A Manual for Conducting Georeferenced Photo Transects
Contents
1. Filamentous cladophora MA A FO Foliose Ulva dictyota MA A CO Corticated Caulerpa MA A LT Leathery Sargassum MA A CA Calcareous Halimeda MA A E Crustose red crustose MA RC cor Corraline on rock RC RC turf Turf on rock RC RC cl Rock clean RC SD Sand Su RB Rubble Su OT Other OL DCOR Diseased coral DC TAPE Tape TWS WAND Wand TWS SHAD Shadow TWS NOTES NOTES NOTES GPS Photo Transect Manual 3 0 October 2009 27 33 ASP Aspergillis NA BL Bleached coral point NA BBD Black Band Disease NA OD Other disease NA PLA Plague Type II White Plague Type II NA WBD White Band Disease NA YBD Yellow Blotch Disease NA GPS Photo Transect Manual 3 0 October 2009 28 33 5 3 C CPCE example class file Not Detail Benthic Category 7 C Coral SC Soft Coral MA Macro Algae SG Seagrass SU Non Living Substrate OV Overview TWS Tape wand shadow CO Coral Dominant C COMA Coral and Macro Algae C COSG Coral and Seagrass C COSD Coral and Sand C CORU Coral and Rubble C CORM Coral and Reef Matrix C COSC Coral and less Soft Coral C CODC Coral live and dead C SC Soft Coral Dominant SC SCMA Soft Coral and Macro Algae SC SCSG Soft Coral and Seagrass SC SCSD2. Figure 17 Screen grab of photo analysis CPCE program On the right is table with one box for class assigned to the whole photo On the bottom the colour bar represents the different benthic photo categories that can be assigned cccceccccsececeececeeeeceeeesseeeeseeeeseeeesaeees 23 Figure 18 Example output of GPS Photo Linked in ARCGIS eeeeseeeeseeessss 24 Figure 19 Example output of kml file created with GPS Photo Link for use in Google Earth 24 GPS Photo Transect Manual 3 0 October 2009 3 33 Summary This manual describes the methods for gathering still photos or video frame of the benthos horizontal or vertical that have a known position in time and space Photos can be used to quantitatively or qualitatively assess the benthos by determining percentage horizontal projective cover herein referred to as cover species composition e g coral algae and seagrass of benthic environments e g sandy or rocky beaches inter tidal and rocky or coral reef areas or indicators of health e g coral bleaching coral diseases The method involves a GPS being towed by snorkeller diver that is taking photos along a freely planned track At set intervals kick cycle or time estimates horizontal projective photos or seascape photos are taken from the seabed GPS coordinate are continuously recorded while towing the unit when swimming a transect and collecting photos Photos are then linked with GPS
3. GPS Photo Link User Manual www geospatialexperts com Acknowledgements The following people need to be acknowledged for helping developing the techniques described or providing alternative options Karen Joyce Kevin Kohler Ray Berkelmans Jens Kruger Salesh Kumar GPS Photo Transect Manual 3 0 October 2009 7 33 1 Equipment Needs The equipment presented is an example that has been used by the authors of the manual however other handheld GPS s that can track and download in combination with underwater cameras could do the job as well 1 1 Hardware Figure 2 Alternative float set up with GPS place in plastic box within a float and connected to reel photo Ray Berkelmans AIMS Figure 3 Snorkeller and diver towing the GPS drybag float system GPS Photo Transect Manual 3 0 October 2009 8 33 Equipment Purpose Example Prerequisites Digital To take pictures Canon a240 with Olympus housing with Anything camera of the substrate two AA batteries and two 3 Gb cards equivalent to this which fits in a housing and is easy to handle Recommended to have sufficient battery life and memory stick The bigger the better There is a variety of different digital cameras available Olympus Canon Ricoh or See in appendix our considerations for buying a new camera Housing for Keep the Marine Pack Housing Easy to handle digital camera dry transparent not to camera P much buttons stick out fits in B
4. Soft Coral and Sand SC SCRU Soft Coral and Rubble SC SCRM Soft Coral and Reef Matrix SC SCHC Soft Coral and less Hard Coral SC MA Macro Algae Dominant MA MASG Macro Algae and Seagrass MA MASD Macro Algae and Sand MA MARU Macro Algae and Rubble MA MARM Macro Algae and Reef Matrix MA MADC Macro Algae and dead coral MA SG Seagrass Dominant SG SGSD Seagrass and Sand SG SGRU Seagrass and Rubble SG SUSD Sand Dominant SU SURU Rubble Dominant SU SURM Reef Matrix Dominant SU SUMS Mud Silt Dominant SU SUSR Sand Rubble Dominant SU SUDC Dead Coral Dominant SU OVCO Overview Coral Dominant OV OVMA Overview Macro Algae Dominant OV OVSG Overview Seagrass Dominant OV OVSU Overview Non Living Substrate Dominant OV GPS Photo Transect Manual 3 0 October 2009 29 33 Tape Tape Slate Out of focus GPS TWS NOTES NOTES NOTES R1 Rugosity 1 N R2 Rugosity 2 N R3 Rugosity 3 N GPS Photo Transect Manual 3 0 October 2009 30 33 5 4 D Check List Equipment and Field Steps In the office Download cable GPS and camera Charger batteries GPS and Camera Silicon grease for O rings Laptop GPS Photo Linking software Drivers for cable if applicable GIS software ARCGIS or Google Earth CPCe to analyse photos pa On ee Wet n the field GPS with free memory space and full batteries a
5. iF ou know Ehe difference between the GPS time and the camera time CameraJP5 Time Matching Method of Time Synchronization fe Use photo of the GPS receiver Manually enter GPS Camera time seconds Iw Use GPS position only iF within 60 seconds Matching lInterpolate between closest GPS points Figure 10 GPS Photo Link Time Synchronise Window 2 8 Synchronise GPS time stamp to photo stamp by selecting use photo of GPS receiver and tick of use GPS position only within 60 sec select for matching Interpolate between closest GPS points Closest in time press next GPS Photo Transect Manual 3 0 October 2009 18 33 2 9 The GPS time and Photo time calibration window occurs Ed GPS Photo Link GIS Pro Time Offset Entry ok ll UK jw Use this photo far time entry Cancel GPS Time 21 08 2009 E 5t23AM Note Be sure to enter exactly how the time appears an the Photo Time 21 09 2009 51 41 AM picture of the GPS screen including the date time and Fitimage Calculated Offset 13 sec am pm bo screen Select Photo Picture from Camera Canon Canon PowerShot G10 Help pERT r Figure 11 GPS Photo Link GPS Camera time calibration 2 10 Look up the photo of the GPS time screen read the time of and enter it in the GPS time box This will automatically calculated the offset time Press then enter 2 11 The photo comments window occurs where
6. strobe off Submerge camera in bucket with freshwater to check for leaking Calibrate plump line so that the photo foot print covers the required surface area 2 lime synchronisation Take picture of GPS Time screen 3 Prepare GPS Dry bag e 4 e Place GPS in GPS dry bag Place GPS with GPS dry bag on float so that you can read GPS screen Place weight on bottom of float Place weight with float and GPS in big dry bag Close big dry bag and check for leakage Connect GPS dry bag to reel or line Enter water with GPS with float in dry bag and reel Magna doodle Camera with plumb line and wide angle lens GPS Photo Transect Manual 3 0 October 2009 14 33 2 2 Step by step in water Go to site Turn on GPS Descend to survey start point constant profile depth While under water check housing regularly on leaking to prevent flooding Write on slate site name start time depth date and possible direction Oo or wa N Take picture of slate Figure 4 Photo of slate and its data at start of transect 7 Take picture of start transect 1 m above the bottom Depending on visibility and detail needed and camera lens field of view Use plumb line to get right distance Figure 5 Snorkeler or Diver takes photos of benthos and holds reel connected to GPS in hand 8 Repeat this for every 2 m interval until the end of transect line or every 4 kick cycles till end of planed line GPS Photo Transect Manual 3 0 October 200
7. the temperature change is reduced Having sufficient memory space and battery power or having another identical setup can take care that no batteries or cards need to be changed in the field When aligning field data with image data the accuracy of the image georeferencing should be similar to that of the field data ARC Explorer cannot be used to add information to each of the points this has to be done in the DBF file which is then transformed to shape files Tips when using GPS Photo Link Download photos first using standard windows software and rename photos to yyyymmdd site transectno photono jpg this to take care the photos have a logical name GPS Photo Link can only give it a fixed name with only the date init so no site information 4 Safety Consideration 4 1 Snorkelling e Snorkeller should bring safety sausage and acoustic signalling device e onorkeller should always be accompanied by other snorkeler or within range of view of a surface lookout on boat or shore e ransect should be planned with the current and not against it 4 2 Diving e Diving should have standard diving equipment including safety sausage and acoustic signalling device e Diving should not be done solo e Surface float with GPS can function as a surface marker buoy for the boat to follow e It s not recommended to plan transects perpendicular to contour lines e ts not recommended to plan transects that require diver to change depth regularly f
8. you can enter information to plot on each photo separately which is optional Then press next Ed GPS Photo Link GIS Pro Data Entry Photo Edit BEES i All Tie ter All Photos oubTitle for All Photos i Photos mE 0 Selected Photo Comment Load From File Direction Manual Lat Lon Hep Photo D Hil BEEN eS Fit image v to screen Internal Lon Cancel Figure 12 GPS Photo Link Add comments to Photo window occurs GPS Photo Transect Manual 3 0 October 2009 19 33 2 12 The output format window occurs GPS Photo Link GIS Pro Output Options 2009 09 27 Web ward Output watermarks Google Misc Heading Distance GeoSpatial j EXPERTS Map Source GPS Photo Link zoom Level High Size of Maps Select output formats icon File Watermarked Photo web Pages HTML v Text File CSV W GPS Exchange GP Google Earth KMLIEMZ Word Report DOC TIIESRI Shape File 5HP Help About Exit z Back Figure 13 GPS Photo Link Output format window 2 13 Here you can select if you want to create a shape file with hotlinks to photo for ARCGIS or Arcview and or a kml file for use in Google earth You also select if you want hotlinks to a thumbnail or to the original photo 2 14 After you pressed enter the photos will automatically linked to GPS coordinates The program will generate several files which will be stored in the folder where th
9. 9 15 33 Figure 6 Example photo of benthos with plump line for set distance from camera to bottom 9 Write on slate site name end time depth date direction 10 Take picture of slate Figure 7 Photo of slate and its data at end of transect 11 Ascend complete dive when finished 12 Turn GPS off tracking is stopped then 13 Go to next transect when needed and start again GPS Photo Transect Manual 3 0 October 2009 16 33 2 3 Data Processing Downloading 1 Download photos and rename photos to site yyyymmdd transectno photono jpg 2 Download GPS Track and link to photos Detailed description in software manual 2 1 2 2 2 3 2 4 2 9 Connect Camera and GPS to computer Start GPS Photo link and Download Camera window below appears GPS Photo Link GIS Pro Select Photos Select photo source either From the camera an existing Folder or any Folder GeoSpati EXBRERTRE Camera Folder Select the Folder that contains the photos GPS Photo Link ett the output Folder under the Photo Root Folder to store the processed photos and output files Load Photos from Camera Folder Camera Folder Photo Source f Camera Folder Save Output Ta C Existing Folder Fhoto Rook Folder Any Folder JC tDatalkubulauiGIs shapefiles Fieldwork 2009 l Mew Folder to be created under Fhoto Root Folder 2009 09 22 Original Photo Action No action hl Help About Exit Next Fi
10. A Manual for Conducting Georeferenced Photo Transects Surveys to Assess the Benthos of Coral Reef and Seagrass Habitats 1 October 2009 Version 3 0 Centre for Remote Sensing amp Spatial Information Science School of Geography Planning amp Environmental Management University of Queensland Brisbane Queensland AUSTRALIA 4072 e mail c roelfsema ug edu au Ph 61 7 3365 6081 and Fax 61 7 3365 6977 GPS Photo Transect Manual 3 0 October 2009 1 33 Table of Contents UUM TINE SP EET aac E E QU PEERS EN 4 1 elei COS ae i cha Seca eae i neces esses cadets 8 wE 2 19 8 2 ttm DS 8 AS on cU 13 2 Wlellods DeschpOll essunstasontu s yandeoven eneneensiveasnedsndeasedencsuasiadsaidecheiesentusuetarenenndseneneiauesiels 14 ZW ECO AL AU OM TEUER 14 2 2 Olep DV Step II WAGE sirien e aeneo eic ere t TU ee dicm ced newts ete ead emis 15 2 3 Data Processing Downloading secesie EE OE 17 2 4 Data Processing Photo Analysis with CPCe ccccccccccesseeeeeeeeeeeeeeseeeeeeesaeeeeesaaees 21 2 4 1 Photo Analysis Detailed by assigning benthic cover type to x points in each photo 21 2 4 2 Photo Analysis Not detailed by assigning one benthic cover category to NYGIV IQUE llo n To 0 NP NER OE EEUU 23 2b DWata Processing GS EHVIFOTfae ribs eere IR a ved nia be tentis 24 3 WU v ianinneaies 25 A AICI Considera ON T nut cc mum m 25 Aly SNOKEN EE o LEE 25 Ar D QC PU E 25 SE ioo CIC d
11. CD pocket Wide angle Being able to Sea amp Sea 16 mm external wide angle Wide as possible lens be close to the but still low cost benthos and i m and easy to handle photograph a d 1 under water large area 1 Underwater removable in case other pictures are needed Plumb line Piece of thin line with weight fishing Thin to not be GPS Photo Transect Manual 3 0 October 2009 distance from the camera to the bottom to ensure same area covered by photograph Handheld Logging way GPS points and tracking the surveyors track GPS drybag Garmin 72 or 76 Map Keeping the GPS unit self extra dry Float Needs to keep GPS unit above water surface for most of the time GPS Photo Transect Manual 3 0 Aquapack Any styrofoam or other floating material that can be found October 2009 obvious in the picture heavy enough to form a straight plumb line long enough for the distance needed Long battery life 8 or more channels up and download capability logging tracks and waypoints adjusting logging times e g every 10 s adjusting projections and datum Transparent fits GPS oufficient floating device to keep GPS a t surface 10 33 1 kilo Weight Needs to hold Divers weight or any other object which Anything that is the GPS in the makes up 1 kilo e g coral rubble small and weights right position u NN around 1 kilo Function as the E keel of a boat Drybag Needs to hold Transpar
12. ate difficulties identifying features Diver can entangle him her self in line to surface float on GPS Diver towed GPS tricky in survey areas with steep slopes walls or against currents Not suitable for validating low spatial resolution imagery i e pixels gt 100m x 100m Cost of the software The horizontal offset between camera and GPS needs to be ideally nil which can be challenging when diving Camera angle will deviate as not used a fixed frame Interval between photos can vary only transect tape can provide a consistent interval GPS Photo Transect Manual 3 0 October 2009 6 33 Diver snorkeller towed GPS tracking for other purposes Following edges of large characteristic features of submerged rocky reefs to determine the main components e g gullies overhangs of a habitat for the endangered grey nurse shark in South East Queensland Australia Following edges of coral reef and seagrass features to use for checking the field GPS coordinates in relation to its location in a satellite image Following edges of marine features e g seagrass beds algal blooms to determine its spatial extent Following a fish for a set time span to determine the area covered by this fish This by using a diver towed GPS and noting begin and end time Downloading the track and determining extent of areas covered by the track Recommended reading Roelfsema C M and S R Phinn 2007 Queensland Researchers Develop Photo Mapping Technique fo
13. coordinates using of the shelve software e g GPS Photolink or other This software enables synchronisation of camera and GPS time after which photo position is determined through interpolation based on closest in time GPS positions The photos can be viewed at its position in space in a GIS environment such as ARCGIS Google Earth or other Photos are analysed using standardized peer reviewed software Coral Point Count excel Kohler et al 2006 The method was initially developed to collect data intended to be used for the analysis of remotely sensed images airborne and satellite images of coral reef and seagrass environments The method described can be used in the following situations e In water surveys Snorkelling Diving or Reef walking e Boating surveys using o Drop video or still camera where GPS is in boat o Towed video where GPS is located in boat are on float above video The following is a brief summary a detailed description of all equipment software and methods are provided in the remainder of the manual For any recommendation or further for information contact the authors Referencing The manual should be referenced as Roelfsema C M and S H Phinn 2009 A Manual for Conducting Georeferenced Photo Transects Surveys to Assess the Benthos of Coral Reef and Seagrass Habitats version 3 0 Centre for Remote Sensing and Spatial Information Science The University of Queensland Brisbane Australia Peer reviewed pap
14. e T TT 26 Se CE luem 26 5 2 BCPCE example class file Detail Benthic Cover Type sesesesssssssse 27 5 3 CCPCE example class file Not Detail Benthic Category see 29 5 4 D Check List Equipment and Field Steps seeeeeseeeeeseeeee 31 59 E PAO LIKING SOMWANC crisan ouis aid orit aue Sou I ge ES Roe vd Ute Pun QOv ub ger ds 32 5 6 E Considerations for digital camera and housing cecceeeeeeeeeeeeeeeeeeeesaeeeeeaeeeeas 33 GPS Photo Transect Manual 3 0 October 2009 2 33 List of Figures Figure 1 Drybag setup with GPS and Reel 0 cecccccecseeceeseeeeeeeseeeeeeeseeeeeeesaeeeeesseaeeeesaaaes 8 Figure 2 Alternative float set up with GPS place in plastic box within a float and connected to reel photo Ray Berkelmans AIMO noise t Maine nance lia eect 8 Figure 3 Snorkeller and diver towing the GPS drybag float system sese 8 Figure 4 Photo of slate and its data at start of transect seesssseseseeeeeennneee 15 Figure 5 Snorkeler or Diver takes photos of benthos and holds reel connected to GPS in giro HH pL TT 15 Figure 6 Example photo of benthos with plump line for set distance from camera to bottom eT TR OPERE TERMS 16 Figure 7 Photo of slate and its data at end of transect seeesseeseeeeeeee 16 Figure 8 GPS Photo Link Start p WITIGIOW eso aee ee ee tend 17 Fi
15. e thumbnail are or original pictures are Two shape files 1 Track file with the track and 2 picture file with per record a photo and coordinates and meta data of the photo It also generates a kml file which has the track The following can be done to check the quality e all the photos taken should be linked it the number of photos is different the number of photos linked there is something wrong with the time offset calculated e When plotting the photos on an image one can check if the photos are taken at the spot you expected Our experience is that the photos are within 5 m of the actual target The mis registration is due to error in GPS position but also of the image position GPS Photo Transect Manual 3 0 October 2009 20 33 2 4 Data Processing Photo Analysis with CPCe 2 4 1 Photo Analysis Detailed by assigning benthic cover type to x points in each photo oee CPCE manual for explanation 1 Decide on classes at least 100 categories possible do we include our system as an example that need to be distinguished this needs to be in a txt file format that is suitable to read by the CPCE program See appendix for example 2 Decide on the number of points per photo which need to be labelled can be up to 500 in grid or random 3 Select then photos per transect 4 Start analysis 5 Select photo and label each of the points circle e when circle is green then label has been assigned e whencircle is yellow current label has ye
16. ends on detail required Downloading and Download and link photos and GPS coordinates linking photos to using GPS Photo Link which creates automatic GIS GPS coordinates file with hot linked photos Photo Analysis Detailed Analyse by a benthic specialist photos by 180 200 Detailed assigning benthic cover types values to 24 points in CPCE Coral Point Count Excel Extension photo analysis software and summarise the results in an Excel graph Photo Analysis not Not Detailed Analyse by a benthic specialist detailed photos by assigning benthic category to individual photo CPCE Coral Point Count Excel Extension photo analysis software and summarise the results in an Excel graph GPS Photo Transect Manual 3 0 October 2009 5 33 Advantages of approach Photos can be Viewed at its position in GIS environment e g ARCGIS Google Earth and its derived benthic data as well as its position is known in time and space on top of georeferenced remote sensing imagery or any spatial data set Analysed when needed in the field on a laptop or in the office on the desktop Analysed to a suitable detail or archived and analysed in years after Used to provide information on various aspects of the benthos depending on the detail provided by the photo Compared to video photos can have higher resolution and are easier to process Transfer of skills and level of required experience Transfer is easy if suitable experience is pr
17. ent water the GPS in proof bag e g small dry back Ortlieb 10 litres on top of float with weight GPS Photo Transect Manual 3 0 October 2009 11 33 GPS Photo Transect Manual 3 0 Needs to be connected to float and diver To note and then photograph begin time End time begin depth end depth transect direction date transect name Magnadoodle pro from Fisher Price October 2009 Reel with thin rope long enough for the working depth of the survey transect easy to role up and easy to stop the line from rolling further small rope strong enough to pull the float at the surface Enough space to write on and easy to wipe out in or underwater and cheap in case of losing Magnetic slates are ideal 12 33 1 2 Software Software Purpose EXAMPLE Prerequisites Up downlo Up load GPS FREE DNR Garmin extension ad GPS coordinates for transect location and to download tracks and waypoints Any program which can up or download the GPS and translate it into file format for any GIS package you use Program which downloads and uploads from Garmin GPS and turns it into shape file directly suitable for ESRI GIS software http www dnr state mn us mis gis tools arcview extensions DNRGarmin DNRGarmin html Standard computer with USB port Standard laptop software and USB port camera drivers Download To download to camera cameras on to computer Standard computer and software w
18. er describing the manual should be referenced as Roelfsema C M and S R Phinn submitted Calibration and Validation of Coral Reef Benthic Community Maps Integration of Field Data with High Spatial Resolution Multi Spectral Satellite Imagery Journal of Applied Remote Sensing GPS Photo Transect Manual 3 0 October 2009 4 33 Personnel requirements Field work One snorkeller comfortable swimming or experienced diver for taking photos and towing the GPS Processing One person with sufficient knowledge to up and download the GPS and or identify the different benthic cover type classes in the photo Minimum equipment requirements e To link photos to GPS coordinates Handheld downloadable GPS Dry bag and reef e To capture photos Basic digital camera in housing with sufficient memory space and battery life Wide angle lens recommended Plumb line to keep consistent height e o process GPS coordinates and photos Laptop amp Software all sources are listed in Section 1 2 Software to download and link GPS and photos and create GIS files Analyse photos or video frames CPCe and map the results using Google Earth or ARC GIS Time needed Example for 500 m transect with 200 250 photos at 3 kick cycles or 2 m interval Component Description Time needed Min Preparation checking batteries and memory and 20 30 jump in the water and turn GPS on One snorkeller or diver takes photos every 3 kicks 2 m interval dep
19. esent Field component person with any experienced fit snorkeler or diver Downloading and storage of GPS and camera any person with basic computer experience Analysis of photos by person experienced with identifying benthic cover types GIS processing by person with basic GIS knowledge Equipment and software needs Most of the equipment is used already by most survey teams e g handheld GPS laptop digital camera in housing and does not need extra purchase Software package described are low cost or for free except ARCGIS Coral Point Count Excel Extension CPCE is an efficient and a flexible software package for any classification scheme or number of points to be counted on photos which isvery well documented GPS Photolink can create automatic ARCGIS shape and Google Earth format file with geotacked photos which improves image interpretation General Method is flexible can be adjusted for variety of transect length and photo intervals e g 100 m length amp 2 m interval or 20 m 5 m or 25 m 1 m depending on detail needed Length of transect can vary 50 m 300 m 1000 m or more No transect line need to be deployed which saves time and increase safety Direction can be determined while in the field Disadvantages of approach When finished field survey photos first need to be analysed to determine benthic cover which is a time consuming process in comparison to in water assessment of cover No 3D view of benthos which can cre
20. gure 8 GPS Photo Link Start up window Determine Photo location on camera or in directory on computer Determine output location of photos and thumb nail photo directory create new folder and press next The GPS download window occurs GPS Photo Transect Manual 3 0 October 2009 17 33 Ed GPS Photo Link GIS Pro GPS Data 2009 09 22 Select GPS data source GPS Data Source Track Logs Waypoints or Files EXPERTS f Download Garmin Track Logs on pork Auto GPS Photo Link Use GP S data in File eSEE f Use GFS data in photo or manually enter latylon Timezone Local Timet Time zone GMT 4 12 00 Fiji Kamchatka Marshall Is m W Auto adjust For daylight saving time iF needed Datum Position Format Lat Lan Select Datum Was di Position Format Help About Exit z Back Figure 9 GPS Photo link GPS down load window 2 6 Determine the GPS connected or select a track file and determine the datum format the program will automatically calculated geographic and UTM coordinates Press next 2 The time synchronise window occurs GPS Photo Link GIS Pro Time Sync 2009 09 22 Matching the digital photos to the GP S location is done by synchronizing the Camera and GP S time Choose the method of time synchronization ERT S M S Use photo of Ehe GPS receiver lets vou enter the time from a GPE Phnoto Link photo of the GPS screen Manually enter GP5 Camera time
21. gure 9 GPS Photo link GPS down load window c ccseccecceeeeecceeeeeeceeeeeesseeeeeeeseeeeetens 18 Figure 10 GPS Photo Link Time Synchronise WINdOW ccccsseccecesseeeeeeeeeeeeeseeeeeeseaeeeeeeas 18 Figure 11 GPS Photo Link GPS Camera time calibration eseessseeeessssss 19 Figure 12 GPS Photo Link Add comments to Photo window occurs sese 19 Figure 13 GPS Photo Link Output format window eeeeseeeseseeeennnennmnn 20 Figure 14 Screen grab of photo analysis CPCE program Main photo with circles in different colours green label assigned red label not assigned yet yellow label currently assigned On the right is table with point numbers and its assigned classes On the bottom the coloured bar represents the different categories that can be assigned 21 Figure 15 Screen grab of photo analysis CPCE program Main photo is a zoom in of the point that needs a class assigned Circles in different colours green label assigned red label not assigned yet yellow label currently assigned On the right is table with point numbers and its assigned labels On the bottom the coloured bar represents the different category that can be assigned Program will automatically jump to next point dare iaWereani E iciegem t e 22 Figure 16 Benthic cover per photo per transect cccccccsecceseeeeeeeeeseeeesseeeeseeeeseeeseeesseeeesees 22
22. hich can present spatial data FREE Google Earth or ArcExplorer http www esri com Mapping To view the GIS downloaded track on a image or map and to check its Works perfect for just checking track on location map or image We mostly use ARCGIS needs licence but has more capabilities then only showing the track on a map FREE CPCE Coral Point Count Excel Extension Photo To determine any Any other analysis characteristics program which needed for the suits to get the research 96 cover This program provides an easy way to desired bottom type analyse photos and place results information species automatically in Excel spread sheet composition sediment colour algal cover etc http www nova edu ocean cpce Can link GPS tracks with Download Downloads GPS GPS Photo Link and link coordinates and photos and Photos and link GPS and them automatically create GIS output ARCGIS files shape file or Google Earth File GPS Photo Transect Manual 3 0 USB port camera driver software Alternative see appendix E October 2009 photo and outputs a spatial data file on standard computer 13 33 2 Methods Description 2 1 Preparation 1 Prepare camera and GPS Place batteries in camera and GPS Check memory space in camera and GPS Check and set correct projection e g UTM and Datum e g WGS84 on GPS Set GPS menu on logging track every 5 sec Set camera photo resolution to the maximum and turn
23. igure 18 Example output of GPS Photo Linked in ARCGIS 2 When using Google Earth a kml file can be generated the ability to view the photos in Google Earth Error Reference source not found cS Cum ANE Google L Figure 19 Example output of kml file created with GPS Photo Link for use in Google Earth 3 3 1 3 2 4 Linking analysed photo data to coordinates Open shapefile named picture dbf file and open the excel file with the data from the photos which were analysed in CPCE Copy the coordinates from the picture dbf file to the excel file for does records where the photo name is the same Import data in ARCGIS by using XY data command GPS Photo Transect Manual 3 0 October 2009 24 33 3 Tips Download tracks and GPS daily to secure data and back up to a separate USB drive Check tracks and photos daily to secure quality Check tracks were conducted at planned positions Place desiccant gel packs in dry bag and inner bag to absorb moisture Check GPS constellation on dates of planned to survey to ensure there are at least six satellites visible Cool GPS between dives snorkels since it can get hot in dry bag Have one person analyse photos to ensure consistency in analysis Create meta data file which consist of information who took photos rolled out line analysed photos downloaded GPS and photos Camera sometimes fogs on the inside of the housing By placing camera between surveys in water bucket in the shade
24. l camera Optional External wide angle lens Optional External strobe Button and levers not to big so that it does not get entangled in survey dive gear Easy to grease o rings Waterproof to at least 30 m Transparent easy to check for water getting in GPS Photo Transect Manual 3 0 October 2009 33 33
25. nd uploaded study sites GPS dry bag with real for diving or 2 m line for snorkelling Float for GPS with counter weight Camera free memory space and full batteries Extra memory cards and batteries Plump line Underwater housing with optional wide angle Underwater slate to write down info Grease and dry cloth for camera maintenance OONDOOARWD GPS Photo Transect Manual 3 0 October 2009 31 33 5 5 E Photo Linking software Software name Provider Fletormat Remark Cost DNR Garmin DNR Shape file text No Free file dbf automatic viewing in ARCGIS or Google Earth ARC Photo ex ESRI shapefile No Free ArcScripts automatic viewing in Google Earth GPicSync sourceforge net GPX format Google Free Earth Output Media Mapper 5 3 Red Hen Mapinfo table Additional Ask Processing oystems format software provider to view in ARCGIS GPSPhotoLink Spatial Experts Shapefiles Has tool in 350 AUS GPX KMZ arcgis GPS Photo Transect Manual 3 0 October 2009 32 33 5 6 E Considerations for digital camera and housing Digital Camera Needs an existing underwater housing Standard memory card Large storage space Small Large battery capacity 6 mega pixel or more Date time stamp on photos Easy to use Does not need to stay on power when in the housing Large LCD screen Internal strobe USB download Underwater housing Small so it almost fit in dive gear pockets Easy to instal
26. or instance following a straight line along a spur and groove system e tis strongly recommended to plan transect along a depth contour e ransect should be planned with the current and not against it GPS Photo Transect Manual 3 0 October 2009 25 33 5 Appendix 5 1 A Example results Seagrass Transect Data July 2004 Source UQ a T cover i Species 1 10 ERR Zostera e 10 40 H ovale 40 70 H spinuiosa a 70 100 Synngadium a0 Cymadosea Hea bored ibe Bora ss ey ime O Lew B High Medium low Bi High high B Medium B No data Transect 700 m transect p Mb a a GPS Photo Transect Manual 3 0 October 2009 26 33 5 2 B CPCE example class file Detail Benthic Cover Type 8 C Coral DC Dead Coral BC Bleached Coral RC Rock MA Macroalgae OL Other live Su Substrate Base TWS Tape wand shadow HCB Hard Coral Branching C HCM Hard Coral Massive C HCT Hard Coral Table C HCE Hard Coral Encrusting C DCB Dead Coral Branching DC DCM Dead Coral Massive DC DCT Dead Coral Table DC DCE Dead Coral Encrusting DC DCA Dead coral with algae DC HCB BP Bleached Hard Coral Branching BC HOM BP Bleached Hard Coral Massive BC HCT BP Bleached Hard Coral Table BC HCE BP Bleached Hard Coral Encrusting BC SC Soft Coral C A CY Cyanobacteria MA A FI
27. r Benthic Habitats Position Magazine Oct Nov 2007 Kutser T E Vahtmae C M Roelfsema and L Metsamaa 2007 Photo Library Method for Mapping Seagrass Biomass Estuarine Coastal and Shelf Science 75 559 563 Roelfsema C M Joyce K E and Phinn S R 2004 Evaluation of benthic survey techniques for validating remotely sensed images of coral reefs In Proceedings of the 12th International Coral Reefs Symposium Okinawa Japan June 29 July 2 English S Wilkinson C Baker V 1997 Survey Manual for Tropical Marine Resources Townsville Australian Institute of Marine Science Ford S Langridge M Roelfsema C M Bansemer C Pierce S Gomez K Fellegara l McMahon K Keller M Joyce K Aurish N Prebble C Surveying habitats critical to the survival of grey nurse sharks in south east Queensland 2003 Unidive University of Queensland Underwater Club htto clubs ugsport uq edu au unidive Hill J and C Wilkinson 2004 Methods for Ecological Monitoring of Coral Reefs Townsville Australian Institute of Marine Science and Reef Check Kohler K E and S M Gill 2006 Coral Point Count with Excel extensions CPCe A Visual Basic program for the determination of coral and substrate coverage using random point count methodology Computers and Geosciences 32 9 1259 1269 Oliver J N Setiasih P Marshall and L Hansen 2004 A global protocol for monitoring of coral bleaching WorldFish Center and WWF
28. t to be assigned e when circle is red label has not been assigned i te TITHTTITIT zzcigeecemace E H iP da T m m H m d mI T Figure 14 Screen grab of photo analysis CPCE program Main photo with circles in different colours greenz label assigned redzlabel not assigned yet yellow z label currently assigned On the right is table with point numbers and its assigned classes On the bottom the coloured bar represents the different categories that can be assigned GPS Photo Transect Manual 3 0 October 2009 21 33 Figure 15 Screen grab of photo analysis CPCE program Main photo is a zoom in of the point that needs a class assigned Circles in different colours green label assigned red label not assigned yet yellow label currently assigned On the right is table with point numbers and its assigned labels On the bottom the coloured bar represents the different category that can be assigned Program will automatically jump to next point when point is assigned 6 Process whole transect to excel file and name yyyymmdd_site_transectno exl This file contains six sheets per transect 1 raw data per photo 2 summary report per photo 3 summary report per transect 4 raw data per photo organized per row 5 Summary report per photo organized per row and 6 Summary coverage Summary report contains the calculated for each of the benthic categories and standard deviations 7 Create graphs of informa
29. tion per photo not standard in software 100 4 90 80 70 60 50 4 40 30 20 eo eo eo eo o o eo eo eo eo eo l 00 ME O7 EE NN 4 X Q5 X X5 qq Y 5 qq Y Y X X Y 45 Q5 X qq qq Y y qq Y X X qq Q5 X q y Y q Y y X y y E Coral Bi Dead Coral m Bleached Coral gi Rock m Macroalgae Other live Substrate Base Figure 16 Benthic cover per photo per transect GPS Photo Transect Manual 3 0 October 2009 22 33 2 4 2 Photo Analysis Not detailed by assigning one benthic cover category to individual photo 1 Decide on classes at least 100 categories possible that need to be distinguished this needs to be in a txt file format that is suitable to read by the CPCE program See appendix for example Number of points per photo is one select then photos per transect Start analysis oa A C N select photo and assign label to photo Figure 17 Screen grab of photo analysis CPCE program On the right is table with one box for class assigned to the whole photo On the bottom the colour bar represents the different benthic photo categories that can be assigned GPS Photo Transect Manual 3 0 October 2009 23 33 2 5 1 Data Processing GIS Environment When using ARCGIS a GPS Photo Link extension can be integrated in the ARCGIS environment Which gives the ability to view the photos on top of the analysis of the photo Figure 21 E E me eem m n c m lao a L UE Pu F
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