relative to The flux variations within the source beam may be expressed as a normalized relative flux distribution function h 2 that takes non zero values only in directions included in the solid angle beam pattern Similarly the angular response function of the the detector may be written A cQ All To generalize the weighting functions to account for arbitrary source beam and detector FOV geometries and relate the phase function to incremental detector responses AD AV 2 e i l Multiply the right hand sides of equations 5 1 and 5 2 by h amp x 9 and carry this factor through subsequent substitutions 69 Ocean Optics Protocols For Satellite Ocean Color Sensor Validation Revision 4 Volume IV 2 Substitute using the relationship AD AV X c h amp amp x eQ Jao AV X c on the left hand side of 5 7 to relate p w x to the incremental detector response 3 Absorb the source flux and detector responsivity distributions into the weighting function W x c by multiplying the right hand side of 5 7 by the product A amp x e O0 h 8 x 9 The numerical implementatio
334. ze scattered photons escaping from the beam in all directions but this would not indicate the directional nature of the scattering losses Instead the scattering process is schematically illustrated in Fig 1 4 as a mottled shaded path of photons scattered in a particular direction v c at a single location X in the beam At this on axis location X similar beams could be drawn in any other direction to visually indicate scattered flux intensity and its subsequent transmittance and attenuation in the new direction The same type of graphic could be drawn anywhere along the optical path and if many were combined we d generate the aforementioned photon cloud masking any indication of the vector nature of the scattered radiant field Nevertheless that mental construct is adequate for considering transmission measurement concepts If the pathlength r is short enough that photons initially scattered out of the beam have a negligible chance of undergoing two or more additional scattering interactions that could return them to the beam then it may be assumed that they will not be detected by Detector 1 Fig 1 4 When the IOP are used in the context of a radiative transfer model on the other hand the translations and rotations relating local coordinates used to describe scattering interactions e g as at position X in Fig 1 3 to global coordinates describing locations and directions in the medium as whole become criti

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