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Acoustic manual PGNAPES PGHERS version 2.1

1. Right click on the single echo window which opens the single target detection dialog Then click calibration In the calibration window open the calibration file made during calibration Click update beam data to upload calibration data into the echosounder The echosounder should then be ready for use 4 4 Interpretation of acoustic images Scrutiny The process of echogram scrutinisation is a largely subjective process that should be at the very least carried out in the presence of someone who is experienced not only with the process but also with the survey area and the target species Species aggregation tactics may vary greatly between species in addition to temporal and geographical variation As a result the allocation of NASC to species always needs support of trawl information However it should be noted that catch composition is influenced by the fish behaviour in response to the gear It is therefore necessary to judge whether the catch composition is a true reflection of the real species composition of the logged school or layer data and whether the allocated percentage species composition needs to be further investigated An effort should be made to scrutinize to the species level where possible and adhering to ICES three letter species codes for data submissions Probability classifications are being used in the North Sea herring survey definitely probably and possibly classes During mixed spec
2. 7 F Gonad length in relation to body cavity size Conversion from 8 to 4 stage key 8 point scale 4 point scale 7 Immature fie M Mature R Running Go l S Spent and resting ke n Appendix D Mesh size measurements Appendix E PGNAPES database format Logbook Country Station National station number 22 StType Geartype activity one line per activity at the same station National definition of station type A d EN Acoustic Post code 2 chars according to countries table Month MM gt O Day PA Decimal degrees negative latitude south 0 0 0000 The position refers to the beginning of the interval Decimal degrees negative longitude west of 00 0000 The position refers to the beginning of the interval Sv Threshold OB AcousticValues Month MM Day LD0 Species LBpeces code HER BLU Acoustic readings m nm Hydrography Post code 2 chars according to countries table Call sign 2 or 6 digits acc to Vessels table Cruise identifier Station Nationaal station numbers StType Geartype activity National definition of station type YYYY 4 digits Plankton Post code 2 chars according to countries table Call sign 2 or 6 digits acc to Vessels table Cruise identifier National station numbers Station o StType Geartype activity National definition of station type YYYY 4 digits Upper station depth m Lower station depth m if only one d
3. If not this might be due to freak start so add extra file at the beginning of file set 4 Save as using cruise and daily file name into a logic directory structure 5 Update calibration settings in all frequencies to be used Check if this is set to automatically 6 Block out bad data define analysis area Tip open cruisetrack while blocking out bad data Minor bottom integrations can cause a huge amount of unwanted biomass Potential sections to block out e Period with no daylight e All trawling activity The restart position can be estimated in the Cruise Track Window where the track crosses start position on restarted survey Any other periods not to be included such as extra stations steaming periods or sections between transect 7 Assign bottom and surface lines below bottom and entire near field need to be blocked out For a standard 38kHz near field is set to approximately 7m 8 Scrutiny see below 9 Check export settings if not already in the template and export LSSS software post processing procedures BI500 BI60 software post processing procedures Thresholding remove unwanted echoes and keep target species An advantage of using a post processing systems like BEI or EchoView is the ability to change the Threshold value of the received echoes By changing the Threshold the non target species plankton in particular can be filtered out The Threshold used may differ depending on a variety of conditions incl
4. The results of measurements of the first winter zone cover on average 53 measuring units at calibration 12 12 marks per 2 mm This may be used as a guide In older fish the first zone that is counted is normally distinct Bower s zone and other checks on the inside are distinguished from the other zones because they appear thinner and are often broken Figure 5 4 shows an example on a blue whiting otolith and how the number of winter ring can be read Figure 5 4 Blue whiting otolith 5 2 4 Maturity stages Maturity of herring and blue whiting should be determined according to fixed scales although reporting of the data varies according to participants See Appendix C for details The 8 point scale is based on Bowers and Holliday 1961 A conversion between the 8 point scale and the 4 point scale is presented in Appendix C Comment L3 Scale and otolith reading is and should also be done by experienced people who are familiar with SOPs Thus these paragraphs can be omitted 5 3 Deepsea species A deep sea species photo guide has been created during the blue whiting surveys of 2007 and 2008 This photo guide will be available as a stand alone document to all PGNAPES and PGTIPS coordinated surveys A word of caution is appropriate here All the determinations have been done on board aided by available literature and equipment All identifications are based on Muus and Nielsen 1999 and the three volume compilation
5. EK ER60 manuals and by Foote et al 1987 Ideally the procedure as described in the Simrad manual should be followed with certain exceptions see below Minimum target range for the calibration of a split beam 38 kHz echosounder is 10 metres although greater distances are recommended about 20 m because centering of the target below the transducer is facilitated if the target is suspended at a greater depth An average integrated value for the sphere taken when it is centrally located should be taken as the measured NASC The calculations should be then performed a number of times two or three in an iterative procedure such that the values of measured NASC and theoretical NASC should converge as described in the Simrad manual A choice is then made as to whether the S Transducer gain should be changed rendering absolute NASC or alternatively the S Transducer gain can be unaltered and a correction factor applied to the NASC Only one strategy should be applied during a cruise such that for example the latter option is to be employed when calibration is only possible after the cruise has started If possible the transducer should be calibrated both at the beginning and the end of the survey with a mean correction factor applied to the data If a new calibration differs less than 0 2 dB the sounder system functions acceptably If it differs more than 0 2 dB the system should be thoroughly inspected There are a number of parameters whic
6. Remarks Bhs ge e mp Na m ey AAA r Arras mEn 5 la gt e ol u lt E k gt I Er sse a ris ra Sp As bn Se Zoegtr H 5 J La F E z pe nn WR DH A Fluffy schools to layers Norwegian Sea IESNS Threshold 70dB Sandeel Ammodytes marinus Ammodytes tobianus SonarData Echoview File Echogram View Window Help O kale ICH leed Ol al Es S BS Gal 2114 i 75 0096 4 Primary fileset Sv raw pings T1 Live viewing 0910 20 jul 2005 SYTSE e 288 5n mi aiia il Af IN THU Katiy ny d ft 1 LN i de gH y i W y AEE anta M o K Gel A 38 Khz echogram left panel and the 200 kHz echogram right panel in the North Sea herring spawning survey Threshold 70dB Mackerel will hardly be detected by the 38kHz transducer but will lit up weak on the 200kHz Software post processing procedures Echoview software post processing procedures General checklist 1 Put selected template in Echoview template folder 2 Create new EV file selecting the correct template if one may exist for this type of survey All species names virtual variables used and other settings will be copied from this template 3 Add datafiles Tip create an Echoview file not containing too much raw data files e g one day fileset Tip open cruisetrack for first check Just check to see if cruise track is in the correct place and no files are missing
7. clause Conditions on data selected Example codes are listed in Appendix F CAUTION Always remember to check the results SQL returns exactly what you wrote in the SQL statement And that is not always the same as the results you wanted Tutorials are easily found on the web http www w3schools com sql default asp http www salcourse com http www 1keydata com sql sql html http www geocities com SiliconValley Vista 2207 sql1 html 10 2 PGTIPS Fishframe webbased database Survey data are checked and stored in the North Sea clone of the FishFrame system www Fishframe org Each country is responsible for uploading e Stage 3 data a Abundance AB files b Stock details SD files e Stage 1 data a Trawl information AF files b Scrutinized NASC s AA files After uploading the data each country should double check the data through the data browser and reports When the data are satisfactory they should be released The joined estimate is then calculated by FishFrame and unsampled rectangles are interpolated The FishFrame user manual Jansen amp Degel 2007a and Exchange format description Degel amp Jansen 2006 contains the necessary information on data upload formats and how to upload check release calculate interpolate tabulate map and report in FishFrame For documentation of the calculations please refer to Jansen amp Degel 2007 11 References Bodholt H 1999 The effect of t
8. coordinator should be appointed for each coordinated survey preferably during the PGNAPES meeting the year before the survey Survey coordinator then has the responsibility to carry planning further for example to update the survey plan as more detailed information on commitments becomes available Survey coordinator is the main contact person for information exchange before during and after the survey until finishing the survey report similarly Survey coordinator must keep other participants updated about the planning It is also the responsibility of the survey coordinator to find suitable dates and venue for post survey meeting if such meeting is arranged Contact details for survey vessels involved are given in Appendix A 2 3 Coordinating vessel During the survey one vessel will act as the coordinating vessel Usually this will be the vessel where the survey coordinator is Coordinating vessels is the hub for information exchange during the survey Contact details for a number of vessels can be found in the table below A coordinating vessel will be chosen during the survey planning phase Contact details for survey vessels involved are given in Appendix A 2 4 Information exchange PGNAPES Data exchange during and after the survey is relatively smooth due to improved adherence to the PGNAPES data exchange format Further improvements to the data exchange and database format were discussed It was agreed that proposed changes of data fo
9. data are combined to yield age and length stratified stock abundance estimates for individual species The methodology is in general terms described by Toresen et al 1998 and in more technical terms and detail by Simmonds amp MacLennan 2005 Theory The core of the analysis is the conversion of acoustic backscattering density estimates expressed in units m nm and variously denoted as sa or NASC to estimates of fish density relying on knowledge on average length of the fish and their length dependent acoustic target strength Acoustic target strength of fish varies with fish size and various other characteristics of individual fish but in practice only length dependence is taken in to account This is expressed with the so called target strength TS relationship TS a b Log L 1 where L denotes length and a and b are regression coefficients for species Some canonical coefficients are in the table below these values apply when length is expressed in centimetres Target Strength Equation Coefficients Species bi ai Herring 20 0 67 5 Blue whiting 21 8 72 8 Mackerel 20 84 9 Horse mackerel 20 71 2 Physoclist species 20 0 71 9 Acoustic cross section of a single fish lt o gt units metre squared is given by the equation o Gei Arr pllarcnpee ll 2 where the term in the exponent is the TS relationship This can be simplified to 42107 HTH division by 10 is an anachronism coming from the conversion of
10. docs Database worksheets PGNAPES_official_c 4 J Work docs Database worksheets PGSPFN_Full Pages Catch Countries Exit Macros DATABASECONTENTS Modules Hydrography Hydrography Groups ICESsquares Groups ICESsquares EZ Favorites 16055 Ea Favorites _ m MAPINFO_MAPCATALOG MAPINFO_MAPCATALOG Paste Errors Paste Errors Plankton Plankton Species Species StationTypes StationTypes Vessels Vessels amp Export Text Wizard A amp Export Text Wizard This wizard allows you to specify details on how Microsoft Access should export your data What delimiter separates your fields Select the appropriate delimiter and see how your text Which export format would you like is affected in the preview below Choose the delimiter that separates your Fields C Tab C Semicolon Comma C Space C Other D Text Qualifier i gt Fixed Width Fields are aligned in columns with spaces between each field Sample export format RO OW2252 0332 03320001 HYDR 300 HCSBC 200 Country Vessel Cruise Station StType Year Eo OW2252 W 0332 wi 03320001 PLKT 400 HUP2B 200 For r rOW2252 e 0332 WI 03320001 HYDR 300 HCSBC vw 2003 P FO 0W2252 0332 03320002 HYDR 300 HCSBC 200 Fo OWZ252 0332 03320001 PLKT 400 HWP2B 2003 rO 02252 0332 03320002 PLKET 400 HUP2ZB 200 Fo OWZ252 0332 03320002 HYDR 300 HCSBC 2003 error oWw2252 d 0332 m 03320003 D
11. of fish in the net during every haul If a target is missed during a haul the catch composition should not be used for species allocation 5 2 Biological sampling procedure The first step of trawl catch anaylsis is to determine species composition This can be carried by breaking the total catch into species components by weight either by exhaustive sampling sub sampling raising to the total catch or by a combination of both Second step is to record biological parameters of the target species within the catch age sex sexual maturity and individual weight measurements Table 5 1 Sampling levels for all target species O otoliths S scales L length M maturity G gender West of West of Scotland Scotland herring survey herring survey Irish ES A Blue whiting OLMG_ AMG gt Hering TC SLMG CT OLMG ST OLMGT LMG Dealfish we LMG II 5 2 1 Total catch treatment The Condition and Quality of the catch should be recorded by the person in charge of the biological sampling in consultation with the officer in charge or the fishing master according to a standard classification Table 5 2 Condition Inspecting the gear when it comes back on deck Quality Observe how the fishing was carried out and how the gear performed Table 5 2 Condition and quality categories Condition aye H Condition of the gear after the haul is finished Not inspected No damage or minor damage of the gear nothing of consequenc
12. of previous calibrations if erroneous values are entered by mistake A calibration report for all survey calibrations should be included in the final cruise report Caution Before starting a calibration make sure that the transducer has been given time to adjust its temperature to the surrounding water temperature The transducer settings of the EK ER60 can be found in Install Transceiver installation Transducer parameters To get the calibration report from EK ER60 Open the calibration program C Program Files Simrad Scientific EK ER60 Bin Calibration exe Open the file created with the calibration of your primary transducer and Print as PDF gives you the possibility to have the first part of the file containing calibration settings and results as an image in stead of a table The format is fixed and it can be used in reports easily 4 2 2 Calibration procedure for Simrad EK500 echosounder It is evident that all versions of the EK500 up to and including version 5 do not take account of the receiver delay in the calculation of target range see Fernandes amp Simmonds 1996 This is particularly important when calibrating at short range 10 m as it can lead to a systematic underestimate of biomass of 3 The correct range to the target should therefore be applied in calibration see below The equivalent two way beam angle w should also be corrected for sound speed according to Bodholt 1999 Receiver delay At This is v
13. possible to assign schools echo traces to species directly e g where the haul contains a mixture of species and no clear differentiation can be made between the observed schools In such situations the integral is assigned to a species mixture category according to the trawl results This is defined as percentage by number or weight taking into account the correct conversion to scattering length post processing software is then used to apply weights and lengths There are two main problems with using trawl data to define acoustic mixtures e Different species are known to have different catchabilities when encountering fishing gear so the exact proportions in the trawl are unlikely to be an exact sample of the true mixture For instance herring are likely to be faster swimmers than blue whiting e PGTIPS For instance herring are likely to be faster swimmers than Norway pout e A target species may also be encountered within a multi species mixed layer In some instances the non target species may be small enough to pass through the gear meshes thus providing a bias in the trawl catch to the actual content of the school layer Mesh size calculations are given in Appendix D e PGTIPS Herring are often found in a mixture with 0 group pout which are mostly lost through the meshes This may also occur with other small gadoids In this case the exact proportions are unavailable and the operator must make an informed guess Target species
14. submission deadlines for all participant countries need to be established for uploading of herring and blue whiting acoustic data to the PGNAPES database At present not all countries submit data in the required format on a pre agreed timescale In some cases data from previous years is still outstanding 10 1 2 PGNAPES database table description Tables and table constraints Ed Microsoft Access Relationships BEA og File Edit View Relationships Tools Window Help E lal x Denglai zlnpesl lp ax Bt 0 MA IO Vessels DATABASE Countries Hydrography IGOSS 2 ys y i 1h n VessellD ER QF VesselName E Mess Interpretation Maturation StomFullness Stomachwt Wi d OR ele StationTypes SpeciesName wegen StType GearType GearDescription Appendix E lists all variables with the correct notation Parameters in bold indicate primary key variables and used together they form a unique key from the logbook to the other sheets except to the acoustic table The acoustic table can be linked to the logbook by the cruise identifier together with country vessel Cruise log year and month 10 1 3 Example of data export from Access As the PGNAPES participating nations have agreed on using the new database format it is recommended to use the PGNAPES database as a working tool while on a cruise Using the database actively putting all relevant cruise data into the base during the cruise will ensur
15. way beam angle should be calculated Gd dB 10log w dB o 5800 Were f and Bo are the values measured by the calibration program If the environmental conditions of two calibrations differ or differ from the measurement conditions a conversion of angle sensitivity beam width transducer gain and two way beam angle is needed Now the index e g Co means sound speed at calibration condition Beam width Appendix C Maturity classification for herring O undefined 1 virgin Immature testes are long very thin translucent and transparent ribbons lying along an unbranched blood vessel no sign of development round end 2 maturing M ribbons are already larger reddish colour smooth and transparent or development clearly started whitish creamy colour of the gonades gonads are more and more filling in the body cavity sperm milk still cannot be extruded using moderate pressure has 3 Spawning Running sperm milk is flowing out or is extruded using moderate pressure to the fish body 4 spent S gonads are shrunken drained transparent and reddish residues of sperma milk showing no development Dutch Code I M R S between brackets Male herring Netherlands amp Norway Scotland amp Denmark Germany undecided GE 1 immature a juvenile phase gonads thread like thin completely transperent and colourless sex difficult to determine 2 immature b somewha
16. with air bubbles under the ship and resultant loss of signal although this problem is somewhat alleviated by the use of a dropped keel mounted transducers Acoustic recording depth PGNAPES Is set to 750 meters No blue whiting or herring is expected to be at greater depths PGTIPS Is set to the bottom for North Sea surveys To be updated by PGTIPS members Day night operations It is recommended if time permits during the survey to study the diurnal behaviour of fish schools in order to determine at what time during the 24hr period the fish may not be available to the echosounder Listed below is the current survey operand e PGNAPES 24 hour operations e PGTIPS During North Sea West of Scotland and Irish herring surveys operations are conducted during the hours of daylight in the areas covered by the German Dutch Scottish and Irish vessels Surveys in the Danish and Norwegian areas are executed according to a 24 hours scheme 4 Acoustic sampling 4 1 Mounting acoustic equipment Transducer The standard transducer used in fisheries acoustics is the 38kHz ES38B from Kongsberg Simrad In order of preference it is advisable to mount the transducer in a dropped keel a towed body or on the hull of the vessel Steps should be taken to ensure that the flight of the towed body is stable and level this should ideally be achieved with the aid of a motion sensor Drop keel mounting Modern research and certain commercially chartered ves
17. 0 60 m the same procedure may be used Here NASC are normally assigned to schools of fish after filtering out plankton by putting the Threshold in the range of 48 to 51 dB In the layer below 60 m a Threshold of 54 to 60 dB may be applied In the deeper parts of the area gt 150m a lower Threshold than 60 dB may be applied At these depths often close to the bottom herring schools are normally larger and easier to recognize After scrutinizing the whole analysis area can be allocated to plankton and fish in order to define plankton after subtracting the individual regions fish Also this method will give you the opportunity to have all surveyed cells in your output files Multi frequency use The echosounder frequency routinely used for abundance estimation is 38 kHz However many vessels now operate multiple transducers with working frequencies of 18 120 and 200 kHz At present these data are used more for species recognition than for abundance estimation For instance herring and mackerel may have different target strengths at different frequencies Mackerel is backscatter more strongly visible at 200 kHz than at 38 kHz Fig 4 5 Stronger at 38 kHz 200 kHz Stronger at 200 kHz Figure 4 5 Echogram showing example of multi frequency pproach To process the data for extraction of schools the variable computation method available in Echo View is being used by many labs The method has been used in 2001
18. 2003 and was developed under the EU program SIMFAMI Previously when processing by hand 2000 and before a small background value for scattered fish was removed from integrator layers with many fish schools lt was noted that fish schools appear consistently on 38 120 and 200kHz echograms while other features such as plankton may be strong on some frequencies and weak on others Use of single target TS distribution data PGNAPES During blue whiting spawning stock surveys TS distribution is often useful in separating blue whiting from mesopelagics in the upper layers If blue whiting is present one usually expects to see a prominent peak somewhere around 35 dB Allocation to mixed layers or mixed schools Sometimes fish occur mixed with other species in aggregations of smaller schools In this case species allocation is based on the composition of trawl catches Those schools are separated from other fish using the standard scrutinising procedures see above and or the allocation of the proportion of the different target species on the basis of catch composition Important The weight based catch composition does not always resembles the acoustic image of the schools layers targeted See an example below Table 4 3 Catch composition in kilograms converted to catch composition in sA values The sA correction factors are taken from Simmonds and McLennan 2007 NA Catch composition sA correction fctor Catch composition a kg
19. CTD or TRAWL mandatory Geardescription Informative desription of gear Appendix F PGNAPES database extraction codes Copy and paste these selects into the SQL query webinterface Planktonstations Trawlstations CTDstations select I from logbook I stationtypes s where l sttype s sttype and s geartype PLANKTON select from logbook I stationtypes s where I sttype s sttype and s geartype TRAWL select I from logbook I stationtypes s where l sttype s sttype and s geartype CTD Herring SA sum pr acoustic log Herring Average SA per statistical square Select a country a vessel a cruise a log a y ear a month a day a Hour a min a a clat a aclon nvl sum b SA 0 HER SA sum pr Acoustic log from acoustic a acousticvalues b where a country b country and a vessel b vessel and a cruise b cruise and a log b log and a year b year and a month b month and a day b day and b species HER group by a country a vessel a cruise a log a y ear a month a day a Hour a min a a clat a aclon SELECT b Rect b lat b lon b Area_sqnmi Sum c logint a WHB SAsum pr Acoustic log Sum c logint SA weighted by nmlog Count c Logint CountOfLogint FROM select a country a vessel a cruise a log a year a month a day a Hour a min a aclat a acl on nvi sum b SA 0 WHB SAsum pr Acoustic log from acoustic a acousticvalues b where a country b country and a vessel b vessel and a cru
20. F is the estimated area density of species i The quantity is the number or weight of species i depending on whether o is the mean cross section per fish or unit weight ci K lt c gt is the integrator conversion factor which may be different for each species Furthermore c depends upon the size distribution of the insonified target and if this differs over the whole surveyed area the calculated conversion factors must take the regional variation into account K is determined from the physical calibration of the equipment which is described in section 1 above K does not depend upon the species or biological parameters Several calibrations may be performed during a survey The measured values of K or the settings of the EK500 may be different but they should be within 10 of one another Conversion factors for a single species The mean cross section lt o gt should be derived from a function which describes the length dependence of the target strength normally expressed in the form TS a b Log L 2 Where a and D are constants for the ith species the recommended target strength relationships for herring surveys in the Norwegian Sea and blue whiting surveys in the North east Atlantic area is given below Target Strength Equation Coefficients Species bi ai Herring 20 0 67 5 Blue whiting 21 8 72 8 Mackerel 20 84 9 Horse mackerel 20 71 2 Physoclist species 20 0 71 9 The equivalent formula for the cross section
21. ICES Planning Group on Northeast Atlantic Pelagic Ecosystem Surveys PGNAPES ICES Planning Group of Temperate International Pelagic Surveys PGTIPS MANUAL FOR HYDRO ACOUSTIC SURVEYING IN THE NORTHEAST ATLANTIC NI DRAFT ONLY till PGNAPES 2008 III Version 2 1 May 2008 International Council for the Exploration of the Sea Conseil International pour l Exploration de la Mer H C Andersens Boulevard 44 46 DK 1553 Copenhagen V Denmark Telephone 45 33 38 67 00 Telefax 45 33 93 42 15 www ices dk info ices dk Table of Contents 1 INTRODUCTION ege 5 2 SURVEY COORDINATO Nn ee 6 2 1 LEVEY ele e a RE 6 2 2 A o O O E nnair SARRATEA ARESE 6 2 3 Coordinating MESS E E A conaaseaecaacaaaseacacaea EEEE EE REEE Y 6 2 4 attente te Renate 6 2 5 EI EE 7 3 SURVEY DESIGN iii A E 7 3 1 IS EE 7 3 2 SUVS Y Tue E e E 8 A AGOUSTIG SAMPLING E 10 4 1 Mounting acoustic equipment EE 10 4 2 A 10 4 3 Inter ship comparison INterGallbralOn ET 13 4 4 Echosounder operation GE 14 4 3 1 Operation procedure for Simrad EK500 cccccsscceeceeseeeeeeeseeeeeeeeeeeceneeeeecceeeeeeeeeseeneeeeeesnaseeeeessennees 14 4 3 2 Operation procedure for Simrad EK ER6O oooocccononoccccncconoccconcnnnoccncncnnanoconcnnannnnnnnronannnnnnnrnnnnn rra ranannnnos 15 4 4 Interpretation of acoustic images SCIUTINY e 16 5 BIOLOGICAL SAM PLING E 24 5 1 Re Ve Le DEE 24 5 2 Biological sampling polio AAA In CULL eect ceeeeeceeentrs 24 5 2 1 Re e is oo
22. Simmonds 8McLennan 2007 LI SA Whiting 10 0 0 100 37 34 PGNAPES This procedure is normally not applied during the PGNAPES surveys but can be used if necessary 5 Biological sampling 5 1 Trawling Proper species allocation of the acoustic records is not possible if no trawl information is available The general rule is to make as many trawl hauls as possible especially if echo traces are visible on the echosounder after a blank period If surface schools are known to occur in the area it is often advisable to take occasional surface trawls even in the absence of any significant marks The principal objective is to obtain a sample from the school or the layer that appears as an echo trace on the sounder by means of directed trawling figure 5 1 The type of trawling gear used is not important as long as it is suitable to catch a representative sample of the target school or layer Gear details for survey vessels involved are given in Appendix A SSS E Figure 5 1 Schematic overview of how to shoot the gear when back trawling Information about the most important dimensions of the trawls used should be included in the survey report from each of the participating vessels During trawling it is important to take note of the traces on the echosounder and the netsonde in order to judge if the target school entered the net or if some other traces contaminate the sample It is recommended that notes be made on the appearance and behaviour
23. Splitting total acoustic densities to species specific densities is at the responsibility of reporting vessels Acoustic densities are nominally expressed at the spatial resolution of 5 nautical miles but in practice there has been a deal of variation around this norm In future surveys the standard spatial resolution is 1 nautical mile For conversion from acoustic density Sa m n mile to fish density p the relationship p sA lt o gt where lt o gt is the average acoustic backscattering cross section m The total estimated abundance by stratum is redistributed into length classes using the length distribution estimated from trawl samples Biomass estimates and age specific estimates are calculated for main areas using age length and length weight keys that are obtained by using estimated numbers in each length class within strata as the weighting variable of individual data BEAM does not distinguish between mature and immature individuals and calculations dealing with only mature fish are therefore carried out separately after the final BEAM run separately for each sub area Proportions of mature individuals at length and age are estimated with logistic regression by weighting individual observations with estimated numbers within length class and stratum variable popw in the standard output dataset vgear of BEAM The estimates of spawning stock biomass and numbers of mature individuals by age and length were obtained by
24. __ _ _ Faeroe Islands Vessel Vessel TI Iceland Vessel Vessel e Ireland Vessel Norway Russia Vessel Vessel Pranger LFungng II Spain Funding Expertise feo For all surveys mentioned above at least the following research methods are being applied e Hydro acoustic sampling e Trawl sampling e Plankton sampling e Hydrographic sampling For a more detailed description of the work carried out by the planning groups and to review current reports please refer PGTIPS former PGHERS http Awww ices dk iceswork wgdetailacfm asp wg PGHERS PGNAPES http www ices dk iceswork wgdetailacfm asp wg PGNAPES 2 Survey coordination 2 1 Survey planning The main forum for survey planning are the PGNAPES PGTIPS meetings the year before the survey Planning will usually start before the meeting and continue until the time of the survey By the time of the meeting participating countries must decide the resources that they can offer for a survey at the level of detail that allows the group to effectively plan the survey Details about the resources include e Vessel s e Vessel time effective survey days e Possible impossible dates and areas of operation e Possibilities for sharing expertise through exchange of personnel Based on the available resources for the survey allocation of survey effort in terms of areas and dates is decided during the PGNAPES and PGTIPS meetings 2 2 Survey coordinator Survey
25. are used in data analysis see the figure below These procedures are available within PGNPES as R codes If the 95 confidence limits do not include unity as in the example below this suggests that one ship is producing biased results and the reason for this discrepancy should be investigated D 5290802 ue Vessel A F 5663757 M ssel A Fai 1 al M i A vessel B Aa i Deeg Vessel H e MJ j Ly U f a j EE Mawtical mile Haag ai mile 4000 S000 Fridtjof Nansen 200 3000 U WER 2000 3000 4000 5000 5 b f D Figure 4 4 Results from an inter vessel comparison vessel A against vessel B The regression slope is 0 56 showing a significant difference between the vessels The upper panels show sequential data along the cruise track the lower panels are scatter plots comparing concurrent measurements on the two vessels The left panels show original values whereas the right panels show these same values on a log scale 4 4 Echosounder operation There are a number of settings that are made during calibration that have a direct influence on the fundamental operation for echo integration and target strength measurement and therefore affect logged data Once set according to the particular transducer these should NOT be changed during the survey It is recommended that each year the same settings be used for the survey in order to facilitate comparison across years 4 3 1 O
26. ate pressure to the fish bod 4 spent gonads are shrunken drained not translucent reddish lightly ribbed residues of eggs showing no development Female herring Norway O undecided checked 1 immature a thread like thin completely transperent and colourless Sex difficult to determine 2 immature b somewhat larger in volume sex easier determined still transparent with hint of colour 3 maturing a opaque but developed in volume distinct veins ovaries with yellow white eggs in lamellae can occupy half body cavity or more 4 maturing b gonads larger in volume distinct veins ovaries yellowish or white can occupy 2 3 or more of the body cavity depending on fish condition Eggs distinct feel like grain becoming transparent in the front part of the gonad 5 maturing c ovaries fill the entire body cavity most eggs transparent 6 spawning running gonads when light pressure is applied 7 spent gonads loose remaining eggs some 8 resting gonads small eggs not visible difficult to distinguish from stage 2 3 1 Virgin herring gonads very small threadlike 2 3 mm broad ovaries wine red 2 Virgin herring with small gonads the height of ovaries is about 3 8 mm eggs not visible to the naked eye but can be seen with a magnifying glass ovaries bright red colour 3 maturing gonads occupy about half of the ventral cavity breadth of the sexual organs is b
27. by Whitihead et al 1986 If in doubt also http www fishbase org FishBase 2008 was consulted Most if not all of the identification are therefore correct However due to the catch methods some of the species were not in a state that they could be identified immediately and discriminating features had to be taken from various individuals of a group of specimens of which we were confident to represent one species It is thus possible that inconsistencies might occur The user of the guide is encouraged not to view it as a final version but as a product in development and help to expand and improve the list of know species of the investigation area The following references have been used 1 Froese R and D Pauly Editors 2008 FishBase http www fishbase org version 01 2008 World Wide Web electronic publication 2 Muus B J and J G Nielsen 1999 Sea fish Scandinavian Fishing Year Book Hedehusene Denmark 340 p 3 Whitehead P J P M L Bauchot J C Hureau J Nielsen and E Tortonese eds 1986 Fishes of the North eastern Atlantic and the Mediterranean UNESCO Paris Vols LI 1473 p FNAM During each cruise it is recommended to compile a list of species which are regularly caught containing o scientific names o point specific features which discriminate them of other related species o photographs Also make sure to include instruction to identify all species to the exact species name and if this is not possible sam
28. e HYDR 3 OO HCSBC W 200 For OWw2252 Be 0332 Ls 03320002 m PLET 400 HUP2B 2003 P Fo OW2252 wae 0332 03320003 W PLKT rro om2252 Be D332 03320003 m rHYDR 300 HCSBC 2003 y ala D Advanced Cancel lt Back Cancel Finish C The fileformat is ordinary ASCIFformat The datavalues within the fileare arranged as Comma Separated Values csv as shown in the example below Country Vessel Cruise Station StType Year log Month Day Hour Min Lat Lon BottDepth WinDi r WinSpeed FO OW2252 0332 03320001 HYDR 300 HCSBC 2003 5 3 1 11 61 83 7 00 77 45 15 FO OW2252 0332 03320001 PLKT 400 HWP2B 2003 5 3 1 45 61 83 7 00 77 45 15 FO OW2252 0332 03320002 HYDR 300 HCSBC 2003 5 3 3 20 61 66 7 30 130 45 15 10 1 4 Internet access to PGNAPES database Data are stored in an Oracle 10g Express edition database freeware The database server is based in the Faroese Fisheries Lab FFL Torshavn Faroe Islands By executing SQL queries through the Application Express web interface the user can extract data in any form URL http oracle frs fo apex Usernames and passwords are individual pr nation User access is limited to select data from the database Insert update and delete operations can only be performed by the schema owner pgnapes_owner Log in on first page ORACLE Database Express Edition F ORACLE Database Ex
29. e data integrity and that exports of data will come out right To make exports from the base will ensure that data exported are ready to import into the other participants databases Exporting plankton hydrography biology or catch data always implies the export of the logbook table as it is the parent table of these underlying tables Exporting acoustic values always implies the export of the Acoustic tables as the acoustic table is a parent table of the acousticvalues table Is important to have the structure of the database in mind when exporting and supplying other participants with exported data Exporting data from access 1 Mark the table you want to export Figure A 2 Go to File export Figure B 3 Save as TEXT format supply file name 4 Save as delimited 5 Make sure it is comma delimited Figure C and include Fields Names on first row is tagged Figure D 6 Press finish DH Microsoft Access PGNAPES_ official Databas El Microsoft Access PGNAPES_ official Database Le File Edit Yiew Insert Tools Window Help ee File Edit View Insert Tools Window Help vi w DG Open Ctrl 0 Get External Data Leg open BE Design New x Be We EE SS Close Create table in Design view Del ein sas E Save As 7 Create table by entering data i Queries Acoustic 1PGNAPES_official Forms ECTS 2 3 Work docs Database worksheets PGNAPES_official Beete Biology 3 J Work
30. e survey o Scrutiny o Fish taxonomist o Oceanographer technical interpretation o Acoustic technician calibration operation o IT technician Unix windows Ingres network Trajectories to be survey Stations to be sampled CTD Plankton Additional sampling requirements Coordination between vessels Deadlines for partial data results and reports 3 Survey design 3 1 Survey area PGNAPES IBSSS In 2004 2005 PGNAPES produced a plan for achieving the optimum coverage that could be achieved for the spawning area blue whiting surveys This plan was followed in the surveys in spring 2005 and 2006 Based on experiences gained the overall timing of the survey from mid March to mid April appears appropriate although a further review of coordinated survey timing is undertaken each year The spatial confines of the survey although not fixed are defined as core spawning areas and secondary target areas as suggested in 2005 Figure 3 1 Every year the target areas will be allocated to ships but the highest priority will always be target area 1 this area has usually hosted about half of blue whiting biomass in the survey area The survey must follow the standardised survey protocol given in this report Barent Sea Il Central Norwegian Sea Ill Icelandic Zone 12 8 EN o q l South Porcupine Il North Porcupine Ill Hebrides IV Southern Faroese V Rockall and Hatton Banks Figure 3 1 Survey sub areas used in
31. e to selection and 1 catch Gear is damaged Some fish may have escaped the codend 2 Trawl has long gashes or large pieces of net are missing codend intact Codend torn very little catch Codend torned very little catch Gear completely destroyed or lost Indicates to what degree the catch represents the quantity of fish in the area judged according to the manner in which the gear was used and the behaviour of the gear The trawl has been set at a predetermined position the trawl sensors have shown that the registrated schools have been hit The trawl has been set at a predetermined position trawl sensors show problems with the gear e g faulty door distance or other indications of malfunction The trawl has been aimed at an acoustic registration trawl sensors show problems with 3 the traw it has not been fishing properly due to technical problems or the catch is not representative due to large quantities of corals jellyfish or mud In general the complete catch should be worked up with respect to species composition If the catch contains specimens which differ significantly from the main catch e g by size or low abundance these may be set aside from the total catch before handling the remaining catch Decisions regarding the further handling of the catch depend on whether it is possible to get a representative sample without sorting the total catch The final sample amount of each species taken out is either the total a
32. eel 1 round supporting rack bucket and 3 loops for lead weights H 3 Nylon lines for the weight with bridle and snap hook Lead weight of 25 kg The WP 2 plankton net can be equipped with a digital flow meter Optional to determine the amount of water passing through the plankton net After each haul the contents of the net are gently washed with seawater into the net bucket which is subsequently emptied and rinsed into a sieve with a suitable mesh width of 180 200 um depending on the mesh in the plankton sampler 6 2 Processing plankton samples At each station two plankton samples are taken The first sample size fractioned into 2000 1000 and 180 um fractions which are oven dried at 70 C and subsequently weighed The weighing must be done in a laboratory on land but samples must be dried onboard and frozen for storage and transportation Before weighing samples must be dried again for at least 6 hours The second sample is fixed in 4 Comment L4 The old formaldehyde seawater solution buffered with sodium tetraborate to a pH of approximately 8 for later E ee ee analyses species determination E working group agrees on a standard buffering agent that is used by each participant 7 Hydrographical sampling 7 1 CTD operation PGNAPES At the Norwegian Sea survey a CTD profile should be taken every 60 nm at each plankton station Temperature and salinity should be monitored from the surface layer and from t
33. emperature and salinity on split beam target strength measurement Working Document presented to the FAST WG St Johns Canada 1999 Available from the author at helge bodholt simrad no Bowers A B and Holliday F G T 1961 Histological changes in the gonad associated with the reproductive cycle of the herring Clupea harengus L Marine Research Series 5 HMSO Edinburgh esch Degel H and Jansen T 2006 FishFrame 4 3 Exchange Format Description www FishFrame org 22 December 2006 Fernandes P G and E J Simmonds 1996 Practical approaches to account for receiver delay and the TVG start time in the calibration of the Simrad EK500 ICES CM 1996 B 17 8p Foote K G H P Knudsen G Vestnes DN MacLennan and E J Simmonds 1987 Calibration of acoustic instruments for fish density estimation a practical guide ICES Coop Res Rep 144 57pp Jansen T Degel H 2007 and the users of FishFrame FishFrame 4 3 User Manual www FishFrame org 28 January 2007 MacLennan D N and E J Simmonds 2005 Fisheries Acoustics 2 edition Blackwell Science Ltd 2005 Oxford 437pp MacLennan DN and E J Simmonds 1992 Fisheries Acoustics Chapman and Hall London and New York 325pp Nakken O and A Dommasnes 1975 The application of an echo integration system in investigations of the stock strength of the Barent Sea capelin 1971 1974 ICES CM 1975 B 25 20pp Reid D G and E J Simmonds 1993 Image analysis techni
34. epending on the ration in the nearest trawl hauls The rest up to 100 is then given to plankton During blue whiting spawning stock surveys plankton can filtered out using 82 dB as the reference Threshold level below which all increase in backscattering is assumed to come from targets of no interest When increasing the Threshold one expects plankton and mesopelagics to disappear usually around 69 66 63 dB unless these are very dense As a rough rule of thumb if one has a registration that contains blue whiting and that does not coincide with dense plankton mesopelagics registrations proportion of NASC that remains when the Threshold is increased to 66 dB can allocated to blue whiting However further adjustment may be applied if there is evidence that registrations contain further non blue whiting echoes especially in deeper layers where echoes may get cluttered If small individuals of blue whiting are present a lower Threshold may be appropriate Thresholding using the BI60 post processing system PGTIPS In stratified waters mainly in the northern and northeastern part of the survey area there is often a layer of plankton in the upper 50 m In this layer very small dense schools of herring may be found Normally all the plankton is filtered out at 42 dB The remaining NASC may be assigned to herring if clear schools are still visible and of course trawl information indicates that herring are present In the range of 3
35. epth then same as upper Plankton mg dry weigth m in each interval Size graded values 2000 my sieve 1000 my sieve 180 my sieve From 2000 my sieve Catch Post code 2 chars according to countries table Call sign 2 or 6 digits acc to Vessels table Cruise identifier National station numbers Station o StType Geartype activity National definition of station type YYYY 4 digits Species Species code HER BLU Minutes m Knots m Biology Post code 2 chars according to countries table Call sign 2 or 6 digits acc to Vessels table Cruise identifier National station numbers Geartype activity National definition of station type YYYY 4 digits Species code HER BLU Cm with one decimal dot as decimal sign G Year from scale readings Year from otolith Empty means not sexed 1 Female 2 Male 0 not possible to determine sex Maturation scale Herring 1 8 Blue whiting 1 7 Stomach fullness visual scale 1 5 ICES Weight of stomach with content g Recnr Serial number identifying the fish Support tables Countries CountrylD Postal code FO DE NL NO IS RU SE IE DK Values in Countries table Vessels VessellD Callsign Vesselname Vesselname Values in Vesseltable IGOSS poa Quality Flag Interpretation Interpretation Species SpeciesID 3 character code Gear STtype Geartype activity National definition of station type GearType PLANKTON
36. ery specific mainly to the echosounder band pass filters and to a lesser extent to the transducer bandwidth the standard target and the pulse duration which may affect the peak value Target bandwidth and pulse duration specific values for the Simrad EK400 are given in Foote et al 1987 their Table 1 Values for the EK500 can be measured Bethke 2007 provided a result for the narrow bandwidth For the wide bandwidth 3 8 kHz Simrad recommends using 3 sample distances 10 cm This equates to a value At 1 07 ms for narrow bandwidth Ar 0 8 m At 0 39 ms for wide bandwidth Ar 0 3 m The range to half peak amplitude rm This is the measured range between the start of the transmit pulse and the point on the leading edge of the echo at which the amplitude has risen to half the peak value m This is usually determined from experience with the readings from an oscilloscope display For example for a 38 1 mm tungsten carbide standard target insonified at 38 kHz at a colour Threshold setting of 70 dB Sy colour min it is measured as from the top of the transmit pulse to the leading edge of the pink colour on the target sphere echo However range to sphere Fspn may then be calculated to verify the measured results Fon fp Af _ CA 2 Note that in the firmware version 5 2 and 5 3 a correction of 3 samples is already included A simple check can be carried out Two calibrations at the same environmental conditions but a
37. etween 1 and 2 cm eggs are small but can be distinguished with the naked eye the ovaries are organs 4 maturing gonads are almost as long as the body cavity eggs larger than in 3 varying in size and opaque ovaries orange or pale yellow in colour 5 maturing gonads fill the body cavity eggs are large and round some are transparent ovaries are yellowish eggs do not flow 6 Spawning ripe gonads eggs flow freely eggs transparent 7 spent gonads baggy and bloodshot ovaries are empty or only contain a few residual eggs body cavity may contain bloody fluid At this stage there can be difficulty in deciding sex if the gonads are spread out it is easier to view the leading edge sharp for male and rounded for female 8 recovering ovaries are firm and larger than virgin herring in Stage 2 Eggs are not visible to the naked eye The walls of the gonads are striated vertically and blood vessels are prominent Gonads are wine red in colour This stage passes into Stage 3 1 small close column Wine in colour torpedo shaped ovaries about 2 3 cm long and 0 66 mm thick 2 Maturing Virgins Slightly larger than stage 1 still transparent individuals organs vertebral Virgin sexual under 3 Sexual Organs become more swollen occupying about half of the ventral cavity 4 Ovaries become more swollen filling two thirds of ventral cavity eggs not transparent 5 Sexual Organs filling o
38. f the gonads are spread out it is easier to view the leading edge sharp for male and rounded for female 8 recovering testes are firm and larger than virgin herring in Stage 2 The walls of the gonads are striated laterally and blood vessels are prominent Gonads are wine red_ in colour This stage passes into Stage 3 1 A individuals small sexual organs close under vertebral column whitish or greyish brown in colour knife shaped testes 2 3 cm long and 0 66 mm thick 2 Maturing Virgins Slightly larger than stage 1 still transparent colouration 3 Sexual Organs become more swollen occupying about half of the ventral cavity 4 Gonads become more swollen filling two thirds of ventral cavity milt whitish 5 Sexual Organs filling ventral cavity milt is white in colour but not yet running 6 milt running Spawning 7 Spents testes slack baggy and bloodshot 8 Recovering spents Blood vessels showing Netherlands amp German O undefined 1 virgin ovaries are thin whitish translucent and long ribbons no sign of development pointed end 2 maturing ribbons are already larger reddish colour lightly ribbed and milky or development has clearly started eggs are becoming larger ovaries are more and more filling in the body cavity eggs still cannot be extruded using moderate pressure 3 Spawning eggs are freely extruding or developed eggs are extruding using moder
39. g acousticval from acousticvalues group by country year cruise f select country year cruise count station pl from plankton group by country year cruise g where a country b country and a year b year and a cruise b cruise and a country c country and a year c year and a cruise c cruise and a country d country and a year d year and a cruise d cruise and a country e country and a year e year and a cruise e cruise and a country f country and a year f year and a cruise f cruise and a country g country and a year g year and a cruise g crulse order by a country a year a cruise
40. g mm Pt E E q A MA 24 0 E SA a IT AAA Y E IE EEE Lech ESTE CE 00 E E E po E DEED Drang 8 E E E ne AA 25 00 A Country Vessel Power Code Name Type Panels Head Groundr Sweeps Length Circum Mesh sizes in all Codend Height Spread panels wings kW B P 2 4 m m m m m mm mm mm mm mm mm mm m m DEN DAN2 3420 Foto P 60 4 66 4 121 397 3200 1600 800 400 200 100 16 GFR Wan 2900 PS205 PSN205 P 4 504 554 995 843 205 0 400 200160 80 50 10 15 28 NED TRI2 2940 2000 M P 4 64 0 72 0 100 0 140 0 400 Pel Trawl SCO SCO2 3000 PT160 Pel P 4 38 0 38 0 70 115 87 0 256 0 800 600 400 200 100 38 38 12 32 Sampl Trawl IRE CEX 3000 PMT Pel P 4 58 0 58 0 55 0 40 0 330 0 3200 1600 400 200 100 50 20 15 45 midwater trawl Appendix B Angle sensitivity The angle sensitivity beamwidth transducer gain and the two way beam angle are according to changes of sound speed see Bodholt 2002 for equations A key parameter is the angle sensitivity This parameter is used to convert the measured electrical phase shift into the calculated and displayed angles of a target which are used for TS compensation SIMRAD Amplitude versus Phase A KONGSBERG Company 12 135 90 45 0 45 90 135 Data sheets giving measurements of Amplitude versus Phase for individual transducers can be obtained from Simrad on request From Figure 1 we can measure an electrical phase shift of 155 5 between the 3dB points If the corresponding beamwidth of tha
41. h rounding down towards the nearest length interval 5 2 3 Aging Collection and reading of otoliths and scales Collection Scales in herring Figure 5 2 Picture with zone indication on herring where scales should be taken A blotting paper within numbered squares is soaked in water and placed on a tray where the scales are temporarily deposited A sufficient number of scales should be taken from each herring to obtain about 4 5 good specimens for age reading Before the scales are taken submerge the herring in sea water and carefully stroke the body from front backwards to remove any loose scales that may have come from other fish After length weight sex and maturity of those fish had been determined the scales are mounted on microscope slides Each slide will contain the scales of 2 individual fish The slides must be numbered with permanent ink beforehand The first and last slide should also contain information on cruise number station and date The scales are cleaned with water from any adhering tissue and dirt placed on a microscope slide that had been prepared with a layer of gelatine use tweezers The scale is slightly curved and must be placed on the slide with the convex side upwards If the scales cannot be prepared on slides immediately after sampling they must be frozen immediately to prevent them from drying Otoliths If possible 2 otoliths should be taken of each individual If age determination of herring is done b
42. h require knowledge of the speed of sound in water It is therefore recommended that appropriate apparatus be used to determine the temperature and salinity of the water so that sound speed can be calculated see MacLennan amp Simmonds 1992 for equations and entered into the EK500 or the EK ER60 A number of calibration parameters and results tabulated in the table below should be included as a minimum in the final survey report Some of these parameters not included in the Simrad operators manual and are defined below and will be specific to certain operating systems only 4 2 1 Calibration procedure for Simrad EK ER60 echosounder The calibrating procedure for the Simrad EK and ER60 are clearly laid out in the users manual and should be followed as such The determination of sound speed for the ER60 is calculated automatically in the environment dialogue box when the parameters of temperature and salinity are inputted from CTD casts During the actual calibration itself Simrad recommend no less than 150 data points from the standard target sphere per frequency Outlying points above or below the target reference TS value can be removed as required to further refine the accuracy of the result before final acceptance of the data set Updating the beam pattern is the final stage of the calibration procedure and will result in an alteration of the beam pattern parameters The Simrad ER60 allows the beam pattern to be adjusted by loading the results
43. he near bottom or deepest layer regularly for calibration of the CTD sonde It is important to select relatively homogenous layers to take the samples in to obtain good calibration accuracy All countries agreed on performing hydrographic CTD downcasts down to a maximum depth of 1000m Seacable ji AN connection Auxiliary sensor connector Main housing ir release valve 37 4 n 1 SEE Zei temperature sensor SHE 40 conductivity sensor TS duet TC puma A Fritten contagi connectors k 33cm 13 in Coge dopih nal shown 305 one 12 in Figure 7 1 A SBE 9plus Underwater Unit with sensors for C T and P and a submersible pump optional auxiliary sensors left panel and and SBE 11plus V2 Deck Unit right panel During the blue whiting survey at the spawning grounds CTD profiles should be taken at least every 60 nm Temperature and conductivity salinity shall be monitored from the surface to a maximum depth of 1000 m Water samples for calibration of the CTD probe shall be taken regularly Measured variables e Temperature Depth pressure Conductivity Oxygen Fluorescence Comment L5 Hydrographers Please specify what regularly means 8 Data analysis 8 1 PGTIPS approach Theory This section describes the calculation of numbers and biomass by species from the echo integrator data and trawl data Most of this section is taken from Simmonds et al 1992 The symbols used in this sect
44. ies analysis e g during coastal surveys if it proves impossible to accurately determine mixed species aggregations to species level then mixed codes should only be submitted to the group through prior agreement Methods of species allocation are often highly specific to the survey being undertaken The method used depends largely upon the schooling behaviour of the target species and the mixing with other species For example In the North Sea and Division Vla the species allocation is based mainly on the identification of individual schools on the echogram In the Skagerrak Kattegat and Baltic the identification is based on composition of trawl catches A few typical target species echograms are shown below It is obvious that during the scrutinising process subjective decisions have to be made However joint sessions of scientists from participating countries who scrutinised each others data has shown that the deviation between the estimated quantities of herring are within the range of 10 provided that trawl information of the recordings is available Reid et al 1998 The scrutinizing is based on combination of visual clues in the echograms information from single echoes disappearance of echoes when changing lower integration Threshold trawl catches and possibly comparing echoes from different frequencies This is an expert process prone to errors and subject to a large degree of subjectivity Often it is useful to look observations
45. ion are defined in the text but for completeness they are listed together below Estimated area density of species i Equioment physical calibration factor Mean acoustic cross section of species Ei Em Ci TS TSn TSw Dn Dw D L W L fi Wi Ax E Partitioned echo integral for species i En Echo integral of a species mixture Lc Echo integrator conversion factor for species i TS Target strength TS Target strength of one fish TSw Target strength of unit weight of fish abi Constants in the target strength to fish length formula Constants in formula relating TS to fish length Constants in formula relating TS to fish length Constants in the fish weight length formula FL Fish length Total length in Ye cm W Weightin grams IL Fish length at midpoint of size class j f Relative length frequency for size class j of species i wi Proportion of species i in trawl catches A Area of the elementary statistical sampling rectangle k Total biomass Qi Total biomass for species i The objective is to estimate the density of targets from the observed echo integrals This may be done using the following equation from Foote et al 1987 po Ja 1 os 1 The subscript i refer to one species or category or target K is a calibration factor oz is the mean acoustic cross section of species i E is the mean echo integral aalocated to the species in the judging prpcess and
46. ions from pre agreed target areas should only be undertaken after consultation with the assigned survey coordinator Orientation This is specific to the type of survey being undertaken Two aspects should be considered in choosing the direction of transects Transects should preferably run perpendicular to the greatest gradients in fish density which are often related to gradients in bottom topography and hydrography This means that transects will normally run perpendicular to the coast The second aspect considers the direction in which the fish are migrating If there is evidence of rapid displacement of the fish throughout the area it is advisable to run transects parallel to the direction of migration This survey design will minimise the bias caused by double counting PGNAPES note For IBSSS The survey direction is historically from south to north which is NOT in opposition to the known migration patterns Since inter vessel time gaps can be as much as several weeks either survey direction would lead to a bias in the stock distribution and stock estimate and therefore it was decided to continue the historical approach However a strong effort has been made in 2007 to compress the overall survey time window to avoid double counting PGTIPS note For HERAS The northern North Sea is survey in a south north direction while the centre and southern North Sea are surveyed in a north south direction A detailed simulation study of the effects of m
47. is o Arr pllarcnpee ll 3 The mean cross section is calculated as the o average over the size distribution of the insonified fish Thus Lj is the mid point of the j th size class and fj is the corresponding frequency as deduced from the fishing samples by the method described earlier The echo integrator conversion factor is c K lt oi gt The calculation may be repeated for any species with a target strength function lt 0 gt 47m poa a J Note that it is the cross section that is averaged not the target strength The arithmetic average of the target strengths gives a geometric mean which is incorrect The term mean target strength may be encountered in the literature but this is normally the target strength equivalent to lt o gt calculated as 10logio lt oi gt 42 Some authors refer to TS as 10 log ops the definition of o is different from ops and should not be confused Conversion factors for mixed species layers or categories Sometimes several species are found in mixed concentrations such that the marks on the echogram due to each species cannot be distinguished From inspection of the echogram the echo integrals can be partitioned to provide data for the mixture as one category but not for the individual species However further partitioning to species level is possible by reference to the composition of the trawl catches Nakken and Dommasnes 1975 Suppose En is the echo integral of the mixture and wi i
48. ise b cruise and a log b log and a year b year and a month b month and a day b day and b species HER group by a country a vessel a cruise a log a year a month a day a Hour a min a aclat a acl on a ICESsquares b Acoustic c WHERE a country c country and a vessel c vessel and a cruise c cruise and a log c log and a year c year and a month c month and a day c day and c AcLat Between b lat_min And b lat_max AND c AcLon Between b lon_min And b lon_max GROUP BY b Rect b lat b lon b Area_sqnmi order by b rect Blue whiting SA sum pr acoustic log Blue whiting Avg SA pr statistical square select SELECT b Rect b lat b lon b Area_sqnmi Round Sum c logint a WHB a country a vessel a cruise a log a year a mo nth a day a Hour a min a aclat a aclon nvl su m b SA 0 WHB SAsum pr Acoustic log from acoustic a acousticvalues b where a country b country and a vessel b vessel and a cruise b cruise and a log b log and a year b year and a month b month and a day b day and b species WHB group by a country a vessel a cruise a log a year a mo nth a day a Hour a min a aclat a aclon SAsum pr Acoustic log Sum c logint 2 SA weighted by nmlog Count c Logint CountOfLogint FROM select a country a vessel a cruise a log a year a month a day a Hour a min a aclat a aclon nvl sum b SA 0 WHB SAsum pr Acoustic log from acoustic a acoustic
49. length from centimetres to metres For blue whiting and herring the simplified equations resulting from the canonical TS coefficients are une whitine gt 6 59 107 LIT and lt Onering gt 8 11 107 L However for blue whiting a slightly different equation is actually used lt Optue whiting gt 6 72 107 LIT The origin of this discrepancy implying a 72 72 dB is shrouded in mystery All we can say is that using about 2 too high coefficient results in underestimation of blue whiting numbers by that amount relative to the correct coefficient Fish density p in numbers per square nautical mile is now obtained as P Sa lt o gt 3 Estimated numbers are converted to biomass estimate by multiplying them with mean individual weight Age and length distributions are obtained by spreading total numbers to age and length classes using corresponding probability density distributions derived from trawl samples Implementation Here we describe the practical implementation of the above calculations also including how spatial dimension of the data is accounted for In national surveys details may differ and corresponding cruise reports should be consulted for more information The acoustic data as well as the data from trawl hauls are analysed with a SAS based routine called BEAM Totland and God 2001 to make estimates of total biomass and numbers of individuals by age and length in the whole survey area and within diffe
50. lities which might occur for instance if one vessel suffered more fish avoidance due to having a worse noise signature and thus consistently indicated a lower abundance for the same fish ensemble If the comparison nevertheless reveals a large difference the equipment on both ships should be recalibrated as soon as possible in accordance with the procedures described in section 4 2 The inter ship comparison works best when e It is done in an area where there are substantial quantities of fish in layers or dispersed aggregations of varying density e Moving in formation figure 4 3 keeping around a 400m offset astern not being in each others wake not detecting the other vessels echosounder taking the lead in turns in case one ship is more sensitive to weather or avoidance behaviour than the other e Covering a time window of 2 6 hours depending on the spatial distribution and density of fish in that area e Keeping constant radio contact to ensure satisfactory cooperation Figure 4 3 Typical inter vessel comparison track lines where both vessels take the lead position in turns Integration periods need to be synchronized so that they relate to the same portion s of the cruise track Thus the following ship must record the echo integrals over time periods which are delayed relative to those of the leader Keeping track of the log counter of the default way to do this Treatment of results Standard Ricker regression techniques
51. mesh in panel 6 E E O E EE E om 3 3 4 0 A AAA 5 7 P8340 a AA Ar Frideriksson PT TANTA Cou eeng Norway TI Faeroer Netherlands Scotland callsign Y TENA LMEL Qw2252 PBVO DBFI MED OOOO pos ecc ETA TEE e bridge EE IE ME 47 55906440 a BEE EA AAA A AA 31 20 7178827 e DEE general IA IES EE 47 55906443 A AA AAA AAA EE INMARSATAphone IT eono TT amgang 871761651777 871323497310 INMARSATA a gt neona 871 324403315 871 600273653 871323497311 a E E qq A AAA gt gt gt CI E E E E O O E e Internet connection ge __ ______ _ maiaday continuous light mail tday continuous Ebbe hh A ASAS e Power kW feat E Equipment facoustic Echo sounder type SmradEK500 Simrad EK6O_ Simrad EK 500_ TI Smaaeko TT BEE OOOO Primarytransducer ESRB Gap TI mp ES BB po Other Frequencies KHz f 18 120 18 70 120 200 PT 2 E E A itl Se SC EE puppet integration limit ip or po integration threshold dB f ooo d ooo o o ME l using sonar systematically no ft td pain sample depth m tooo too 750 100 PE fp Blue whitingsurvey Fishing gear__ Ciroumference m JP TI om TL ae O NE Atlantic ecosystem survey ae A A eee ese f rrr ry Si A A E ees AA Ss North Sea herring survey Fishing gear type S l i G O ooa _______ NN E EE E A a D A S AAA oOo fe MS ep A OOO A Circumference mm PO po Vertical openin
52. mount or a representative subsample of that species in the catch Since net sorting by size is known to occur it is advisable that subsamples are drawn from different parts of the catch The word sample should be understood as the number of specimens of a species extracted from a catch for closer examination e g Individual sampling or biological sampling is a detailed study of each specimen where various biological parameters are measured length weight sex maturity and age The number of fish in the catch is found by dividing the total weight of this group by the mean weight The mean weight is found by taking the weight of the sample divided by the number in the sample Catch_number Catch_weight x sample_number sample_weight For herring and blue whiting a representative number of individuals 100 fish per species if possible Comment L2 During surveys should be examined for only 50 specimens are taken per Length measured in L cm intervals species and haul onboard some Weigth measured in grammes vessels Sex Maturity maturity key is given in section 5 5 Age in winter rings herring using scale and blue whiting using otoliths VVVVV 5 2 2 Length measurements Representative length measurements of between 150 250 individuals should be taken e Herring and sprat are measured to the 0 5 cm below e All other species to the whole cm below The length measured should be the total length of the fis
53. multiplying the numbers of individuals in each age and length class by estimated proportions of mature individuals Spawning stock biomass is then obtained by multiplication of numbers at length by mean weight at length this is valid assuming that immature and mature individuals have the same length weight relationship 9 Cruise reports North Sea herring survey e cruise reports should be produced following a standardised format e cruise reports appear as appendix in the international report Blue whiting survey e Cruise reports aren t used internationally e Cruise reports are not included in the international report The following can be included in the cruise report gt Itinerary of the survey gt Map showing o Cruise track o Trawling station location o CTD station location o Plankton station location if collected gt Materials and methods o Acoustic data A calibration report for all survey calibrations should be included in the final cruise report o Hydrographical and zooplankton data o Biological data gt Results o Distribution and density of the acoustic data o Size and age distribution of the catches o Age and size stratified stock estimate s o Hydrographic conditions and zooplankton biomass gt Discussion o Acoustics o Scrutiny of the acoustic data o Trawling o Other relevant issues leg weather 9 Data Handling Each individual country is responsible for working up its own survey data before entering
54. nnnnnnnana nan 52 1 Introduction This manual was developed through the ICES Planning Groups on Northeast Atlantic Pelagic Ecosystem Surveys PGNAPES and the Planning Group of Herring surveys PGTIPS as a guide to the methodologies that should be adhered to during the planning execution and analysis phases of ICES coordinated survey programs The results of the surveys discussed in this document are provided in area and time based management units in an attempt to move towards an ecosystem approach in the group The surveys described here are the following PGNAPES surveys The first survey within this group is termed the International blue whiting spawning stock survey for the time being and only in this document further referred to as IBSSS and aimed at assessing the spawning stock biomass of blue whiting during the spawning season in March April as well as to determine the spatial distribution at this time of year This estimate is used as a tuning index by ICES to determine the size of the population The spawning areas of blue whiting west of the British Isles have most actively been surveyed by Norway and Russia Some coordination of these survey activities took place over a number of years until the Russian spawning stock survey was discontinued in 1996 Russia resumed the blue whiting spawning stock survey in 2001 There was however no further coordination between Norwegian and Russian surveys In the Norwegian Sea and Barent
55. o E 25 5 2 2 lalo Me mMer COL Ea p aa ELA ELEA rere 26 5 2 3 Aging Collection and reading of otoliths and SCales ooooococccnnnocccocncononocccconanancnnnnnnancnnncnnnncnncnnnnnnnnos 26 5 2 4 OM LAN 27 5 3 D epsea SS OCN e o o y Eaa a 28 6 PLANKTON SAMPLING searen aran cd 28 6 1 edel Te Blo fol gl ito E 28 6 2 Processing plankton samples APP o A veces veeeseueccunnnecteedeceeenccredes 29 7 HY DROGRAPHICAL SAMPLING Ainiai cai ri 30 7 1 GTB Ope abl OM APA OO oo A 30 8 DATA ANALYSIS telecasts tect aaa S aa EAA a a a a a ia anaE 31 8 1 Pil ellen DE EN 8 2 PGNAPES EE 33 CRUISE REPORTS ee EEN 35 DATA HANDLING ocorren eannan aona acne 35 10 1 PGNAPES Webibased Be Ee 35 10 1 1 Overview and exchange e E 35 10 1 2 PGNAPES database table description EE 36 10 1 3 Example of data ANDOAIN ON 36 10 1 4 Internet access to PGNAPES daiabase Ann 38 10 2 PGTIPS Fishframe webbased database NENNEN 39 11 PEN Ee 39 APPENDIX A VESSELDETA Eeer Ree 41 APPENDIX B ANGLE SENSITIVITY ee AER vuestantedtsewcucssxevesskveus 44 APPENDIX C MATURITY CLASSIFICATION FOR HERRING cccccessseeeesseeeseesseeeeeneeenseeeseeoanes 45 APPENDIX D MESH SIZE MEASUREMENTS cccccccsesseecesseeeeenseeseesseeeeessesseasseesenseeseeseeseeeneees 48 APPENDIX E PGNAPES DATABASE FORMAT s cssssssccsnsseccnnssecennsssesnessscennsseennssseenssesennessoes 49 APPENDIX F PGNAPES DATABASE EXTRACTION CODES cnmococcocnncncccccnnnnenennnn
56. otion on the survey design of North Sea herring is available in Rivoirard et al 2000 Design PGNAPES Due to the extent of geographical coverage carried out during the IBSSS a parallel transect design has been adopted during this survey Based on a review carried out by Rivoirard et al 2000 as referred to by Simmonds and MacLennan 2005 in instances where transect length is twice that of transect spacing a parallel design should be used as the best means of reducing variance Spacing e PGNAPES Transect spacing as agreed during the PGNAPES survey planning phase should be no less than 30nmi or no greater than 40nmi where possible to maintain the integrity of the international time series e PGTIPS Transects are spaced at a maximum distance of 30 nautical miles and a maximum distance of 7 5nautical miles Survey progression in time It should be carried out as determined during the survey planning phase PGNAPES PGTIPS and adhered to wherever possible Live communication with the survey coordinator is essential Contact details for survey vessels involved are given in Appendix A Ship s speed During the survey speed should be maintained at 10 12 knots where possible At higher speeds problems are encountered with engine noise or propeller cavitation These problems however depend on the vessel and the positioning of acoustic transducers In rough weather the ship s speed may be reduced as required in order to avoid problems
57. over some tens of miles at time as some continuity that facilitates scrutinizing can usually be expected Through a process of personnel exchange on surveys and dedicated workshops it is hoped to further develop the existing knowledge base within both PGNAPES and PGTIPS on fish behavior directly relating to echogram scrutinisation Echogram scrutinisation used to be done by measuring the increment of the integrator line on the printed paper output of the echogram This was a simple and efficient way of scrutinising if one deals with single species schools and if there are no problems with bottom integration More generally computer based post processing systems such as the Simrad BI60 or Sonardata Echoview systems are currently being used for scrutinising It is recommended that one depth range be used for the whole area in the printer output and on post processing systems This will ensure that similar echo traces from all parts of the survey area will have the same appearance and hence are visually more comparable For all internationally coordinated surveys a range of ICES three letter species codes have been applied through a common database to ease the flow of data between participant countries Use of trawl information The allocation of echo traces to species is governed by the results of trawl hauls In many cases these are considered together with observations from the netsonde and the echogram during the haul In some cases it is not
58. peration procedure for Simrad EK500 4 3 2 Operation procedure for Simrad EK ER60 The following steps should be checked Settings in header menu Install Transceiver 1 Check if all frequency channels appear in green text If not choose correct transducer in transducer selection Navigation 1 Select serial port of GPS device If nothing present or other check port management in Install port control 2 Select serial port of speed information probably GPS 3 Select distance calculation method probably from speed This box is also used to set the starting number of the overall distance of the survey Environment 1 Set the temperature and salinity of the calibration site Output file 1 Directory enter data recording directory 2 Raw data file size decide on the length of individual datafiles based on distance or file length Operation normal 2 Mode active 3 Set pulse duration sample interval bandwidth combination This pulse duration should be equal to the one used in the calibration file 4 Choose power which to use 5 Set depth of transducer from surface level Operation ping control Choose a ping interval which does not give an error or warning Input of calibration data After completing the above steps you should now be able to view correct echograms of the installed frequencies
59. perience show that for herring down to approximately 50 meters about 60db is suitable However at extremely high levels as experienced in coastal waters a Threshold of up to 54 db maybe required in order to remove unwanted plankton When starting a new 5 mile first a layer is entered which defines the lower depth of the vertical herring distribution This depth is found by looking for herring schools as discrete jumps in the integrator line and include the lowest school We then set the Threshold at a level where all the plankton is removed This is done by varying the Threshold and looking for changes in the coloring of the upper level Herring schools will often appear as very tiny red dots size only a few pixels hardly visible Note that this Threshold applies only for the upper channel down to approx 50 meters A note is made of the NASC when the correct Threshold is found This value is noted and is given to herring after the Threshold has been reduced again to 85 db The Threshold is lowered again to 85 db herring is given the noted value and the rest up to 100 is given to plankton In deeper waters below 50m the procedure for this depth is similar as for the upper layer The Threshold is reduced until the plankton disappears from the screen normally till about 69db sometimes as low as 66db That NASC is kept for blue whiting and mesopelagic fishes Normally 20 30 percent is given to mesopelagics and the rest to blue whiting d
60. ples should be taken for later indentification ashore 6 Plankton sampling 6 1 Sampling plankton The standard equipment for zooplankton sampling is the WP2 net Fig 6 1 with 180 or 200 um mesh size and 56 cm aperture The net is hauled vertically from 200 m or the bottom to the surface at a speed of 0 5 m s It is important not to stop the haul or lower the speed until the net is above the sea surface Figure 6 1 Image of a typical WP2 net and a description of its parts A Nansen release mechanism heavy duty version for operating closing plankton net by a 0 8 kg drop messenger not used during the survey B Three 6 mm Nylon lines with bridle and snap hook length 85 cm C Ring of AISI 316 stainless steel tubing with 3 loops for bridle and weight lines 2 loops for an optional digital counter located in the middle of the opening 1 D 157 cm area of 0 25 m2 D AISI 316 stainless steel clamping fixture E Part a net 180 200 micron Monodur Nytal Nylon net with 6 loops for the 6 mm diameter Nylon line closure rope Cylindrical net length is 95 cm Part b net is identical to a but conically shaped The length is 166 cm F AISI 316 stainless steel clamping fixture G Net bucket based on the Hensen design The bucket is made of a 160 mm diameter Polypropylene tubing with a plastic draining tap 6 openings Total area of 315 cm2 covered by 180 200 micron net material of AISI 316 stainless st
61. press Edition Enter your database username and password User PONAPES OWNER Username Password Click here to learn how to get started Select the SQL button Figure A and select the SQL Commands button Figure B Then write or paste your SQL statement into the SQL text box and press the RUN button Number of rows displayed are default 10 but can be changed in the Display drop down field Saving SQL statements It is possible to save your SQL statements by pressing the SAVE button Retrieve your saved SQL s by pressing the Saved SQL button lts recommended to copy and paste the SQL statements on page 7 and onwards to get a feel of the system Exporting from database It is possible to download data from the database After the SQL is executed the link csv export pops up below the results pane By clicking the CSV export link data will be downloaded to your computer The user will be prompted to choose to look at the data or to store the data locally Note that the format of the browser output and CSV file decimal sign thousands separator text qualifier etc depends on the language settings of your browser Internet Explorer Internet options language Standard Query Language Writing SQL statements is relatively easy Basically a select statement is divided into 3 parts e Select clause What do you want to see e From clause From which table s are you selecting data e Where
62. ques for the study of fish school structure from acoustic survey data Can J Fish Aqu Sci Reid D G P G Fernandes E Bethke A Couperus E Goetze N Hakansson J Pedersen KJ Staehr E J Simmonds R Toresen and E Torstensen 1998 On visual scrutiny of echograms for acoustic stock estimation ICES CM 1998 J 3 6pp Rivoirard J Simmonds E J Foote K F Fernandes P G and Bez N 2000 Geostatistics for estimating fish abundance Blackwell Science Ltd Oxford Simmonds E J F Gerlotto P G Fernandes D N MacLennan 2000 Observations and Extraction of three dimensional information on fish schools Proceedings on the meeting of the annual Journal of Acoustical Society of America Berlin June 2000 Simmonds E J N J Williamson F Gerolotto and A Aglen 1992 Acoustic survey design and analysis procedures a comprehensive review of current practice ICES Coop Res Rep 187 130pp Wileman D 1991 Codend Selectivity Updated review of available data Study contract No 1991 15 Danish Institute for Fisheries Technology and Aquaculture Appendix A Vessel details Survey vessels and specifications of participants involved in surveys coordinated through PGNAPES and PGTIPS gto Rese Dre callsign E gt LDGJ TFEA ee EIGB UANA OXBH Y eau MEC AAA pinro gtel ru_ pidge 84D 871 763 574928 8 954 210 3640 45 98944448 in Hirtshals only 4755906401 PF 45 98945048 in Hirtshal
63. rent sub areas i e the main areas in the terminology of BEAM Strata of 1 latitude by 2 longitude were used The area of a stratum are adjusted when necessary to correspond with the area representatively covered by the survey track For blue whiting this is particularly important in the shelf break zone where high densities of blue whiting quickly drop to zero at depths less than about 200 m To obtain an estimate of length distribution within each stratum samples from the focal stratum are used If the focal stratum was not sampled representatively also samples from the adjacent strata are used In such cases only samples representing a similar kind of registration that dominated the focal stratum were included Because this includes a degree of subjectivity the sensitivity of the estimate with respect to the selected samples was crudely assessed by studying the influence of these samples on the length distribution in the stratum No weighting of individual trawl samples was used because of differences in trawls and numbers of fish sampled and measurements The number of fish in the stratum is then calculated from the total acoustic density and the length composition of fish Species specific acoustic density Sa m n mile for each stratum is estimated as the weighted mean of species specific density estimates reported by all vessels from a certain stratum with length of cruise track behind each value being used as the weighting factor
64. rmats will be sent in before the start of the survey in order for all vessels to use the most up to date format for data exchange An important change in the database format was to switch from common PGNAPES species naming to the use of the standard three letter species code used by ICES All 2006 data will be imported into the database shortly and made available for the survey participants on the web PGTIPS The North Sea and the West of Scotland survey are coordinated by PGTIPS Aggregated data survey data are uploaded in the Fishframe database at least a month before the meeting date normally end of January During the meeting the joined estimates and the survey report are prepared for the HAWG The groups is trying to develop a database containing raw international survey data However regional differences in survey methods induced by the highly variable circumstances by area causes the process of raising the data to aggregated level to be different Thus the data collected in the different national areas are not compatible and the national participants do not give a high priority to the upload of raw data which is complicated anyway knowing that they will have to be dealt with separately anyway At PGTIPS the coverage for the July surveys are planned During the surveys there is daily radio contact between the national vessels 2 5 Cruise plan An annual cruise plan requires at least the following items e Expertise needed during th
65. s Sea the joint survey in late spring late April early June is termed the International ecosystem survey in the Nordic Seas for the time being and only in this document further referred to as IESNS aimed at observing the pelagic ecosystem in the area with particular focus on Norwegian Spring Spawning herring blue whiting zooplankton and hydrography In 2003 ACFM recommended that a coordinated survey be organised covering the main spawning grounds of blue whiting Other countries than those presently taking part in these surveys were invited to take part The coordination of blue whiting surveys is taken care of by an extended ICES Planning Group on Northeast Atlantic Pelagic Ecosystem Surveys PGNAPES including also the blue whiting spawning survey during spring PGTIPS surveys The survey targeting the largest stock within this group is the North Sea Hydro Acoustic Survey for Herring and Sprat HERAS in July It traditionally delivers indexes for North Sea autumn and springspawners spawners and sprat to the ICES Herring Assesment Working Group HAWG Closely connected to HERAS is the West of Scotland Herring Survey which deals with autumnspawners west of Scotland ICES area VIA during the same period Listed in the table below are the contributions since 2004 by country to the surveys coordinated through ICES led PGNAPES and PGTIPS planning groups Table 1 1 Survey contributions Sey Country IBSSS_ HERAS _
66. s constants for one species However a and b could be considered as variables varying differently with stock and time of year as well as species Suppose the target strength of one fish is given as TS a b log L 7 The corresponding function TSy the target strength of unit weight of fish has the same form with different constants TS a b log L 8 The number of individuals in a unit weight of fish is 1 W so the constant coefficients are related to the formulae b b 10b 9 a a 10log 4 10 Abundance estimation So far the analysis has produced an estimate of the mean density of the insonified fish for each part of the area surveyed and for each species considered The next step is to determine the total abundance in the surveyed area The abundance is calculated independently for each species or category of target for which data have been obtained by partitioning the echo integrals The calculations are the same for each category Q AF 11 k 1 The total biomass for all species is Q 2 Q 12 The Fi are the mean densities and Ax are the elements of the area that have been selected for spatial averaging The may be calculated from the shape of an area or measured depending upon the complexity of the area The presence of land should be taken into account possibly by measuring the proportions of land and sea 8 2 PGNAPES approach In this section we describe how acoustic and trawl
67. s only kL AAA EE E NEEN EECH 45 40435479 or 45 30272529 TI E E 48 30250363 INMARSATA phone___ ___ ______ S oa to 87t rwmws FINMARSATAfax o gt gt pp or SE EE E o S G 877321988420 gun ast stat aen 881631450453 O WSAT rte TAS SC E E E E E O E E TE weblink contacts E T o o we we e e e we O weblink technical specs al we vw eee eb i Power kW l NN E gt AE 200 AA AAA pin range e Ap A A ps A pod Primary transducer ES 38B SK_ Essee_ Essee _ ES38B Se a ee LI Ge pf Other Frequencies KHz te 120 200 18t2 to testeo2m e Ee ona ea O pons sare IO O EE O 28 Dee t og interval nm T E a N RA A E E R ee upper integration limit SS o o e e o o e po integration threshold B 2222222 Y d o S o oo _ Using sonar systematical A S o Poo o poo S o Ge sampler PO SBE 32 Pp Rosette sampler Pes po Maximum sample depth m S 1000 1000 1000 fp 1000 re Seabird SBE21E pe l Y See vata Se E e E pO Mesh size in ST unt WE A 2 IM EL q Typical towing speed il 3 3 4 0 3 5 4 0 IAS E er vata igi o E O pO Mesh size in SC IO BC E E besche Typical towing speed kn 3 0 4 0 A EA AAA 3 3 3 9 P8045 ce O EE D CH A E GE __ EEN Ce mee O ET A A E O E E A ET E A 88 E poetical opening mm Pt d SO presea po mesh in panel 2 E ____z gt E q LH feshe HS AAA 9 gt gt gt AO mesh in panel 5 hdl 0 WO pot
68. s the proportion of the i th species calculated from fishing data It is necessary to know the target strength or the acoustic cross section which may be determined in the same manner as for single species above The fish density contributed by each species is proportional to wi Thus the partitioned fish densities are FE wk SES O w lt 0 gt Es 5 The wi may be expressed as the proportional number or weight of each species according to the units used for lt oj gt and ci Consistent units must be used throughout the analysis but the principles are the same whether it is the number of individuals or the total weight that is to be estimated Using weight length relationships The abundance is expressed either as the total weight or the number of fish in the stock When considering the structure of the stock it is convenient to work with the numbers at each age However an assessment of the commercial fishing opportunities would normally be expressed as the weight of stock yield Consistent units must be used throughout the analysis Thus if the abundance is required as a weight while the target strength function is given for individual fish the latter must be converted to compatible units This may be done by reference to the weight length relationship for the species in question For a fish of length L the weight W is variable but the mean relationship is given by an equation of the form W a L 6 Where a and b are taken a
69. sels are now equipped with a retractable drop keel on which acoustic sensors may be mounted Figure 4 1 Direct comparison in bad weather Transducer ef al IA Hull mounted in transducer wa SE e Be 8 hull mounted drop keel mounted rhe Figure 4 1 Drop keel mounting left panel and differ mounting right panel Source http www uib no gosars english background special_features dropkeel_more html Towed body mounting A tow body is an independent towed unit suspended from the main survey platform with a mounted transducer Fig 4 2 As the unit is towed alongside the vessel the survey depth is a function of cable length and vessel speed n_n Figure 4 2 Towed body as used by FRS Aberdeen and IMARES left panel and image of a typical towing depth right panel Source http www acoustics washington edu gauthier Research Sitka towfish1 jpg 4 2 Calibration There are a number of transducer parameters that require knowledge of the sound speed in water The theoretical context is given in Bodholt 2002 It is essential that a CTD cast is used to determine the temperature and salinity of the water so that sound speed can be calculated see Appendix 2 and MacLennan amp Simmonds 2005 for equations and entered into the EK500 or the EK ER60 Calibration of the transducer should be conducted at least once during the survey Calibration procedures are described in the Simrad EK500 manual the
70. specifications Herring Clupea harengus and Sprat Sprattus sprattus Remarks In the western and northern part of the area covered by the survey most of the herring occur in well defined schools often of a characteristic shape as pillar shaped large dense schools or as layers of very small and dense school at the surface In the northern and central part schools of Norway pout and herring are difficult to distinguish from each other In low density areas of the western area mixed layers and aggregation of small schools consisting of gadoids and herring may occur Sprat marks in the North Sea and Vla appear mostly as quite large typical pillar shaped marks usually slightly more diffuse than herring and usually in shallow water Examples of typical echograms Comment sy1 We could decide to leave examples out i d H d a i nah SEET Led uk TO aki Au bottom depth 47 37m Good SYTSE 4 0 KB s 50714 T040544 raw 55 40 09 N 5 13 30 E 147 2005 09 17 56 82 Distinct Northern North Sea SEEE and mixed conan Bi igh 381447 Primary fileset Sv raw pings 3 File Surface layer Norwegian Sea IESNS Threshold 80dB Blue whiting dE poutassou a s a E ve Pe ial ER AR cla tee E R Se 7397 21m Ce oo he v haci Bl i pee ena Distinct layers West of British Isles IBWSSS Threshold 70dB
71. t different ranges have to show the same results Correction factor for pre calibration NASC s on EK500 K Where AG Calibrated Sy Transducer Gain Default Sy Transducer gain Correction factor for pre calibration Sy s on EK K 10 log s correction factor A calibration report as shown in Tale 4 1 should be completed at the end of each calibration Calibration report Frequency kHz gt gt gt Iteration no Transducer serialno IL Time Range to half peak amplitude m a a RS Vessel S pess Range to sphere m OZ O HH Pae Y Theoretical NASC m2 nmile 2 latte TI Measured NASC m2 nmile 2 I I Longitude d Bottomdepth m T Temperature 0 Salinity ppt T Speed of sound m s 1 T TS of sphere dB Pulse duration f Equivalent 2 way beam angle dB 3 Receiver delay s f Time Default S transducer gen Measured TS Calibrated TS gain A T Table 4 1 Calibration report sheet used with EK500 calibration Note All parameters may not be necessary when using the Simrad EK ER60 echosounder 4 3 Inter ship comparison Intercalibration The advantage of inter ship comparison is that it will demonstrate any gross difference in acoustic performance The inter ship comparison is NOT an absolute calibration but it is a useful means of checking that there is no great difference in the respective measurement capabi
72. t larger in volume sex easier determined still transparent with hint of colour 3 maturing a opaque but developed in volume distinct veins testes white or with white spots firm can occupy half body cavity or more 4 maturing b gonads larger in volume distinct veins testes light grey or white milt thick and slow flowing 5 maturing c testes are grey or white The gonads are not yet running however a light pressure on the abdomen causes the milt to run 6 spawning running gonads when light pressure is applied 7 spent gonads loose remaining milt contain 8 resting gonads small difficult to distinguish from stage 2 3 T ed herring gonads very small threadlike 2 3 mm broad testes whitish or grey brown 2 Virgin herring with small sexual organs height of testes is about 3 8 mm testes a reddish grey colour 3 maturing gonads occupy about half of the ventral cavity breadth of the sexual organs is between 1 and 2 cm testes reddish grey or greyish 4 maturing gonads are almost as long as the body cavity testes whitish 5 maturing gonads fill the body cavity testes are milky white sperm does not flow but can be extruded by pressure 6 spawning ripe gonads testes white sperm flow freely 7 spent gonads baggy and bloodshot testes may contain remains of sperm The body cavity may contain bloody fluid At this stage there can be difficulty in deciding sex i
73. t transducer is 6 86 the angle sensitivity is calculated as 155 576 86 22 86 instead of the default value of 21 9 The angle sensitivity of individual transducers can differ from the default value Conti et al 2005 report values of 1 2 4 however for the presented example the deviation was larger than 4 The use of an incorrect angle sensitivity has a significant influence on the TS compensation while the influence on the sa value is relatively small The sa value depends on the square of the angle sensitivity In this case using the default value instead of the measured angle sensitivity introduces an error of about 10 to the measurements H the specific angle sensitivity is not known the default value for the angle sensitivity and the given two way beam angle should be used These parameters have to be converted from the environmental conditions given in the transducer sheet obtained at a given temperature in a fresh water container into a parameter set for the instantaneous environmental conditions by the equations given in Bodholt 2002 Angle sensitivity n C The angle sensitivity has to be converted for EK 500 and EK 60 before the calibration is carried out 2 C Two way beam angle Ur Y SS 0 This two way beam angle should be used even if the calibration results in a different value If the specific angle sensitivity is known only this parameter has to be converted to changed environmental conditions In this case the two
74. the IESNS and IBSS PHTIPS The international area of the North Sea Hydro Acoustic survey is every year the same based on where herring and sprat have been found historically The survey is roughly divided in 5 national areas see figure below These areas may be different from year to year for logistic reasons but also to get to know each others border area sometimes overlap and inter calibrations The survey effort is basically two east west transect through each ICES rectangle However high density area are covered with a double intensity at the cost of areas with low concentrations see figure 3 2 Ds D9 ED El E2 E3 E4 ES E6 E7 E8 E9 FO F1 F2 F3 F4 FS F6 F7 da F9 GO Gi G2 G3 Dil A Sep Sep STA ta ETA mH E Figure 3 2 A Survey area layouts for all participating vessel in the 2008 acoustic survey of the North Sea and adjacent area s IE Celtic Explorer WSC West of Scotland charter SCO Scotia NOR Johan Hjort DK Dana NL Tridens GER Solea B Figure Survey effort in the 2008 acoustic survey of the North Sea and adjacent areas Red 7 5 nautical miles spacing Magenta 15 n mi Cyan 30 n mi 3 2 Survey implementation Transect design Area coverage Pre agreed target area coverage is designed to maximise survey effort and avoid duplication It is dependent on the pre agreed survey areas as assigned during the survey planning phase and should be adhered to wherever possible Agreement Variat
75. these in the international database It is imperative that the results are submitted in PGNAPES format to the Faroese Fisheries Lab FFL as quickly as possible after each survey This to facilitate the processing of numbers for the combined survey report Submit data to Leon Smith email leonsmit frs fo 10 1 PGNAPES web based database 10 1 1 Overview and exchange format At the PGSPFN meeting in Bergen 2001 the group agreed to set up a common database for the data collected in Norwegian Sea since 1996 by the different nations This was due to the fact that the data handling was becoming more and more difficult as the amount of data collected is huge Already then a draft database design was made In 2007 a database web server Oracle 10g express edition was set up at Faroese Fisheries Lab The PGNAPES group has committed itself to submit all relevant cruise data to this central database to achieve easy access to the complete time series The PGNAPES data base was developed on an Microsoft Access platform and the Access version is very usefull during a survey facilitating the collection and organisation of data and ensuring the quality and integrety of the dataset Another great benefit is that the tableexports fits right into the central database on the internet Data files can be interchanged between the vessels in the csv format comma separated values with tables arranged as described by the PGNAPES database format Data
76. uding the water depth more care should be taken at greater depth and the particular size of fish Examples of conditions where certain Thresholds have been applied using the BEI and Echoview post processing systems are described below they should not be used without verification Several institutes have developed or contributed to image processing systems for post processing of echograms This can extract a range in school descriptors energetic morphometric and positional which can be used to define the characteristics of schools of a particular species These techniques are based on a license module called Virtual echogram often accompanied by the School detection module In general such systems can differentiate most observed schools to species however these are usually the schools which an experienced survey operator can also discriminate by more traditional methods These systems are likely to become more valuable in the future when they can be fed with multi frequency data At the beginning of the survey it is advisable to experiment to find the right Thresholds specific to the conditions encountered during the survey This can be achieved by isolating schools and changing the Threshold to leave only the target species Notes should be made to track the action taken specific to each survey Thresholding using the BEI post processing system The main principle has been to use as little threshhold as possible at any time but ex
77. values b where a country b country and a vessel b vessel and a cruise b cruise and a log b log and a year b year and a month b month and a day b day and b species WHB group by a country a vessel a cruise a log a year a month a day a Hour a min a aclat Select all data from a table Select from lt tablename gt a aclon a ICESsquares b Acoustic c WHERE a country c country and a vessel c vessel and a cruise c cruise and a log c log and a year c year and a month c month and a day c day and c AcLat Between b lat_min And b lat_max AND c AcLon Between b lon_min And b lon_max GROUP BY b Rect b lat b lon b Area_sqnmi order by b rect Records in database overview Select a country a year a cruise a log b catch c bio d hydr e acoustic f acousticval g pl from select country year cruise count station LOG from logbook group by country year cruise order by country year cruise a select country year cruise count station jcatch from catch group by country year cruise order by country year cruise b select country year cruise count station bio from biology group by country year cruise c select country year cruise count station hydr from hydrography group by country year cruisejd select country year cruise count log acoustic from acoustic group by country year cruise e select country year cruise count lo
78. varies large ventral cavity with some transparent eggs 6 Roe Spawning running 7 Spents ovaries slack with residual eggs baggy and bloodshot 8 Recovering spents no eggs visible Blood vessels showing Maturity classification for blue whiting Stage Females JE Maier JE blank Undecided not checked Undecided not checked E 1 Immature lt 1 4 Immature lt 1 4 Ovaries transparent and white No visible Testes are thin and transparent eggs Ribs almost invisible 2 3 5 Spent new maturation First time 1 3 Spent new maturation First time 1 2 spawner spawner Ovaries transparent orange red somewhat Testes transparent pink white with spotted some rolls or loops with bags Curl when squeezed Maturing 2 3 Maturing 3 4 Ovaries harder orange pink Opaque eggs Testes opaque white plump distinctly visible Maturing mature Ovaries orange pink gt 3 4 Maturing mature 1 Some hyaline eggs Testes opaque creme white Tightly curved bags or rolls WW Spawning running Spawning running Ovaries pink white Mainly hyaline eggs Testes opaque creme white Easy to squeeze out Easy to squeeze out Spent lt 1 2 Spent Testes yellow white and aa Ovaries spotted pink red bloody Some bloody Small crinkled band eggs remaining Maturing Maturing Ovaries orange pink Opaque eggs barely Testes are in the process of becoming visible opaque pink whit Some blood vesssels 4
79. y scale reading a number of otoliths should also be taken for comparison 100 200 over different trawl hauls per cruise Otolith and scale reading Otoliths and scales may be read onboard using standard procedures for otoltih reading of blue whiting or scale reading of herring or they may be examined at a later stage in the institute laboratories Reading Herring otoliths and scales Count the number of hyaline zones winter zones dark in reflected light on the otoliths number of zones on the scales Figure 5 3 shows an example on a herring scale and how the number of winter ring can be read January 1 is the date on which the fish becomes one year older If otoliths or scales from a fish caught in the autumn have started a new winter zone this zone should not be counted or measured If otoliths or scales from a fish caught in the spring have not yet started the winter zone this should be assigned a year more than the number of zones i e the edge is counted and measured as a winter zone Figure 5 3 Herring scale Blue whiting otoliths It is difficult to give strict rules for the determination of zones the width of rings and zones and the distance between them must be appraised continuously In otoliths of young fish lt 2 years it may be difficult to distinguish between the first winter zone and Bower s zone Bailey s zone and other rings checks particularly for l group fish caught in the year s first quarter

Acoustic manual PGNAPES PGHERS version 2.1

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