zooprocess manual - Observatoire Océanologique de Villefranche
Contents
1. 5 3 6 3 PID_process Pid_results 5 3 6 3 1 PID_process Pid_results Datl_extracted The files extracted by the Extract vignette according to prediction or validation tool are automatically copied there during the extraction process for backup 5 3 6 3 2 PID_process Pid_results Dat1_validated The files processed in the Load vignettes from folder tool are automatically copied there during the process They contain the validated Ids in their last column 5 3 6 3 3 PID_process Pid_results Pid_predicted User should move there the PID files from the Pid_results folder that have been predicted in order to avoid predicting them again in Plankton Identifier 5 3 6 4 PID_process Prediction We recommend saving there the results from the ANLYSIS in Plankton Identifier 5 3 6 5 PID_process Sorted_vignettes The vignettes extracted according to prediction will be stored there in subfolders for later validation by experts 5 3 6 6 PID_process Unsorted_vignettes_pid Not used for UVP5 and FlowCam 14 5 3 7 RAW folder This folder will contain the raw data to be processed 5 3 7 1 UVP5 The folders downloaded from the UVP5 HDRYYYYMMDDHHMMSS must be placed there to be then imported filling the metadata UVP5 download data tool does it automatically 5 3 7 2 FLOWCAM The folders containing the raw images from the Flowcam must be placed there The folders names must start by flowcam_ in order to be detected and imported2. 1 ImageJ is in the public domain 2 5 3 Install ImageJ for Windows system 64bits W7 and W8 This operating system allows to scan and process both Large frame images at resolutions up to 2400dpi and Narrow frame ones at resolutions up to 4800dpi providing that you have 8Gb of RAM There is no improvement in the process speed with more RAM Zooscan models that can run with this operating system e Biotom e Hydroptic V1 e Hydroptic V2 e Hydroptic V3 up to 4800dpi Use the installation files provided for these OS W7_64bits zip amp W8_64bits zip 6 Install first the ORACLE Java machine provided in the install archive jre 6u29 windows x64 exe 7 Install then ImageJ from the same archive 1j141 nojre setup exe ImageJ must be installed in a folder that users can write in like My documents 8 Define the path to the Java machine java exe that you have previously installed It can be done when asked by the ImageJ installer or later modifying manually the ImageJ cfg file from the ImageJ folder C Program Files Java jre6 bin javaw exe Xmx6000m cp ij jar ij ImageJ 9 Set then the memory in ImageJ to 2 3 of the RAM available on your computer 10 Restart ImageJ to check that the memory is well set 2 5 3 1 ImageJ start error message Java Virtual Machine Launcher x amp Could not create the Java virtual machine If you get this message you have can try to modify the memory manually in the ImageJ
3. Use the installation files provided for this OS WXp_32bits zip 1 Install first the ORACLE Java machine provided in the install archive jre 6u29 windows x64 exe 2 Install then ImageJ from the same archive ij141 nojre setup exe and define the Java machine above when asked to Set then the memory in ImageJ to 2 3 of the RAM available on your computer A minimum of 1680Mb is requested to process Large frame images acquired at 2400dpi 3 Define the path to the Java machine java exe that you have previously installed It can be done when asked by the ImageJ installer or later modifying manually the ImageJ cfg file from the ImageJ folder C Program Files Java jrmc 3 1 2 1 6 0 bin javaw exe Xmx1680m cp ij jar ij ImageJ 4 Set then the memory in ImageJ to 2 3 of the RAM available on your computer 5 Restart ImageJ to check that the memory is well set Note to ZooImage users You may also encounter some problems with the ImageJ version which is automatically installed in the ZooImage bin ImageJ folder if ZooImage has been installed You can decide either to upgrade this version and place the Zooprocess macro files in Zoolmage bin ImageJ Macro and Plugins folders or to install a new version in the root program files folder of your PC recommended Check the ImageJ shortcut on your desktop to launch the right ImageJ version Check version as described above It must be 1 410 now About ImageJ iva 1 6 0 14 22MB of 1640MB
4. We recommend to install the computer OS on a small 20 30 Go boot hard drive C or D The computer should have at least an additional large capacity hard drive for images D or E On some computers we observed that a requirement is in the order of the drives the CDROM letter appears in the last position i e F Otherwise you may have an error message when launching the ZooProcess macro We also use Zooprocess on network drives to ease data sharing We also recommend keeping the Zooprocess computer free of software that is not requested for the Systems operation and checks This is the simplest way to avoid any conflict with ImageJ and Java NEVER update ImageJ orr JAVA unless requested by further version of Zooprocess 2 2 Operating System specifications Zooprocess is compatible and tested with the following operating systems e Windows XP pro 32bits SP3 not recommended anymore e Windows 7 pro 64bits e Windows 8 pro 64 bits tested only with V3 model We support ONLY Zooprocess for these systems We know that some users of Windows SEVEN 32bits are running the different tools with no difficulty Even if we DO NOT support Zooprocess on this OS it may be considered as Windows Xp 32bits and utilized with the same installers and configurations Windows 8 users will proceed as for Windows 7 operating system NOTE support can be provided only for the above OS and for the latest release of Zooprocess Check for updates before
5. Java machine 2 ImageJ 3 Tanagra 4 Pid Viewer 5 PKId 6 Xnview 2 1 5 OTHER 1 Java machine 2 ImageJ 3 Tanagra 4 Pid Viewer 5 PKId 6 Xnview 2 2 Install Zooscan driver Connect the Zooscan 2 1 Launch the selected installer epsonxxxx exe 2 3 Turn ON Zooscan 2 3 Install Vuescan 1 Launch the selected installer 2 DO NOT install drivers for old versions 3 Launch Vuescan and enter the license information provided in the documents delivered on the memory stick with the Zooscan Contact Hydroptic if necessary 2 4 Install JAVA USERS must run ImageJ with the provided JAVA machines NEVER update Install ONLY the jre 6u29 windows i586 s exe JAVA machine on 32 bits systems Install ONLY the jre 6u29 windows x64 exe JAVA machine on 64 bits systems 2 5 Install ImageJ 2 5 1 ImageJ version Only the version 1 410 of ImageJ should be used for Zooprocess above version 7 00 2 5 2 Install ImageJ for Windows systems 32bits Xp pro SP3 These systems allow to scan and process both Large and Narrow frame images at resolutions up to 2400dpi The requested size of RAM is 2Gb There is no improvement in the process speed with more RAM Zooscan models that can run with these operating systems e Biotom e Hydroptic V1 e Hydroptic V2 If ImageJ is already installed on your computer check the version e Launch ImageJ e Help e About ImageJ If version is not 1 410 you have to perform installation
6. when filling the metadata The raw images must be named rawfile_xxxxxx tif where xxxxxx is the image index It is recommended to configure the FlowCam application to directly save data AND all raw images there 5 3 7 3 GENERIC The folders containing the raw images from the generic instrument must be placed there The folders names must start by generic_ in order to be detected and imported when filling the metadata The raw images must be named _xxxxxx fff where xxxxxx is the image index The image format fff can be either TIF jpg JPG or BMP 5 3 8 Work folder This folder will contain the folders of the processed samples profiles images 5 4 Fill in metadata tools UVP5 FlowCam amp Generic When launched the tool displays the list of available RAW samples profiles that have not yet been documented and imported Select the profile and fill the information sheet following the recommendations The data from the previous profile are automatically displayed in order to facilitate the filling Do not forget to modify the requested fields A new subfolder containing a metadata file is created in the work directory for each of the samples profiles A global metadata file is filled in the meta folder 15 5 4 1 UVP5 metadata x Filename RAW 20130119091754 Cruise sn008_qualif Ship sagitta i Profile Id must start with alphanumeric characters Stationld ptb on Bottom Depth m CTD refe
7. 1 Introduction This manual has been written as a reference document for the Zooprocess software The new Zooprocess 7 16 and above versions are now fully compatible with the following instruments Zooscan Underwater Vision Profiler 5 including piloting tools Flowcam Almost any other imaging instrument making not too big images microscope ISHS gt generic VVVV Do not hesitate to contact me if you want to add any instrument and use the complete image process and Plankton Identifer system This manual contains gt Installation of Zooprocess gt Use of Zooprocess for FlowCam UVP and GENERIC 1 1 Related documents e User should refer to the Hydroptic manuals for Zooscan and UVPS e General methods are presented in Gorsky et Al 2010 Picheral et Al 2010 e Scanning an processing procedures with ZOOSCAN are described in SHORT MANUAL TO SCAN and PROCESS SAMPLES with the ZOOSCAN e Computer assisted zooplankton sorting protocol for all instruments is described in ZOOPROCESS PLANKTON IDENTIFIER PROTOCOL for COMPUTER ASSISTED ZOOPLANKTON SORTING 1 2 About Zooprocess Zooprocess is a suite of routines in ImageJ macro language It is thus free for all users and everybody can adapt it to its needs We would appreciate if people share the new tools that they develop with the Zooprocess community and inform us if they use it email to marc picheral obs vlfr fr Zooprocess has been developed for our use by
8. 8 2 3 Tostal V escahesesi iriiri EA E ER N 8 24 Jnstall JAVA ceren iaa a a a A aa raaa 8 2 9 Install Image sscrrsisinseoisriceniiesiargnaeoi ene eesi REE EEE EREE TEE 8 2 5 1 ImageJ VersSioh sinorsisessisisiiineiaa nioi EEE E a a aE 8 2 5 2 Install ImageJ for Windows systems 32bits Xp pro SP3 ssesesesessesssssessssesses 8 2 5 3 Install ImageJ for Windows system 64bits W7 and W8 sssssesssesesesesssssrssseessse 9 2 5 4 Install OPTIONNAL RS232 tools UVP5 pilot module only 0 0 0 eee 10 2 5 5 Install Zooprocess first installation ceeeceeeeseeceeneeceeeeeceeeeeceeneeceeeeessteeeeeeees 11 2 9 0 Update ZOO ROCESS sax jane ae E E ne cen ee 11 3 4 5 First start of ZOOPT CES Stn A ete tes date E alleen A E A E 12 Organization Of TOGIS sicsiccsscesdiesncceetarecccadibadsacsgansedaissdraidesascassasdeeedsa AE aS iea riia beaa 12 Zooprocess tools for UVP5 Flowcam amp Generic 0 0 ceeesecesseeceeneeceeeeeceeeeecseeeeeeteeeesaes 13 5 1 USER ADVANCED OPNS ne ra iie EEE aes E EE 13 5 2 LAUNCHING INTERRUPTING ZOOPROCESS ceccceesceeceeeeeteeeeeeeeeeeeeeenaees 13 5 3 Create project UVP5 FlowCam amp Generic sssesssessssseesseesseesseresseessseessresseessee 13 5 3 1 BACK folder FlowCam On1y cisiv icscsavsccsssissdraccutaschesasdevessadbesaceasadeeesstsaveavesdesnctes 13 D2 OMNIS MONET Suk ies ch E E EE deuce E T 13 5 0 0 Confis folder UVES ONIY Jroen i a E eae es 13 5 3 4 Ctd_data_cnv folder CUVPS on
9. CLOSE ALL OTHER APPLICATIONS BEFORE LAUNCHING ZOOPROCESS LET ZOOPROCESS WORK DO NOT TRY ANYTHING DURING PROCESS When started for the first time Zooprocess automatically creates the proper folders and configuration files on the selected drive We recommend installing the Zooprocess root folder on the C drive and the projects folders in a separate large capacity drive There must be at least 1 Gb Windows Xp or 4 Gb Windows 7 of space on the drive that will contain the Zooscan root folder If it is the first time you start Zooprocess or if you had already installed versions below 7 00 of Zooprocess you will get an initial screen asking you to install Zooprocess and select the Zooprocess root folder No data will be saved there except some configuration files and some temporary files Please allow anyhow 500 Mo of memory on the installation drive for temporary files saving Zooprocess will create the necessary files on the selected drive and ask you to choose an instrument This instrument can be later changed in the main menu Zooscan and UVP5 users will be asked to provide information provided with their systems You will then be asked to create a first project for this instrument Zooprocess will not work properly if you do not create import a first project at that step Do not hesitate to create a test project at this stage You will delete it later To import existing project just enter its name in the creation tool removing th
10. Marc PICHERAL CNRS UPMC LOV Station Zoologique BP 28 La Darse 06234 Villefranche mer T l 4 93 76 38 08 Fax 4 93 76 38 34 Email marc picheral obs vlfr fr ZOOPROCESS MANUAL ZOOSCAN UVP5 FLOWCAM GENERIC Laboratoire d Oc anologie de Villefranche sur mer updated for versions above 7 16 2013 10 24 l Tntrog ction seanair ta reina A Ea E A led E RNE EA 3 1 1 R lated documents visiaaravenetaveavuannsednonensase ira eera e sa E E EEEE EEE S 3 1 2 About ZOOPTOCESS ossis aise tec ced et ice diusaceaedctalcgidadanecaadetigeclas ian aelieie oceans 3 2 Tostal Sy A cee eee esac ed E EE E ns tegen twee 4 2al Comp t r SSC INC ALOIS ssisosesiiroeer tinana EEE E E 4 2 2 Operating System specifications eesesseseesreeseesssetererrtesttsrrsrresersrtsrrestessreeresresseeers 4 2 1 Operating System Regional Settings sesseseeesessesersrrsrirsrrssrsersrressrssrerresseseresresseeee 5 2 2 Proyidsd installation files scese EE 5 2 1 Installation seguent siryen E EE E EEE 7 2 1 1 Scanning and working with Zooscan esseessesesesessesseseresressessresrenstrseeeresseesseeereses 7 2 1 2 Working with Zooscan Gata sces iacpociecsis cezeliexssetatfenuiadebeledhiieedsidceeeadeiabedsiagedeenaels 7 21 3 R nnimne UVP ere cense ee E E Re EPES EES Eas 7 2a Working with UVP datassesitoersneen e a E EE 7 2145 OTHER penisie r AE A E E E ERE E E 7 2 2 Jnstall ZOOS ANAM Cl oisi soisencerensi ai e ea aE NEEE EES
11. Marc Picheral who is not a professional programmer It is still in development and new versions will be posted on our Website We consider that the file formats and project architectures will not be modified In any case ascending compatibility will be kept The Zooprocess manual is regularly updated on the Zooscan website http www obs vifr fr LOV ZooPart ZooScan or www zooscan com Please check that you have installed the last version before proceeding We support ONLY the last version Please refer to ImageJ and Zooprocess in your publications The reference publication for Zooprocess is J Plankton Res Gorsky et al 32 3 285 2 Install softwares 2 1 Computer specifications DO NOT USE any BI PROCESSOR computer Multicore computers are OK e 2 Go of RAM is necessary to process the Zooscan 2400 dpi images on Windows Xp pro systems 32bits We no longer recommend these systems which are now obsolete e A minimum of 8 Go of RAM is requested on Windows 7 pro 64bits and Windows 8 to process the 4800dpi images e A 1280 x 1024 monitor is a minimum for the Zooscan We recommend 1680 x 1280 for better image viewing The minimum vertical resolution is 1024 dpi for the ZOOSCAN tools limiting the use of most laptop PC e The computer should have a good graphic card e A mouse fitted with a roll button is requested for most of the manual graphic tools measurements tag separation identification vignette display from graph
12. an Biotom amp Hydroptic V1 8 4 57 8 3 23 4 Vuescan Hydroptievs NA Drivers Biotom amp Hydroptic V1_ epson12181 exe Drivers Hydropticv2 epson13552 exe DriversHydroptic vs wA ij141 nojre setup exe JAVA machine installer jre 6u29 windows i586 s exe PKId Installer PkID_Setup126 exe Pid viewer installer PID_viewer_Setup exe Tanagra installer setup_tanagra exe vuesca8457 exe vuex6490 wex6490 exe nat tested not tested 9 0 51 not tested nat tested epson15196 exe 8Gb ij141 nojre setup exe ij141 nojre setup exe PkID_Setup126 exe PkID_Setup126 exe PID_viewer_Setup exe PID_viewer_Setup exe jre 6u29 windows x64 exe_ jre 6u29 windows x64 exe setup_tanagra exe setup_tanagra exe RS232 for UVP5 piloting module rs232_w32 zip 1 232_w64 zip not tested See the ZOOSCAN manual for the specific drivers and software and installation Vuescan Install the tools following the list of chapters below 2 1 Installation sequence These sequences must be done following the indicated order N ok ok COON DOES Scanning and working with Zooscan Zooscan drivers epsonXXXXX exe Vuescan Java machine ImageJ Tanagra Pid Viewer PKId Xnview 2 1 2 Working with Zooscan data 1 Vuescan 2 Java machine 3 ImageJ 4 Tanagra 5 Pid Viewer 6 PKId 7 Xnview 2 1 3 Running UVP 1 Java machine 2 ImageJ 3 RS232 piloting tools 4 Tanagra 5 Pid Viewer 6 PKId 7 Xnview 2 1 4 Working with UVP data 1
13. any enquiry 2 1 Operating System Regional Settings You must configure the computer to use dot between integers and decimals Customize Format Numbers Currency Time i Date Example Positive 123 456 789 00 Negative 123 456 789 00 Decimal symbol j No of digits after decimal 2 X Digit grouping symbol X Digit grouping 123 456 789 Xz Negative sign symbol X Negative number format 1 1 X Display leading zeros 0 7 3 List separator 5 X Measurement system Metric 7 Standard digits 0123456789 x Use native digits Never x Click Reset to restore the system default settings for Reset numbers currency time and date 2 2 Provided installation files The table below indicates the files to be used according to your Zooscan version and your Operating System If you install Zooprocess for Other systems than ZOOSCAN you do not have to install Vuescan and the drivers These files can be downloaded on the memory stick provided with the Zooscan and from the Www zooscan com website Operating System Windows Xp pro 32bits Install Archive W7_ 32bits zi RAM minimum recommended 2Gb Compatible Zooscan Biotom Hydroptic V1 Hydroptic V2 N A Windows SEVEN pro 64bi Windows 8 pro 64bits W7_64bits zip W8_64bits zip not tested Hydroptic V1 not tested Hydroptic V2 not tested Vuescan installer vuesca8457 exe Vuesc
14. config file e Open the ImageJ cfg file from the ImageJ folder and manually change the memory reduce it in the third line of the file and try again to start the software Note if you reduce the ImageJ available memory below 1640Mb for Windows Xp 32bits you may experience memory errors during the Image processes of 2400dpi images 2 5 4 Install OPTIONNAL RS232 tools UVP5 pilot module only RS232 for UVP5 piloting module rs232_w32 zip rs232_w64 zip Quit ImageJ Extract the ZIP archive adapted to your OS Move RXTXcomm jar and serial_ext jar into ImageJ plugins folder Move rxtxParallel dll and rxtxSerial dll into Program Files Java jre6 bin folder Restart ImageJ 10 2 5 5 Install Zooprocess first installation 1 Extract the text files from the Zooprocess_version_x xx zip archive from Zooscan memory stick or from Zooscan website into the ImageJ macros folder and replace all previous files 2 Move free_memory class and free_memory java and all class and java files from the ImageJ macros folder to the ImageJ plugins folder 2 5 6 Update Zooprocess If your actual version of ImageJ is suitable for the last version of Zooprocess you can update Zooprocess by downloading only the Zooprocess_xxxx zip archive containing the macros of the software Extract then all files into the ImageJ macro folder and REMOVE the previous Zooprocess_ txt file if exists from the ImageJ plugins folder 11 3 First start of Zooprocess
15. ct They should not be modified 16 5 4 2 Flowcam metadata To do document the fields 5 4 3 Flowcam generic To do document the fields 5 5 Process Background Flowcam According to the configuration file you can either create manually a background from selected images or let the application make backgrounds at regular intervals that you will define The background images are saved in a dedicated folder 5 6 Process DAT BRU PID and VIGNETTES UVP5 This tool accomplishes the necessary processes from the raw data and image to the final dataset It can automatically skip already processed samples profiles and allows batch or individual sample profile treatment e If some profile folders are missing in the work folder they are automatically recovered to allow their process e It sums the different DAT files in a single one removing the wrong lines and changing the separators to and saves the results in the sample folder of the work directory e It sum the different BRU files in a single one removing the wrong lines and changing the separators to and saves the results in the sample folder of the work directory e If the UVP5 raw images are full images not vignettes it extracts the vignettes in a vignettes sub folder of the raw sample folder e If a FULL mode has been selected for the acquisition the BRU and DAT files are reprocessed from the RAW images e It process all vignettes and crea
16. e instrument name and the following _ Be careful when connecting network or external drives containing backup copies of projects Select the proper on to work with in the starting page of Zooprocess 4 Organization of tools The Zooscan users should refer to the dedicated manual We describe below the use of Zooprocess for other systems The tools for both systems are grouped in 4 sections 1 METADATA filling 2 Image and file process 3 Identification and validation linked with PLANKON IDENTIFIER 4 Settings and other useful tools All the existing projects are automatically listed and become available version 7 00 When you have processed one tool the project remains selected and you are asked again to select a tool and process it in the same project 12 5 Zooprocess tools for UVP5 Flowcam amp Generic Tools are presented in the order they should be utilized for a normal data process 5 1 USER ADVANCED options New created project are set to the default USER mode This mode gives access to all necessary tools for daily work with the selected system Anybody can switch from USER to ADVANCED and back using the corresponding menu The ADVANCED mode provides more tools and more options for many tools We do recommend keeping using USER mode for daily work and limit the use of the ADVANCED mode USER mode tools are described first 5 2 LAUNCHING INTERRUPTING ZOOPROCESS Zooprocess will start automatically when you
17. her instrument The tool allows switching to another instrument to work with Zooprocess 5 10 Edit Modify Metadata The tool allows selecting to edit and modify the metadata previously entered Almost all files containing metadata will be corrected providing that they are in the proper folder The list and location of all corrected files is displayed at the end of the operation 5 11 UVP5 pilot module e See UVPS manual 20
18. in the Field Of View of the UVP If the FOV is 152 x 114 mm for the 1280 x 980 CCD the pixel size will be 1280 152 0 118 0 174 for sn001 0 118 for sn002 18 Threshold for segmentation will be utilized by Zooprocess to extract vignettes from full images and or to extract objects from the background of vignettes 252 for sn001 235 for sn002 Gamma for vignette display 0 5 5 Utilized to enhance the visual aspect of vignettes It has no effect on measurements Length of scale line mm length of the scale bar in vignettes It utilizes the Pixel size Process option define the number of variables to be measured for each object It should be set to ADVANCEDi to allow the computing of the Areai that is the same than the one issued from the BRU file Minimum depth to start process vignettes m It helps removing the vignettes from the surface standby in addition with the First image OK defined in the metadata for each sample ESD min mm not utilized as the minimum size for the vignettes creation is defined in the modfile by the SMZOO parameter ESD max mm can help remove too big targets Modfile parameters they should all be recovered from the hdr file of the profile The threshold will be utilized for the computing of Areai see above Vignette ratio not utilized Flowcam Configuration file Method to subtract background should be set to Automatic_N Mimg as the rolling ball method is extremely time demandi
19. l BRU files All BRU files from the same profile are added and data lines edited for easy post processing in Matlab Resulting columns are Image Number same as in DAT Object number in the Raw image sorted by decreasing size Surface Area in pixel Grey level 0 256 X position of gravity center Y position of gravity center The resulting BRU file is saved in the Results folder of the project ANRWN PID files Zooprocess creates a unique PID file for each profile The file is saved both in the profile folder and in the Results folder The depth is included as a variable and the Areai too if the advancedi method is selected in the configuration file default after 2011 10 Note There is no relation between the vignette numbering and the image numbering 5 7 Process PID and VIGNETTES Flowcam amp Generic This tool accomplishes the necessary processes from the raw data and image to the final dataset It can automatically skip already processed samples profiles and allows batch or individual sample profile treatment e It extracts the vignettes from the RAW images after background removal and creates o Enhanced vignettes containing scale bar and information o PID files 5 8 Edit configuration file The tool allows modifying or creating a new file which will define the processing parameters for the project 5 8 1 UVP5 Configuration file See the UVP5 user manual e Pixel size mm true size of a pixel
20. launch ImageJ You can also restart Zooprocess pressing the Z key Note that the S key is utilized to interrupt a process waiting automatically to a stage that will allow easy restart without corrupting any file 5 3 Create project UVP5 FlowCam amp Generic This tool creates a project where the RAW data from the instruments will be placed and then processed The project is a directory whose name starts by the drive and instrument s name UVP5S projects will contain the serial number of the utilized instrument automatic We use to create projects associated with cruise legs A project contains different subfolders for different purposes 5 3 1 BACK folder FlowCam only The averaged background images for the FLOWCAM will be saved there in distinct sub folders 5 3 2 Config folder The configuration file defining the processing parameters is saved there User can create different files using the Edit configuration file tool but we recommend keeping only one file to avoid confusion in the process Some zooplankton list of groups is automatically created for UVP5 and FlowCam User can edit them with WordPad and modify them They can also be used by Plankton Identifier to create the learning sets categories We recommend copying these files in the LIST sub folder of the PKId folder program 5 3 3 Config folder UVP5 only Specific uvp5_settings subfolder of Config folder is created with necessary files to pilot UVPS
21. ly ssccisscsdeassccecarasessacetaseaeassactsdaatasusses ancs seectaseasacens 13 5 3 Meta tolder aeiio e inte cc E E oh E S EITS 14 5 3 0 BID Process TOMER a prunon a E T ele aad 14 Ded RAM OE a E A ea teats nanmeenearees 15 dee AW OE foldet inorren ee Mente at teh att Salen Tal sa tats Got oh saath oan ah Maat 15 5 4 Fill in metadata tools UVP5 FlowCam amp GeNneric cccccessescccececeesessneceeeeeens 15 Dic MIN PS Metadata aona a a icon a T E a OA E 16 542 Flowc m metadata coenen e E E A E ues anges R 17 5 4 3 Flowcam pener Cersei aieiaa e Ea RES aE oaii A EEEE 17 5 5 Process Background FlOWCaM ccscccsscssssccesssccssssssessscssssescessacescnenesenasesenscesens 17 5 6 Process DAT BRU PID and VIGNETTES UVP5 cc cecceeeccececceeeesessnteceeeeeens 17 So E Ana a ES E E E 17 5 7 Process PID and VIGNETTES Flowcam amp Genetic ccccssseccceceeeesessnseceeeeeens 18 5 8 Edit configuration file sesreecseso eiennenn aa e a E E E 18 DO UVP COME Suan e ne ics oa o aS a R AA AEE are ERES 18 5 8 2 Flowcam Configuration file nsei i a EEEE E E 19 5 8 3 GENERIC Configuration file sicccvesiscistesdeasssusidasvesgoieis vaceaneadegdadeasusids roan goaate bodtacees 20 5 9 Select another instrument cc eoistcs cits ccsdeak aduesedeaeeassausgaatsy ues can aucgads seca utessuns tanseeseeeds 20 SO Edit Modify Metadata sron enni es e stacey baey a a E saaeonenass 20 SLL HUN PS pilot module e A E a uae Sande ee 20
22. ng Number of images to average in background should not be set above 10 An average of 5 images is correct User will anyhow be asked to confirm this value at the time of the background process Used only for average_image option creating a unique initial background Rolling ball value see above Pixel size for cell 4x um comes from the FlowCam calibration Pixel size for cell 10x um comes from the FlowCam calibration Threshold for segmentation will be utilized to extract objects from the background of images 245 for our Flowcam Gamma for vignette display 0 5 5 Utilized to enhance the visual aspect of vignettes It has no effect on measurements Length of scale line um length of the scale bar in vignettes It utilizes the Pixel size Process option define the number of variables to be measured for each object It should be set to ADVANCED ESD min um minimum size of objects to be analyzed ESD max um can help remove too big targets LUT offset not utilized LUT slope not utilized Maximum number of IMAGES to be analyzed stop criteria Maximum number of OBJECTS to be analyzed stop criteria Remove objects touching sides helps remove truncated objects Remove duplicates helps remove duplicates objects sucked in the cell Grey level auto adjust helps compensate for variations of image intensity over time for one sample 19 5 8 3 GENERIC Configuration file e To be later documented 5 9 Select anot
23. refer to UVP5 manual 5 3 4 Ctd_data_cnv folder UVP5 only Created only for the UVP5 projects the user should place there the CTD files acquired simultaneously with the UVP images The CNV files must include the header 13 5 3 5 Meta folder A unique file containing the metadata of all samples profiles will be created and completed there This file must not be deleted and user must be careful in attempting to manually modify it It is preferable to use the EDIT amp MODIFY METADATA tool for that purpose 5 3 6 PID_process folder This folder contains all sub folders necessary for an easy identification and validation of the specimens User can refer to Plankton Identifier manual AND short user manual on the website http www obs vlfr fr LO V ZooPart ZooScan article php3 id_article 170 5 3 6 1 PID_process Learning_set The different learning sets applicable for the project should be created copied in this repertory This is not mandatory for Plankton Identifier but helps much avoiding confusion It is possible to place there only the LEARN file that will be utilized to predict identification of specimens for the selected project 5 3 6 2 PID_process Pid_results The PID files issued from the process will be copied there The predicted files dat1 txt files issued from the prediction from Plankton Identifier should be placed there for the Extract vignette according to prediction tool Refer to identification tool chapters
24. rence filename Latitude 12 76398 for 12 76 398 S Longitude 135 45325 for 135 45 325 W N First Image OK Last Image OK if not max depth Yoyo Y N Image volume aa Exp Day Night Wind dir degree Wind speed knts Seastate Nebuloussness 99 if not observed Comment Cruise should not be changed issued from the project name Profile Id unique name associated with the profile can include station name There can be many Profile Id performed during a unique station This name CANNOT be later changed Station Id Name of the station where many profiles can be performed CTD reference name can help associating CTD data to UVPS5 data Latitude and Longitude watch the described format just enter it as you read it from GPS replacing by First Image OK to be read in the DAT file of the profile HDRYYYYMMDDHHMMSS_XXX dat This number will be the start of the descent see UVPS pilot tool manual Last Image to be modified if the I O mode has been selected or if multiple profiles have been performed as a yoyo during a unique acquisition sequence Kept set to 99999 if not to be set Yoyo to be set to Y if a single sequence contains multiple profiles CANNOT be later modified All profile metadata of a unique sequence must be filled in the same metadata filling session Image volume aa Exp parameters provided in the documentation of the instrument and filled when you created the proje
25. te o Enhanced vignettes containing scale bar and information o PID files 5 6 1 Resulting files Images All vignettes issued from the source RAW directory of each profile are converted in JPG images A legend is added to detail the scale the profile name the raw number of the source image same than in the DAT file If you have acquired full images instead of thumbnail images of ROIs the vignettes will automatically be extracted from them Note Only vignettes below the minimum depth set in the config file and after the First Image set in the metadata are kept for process The image process will stop after the deepest image or the last image set in the metadata DAT files All dat files from the same profile are included in a single datfile Incomplete lines from the top of the firt DAT file are removed The resulting datfile is also saved in the Results folder of the project index image sensor data nb blobs P G mean area P G mean grey P G nb blobs G mean grey G 1081 20130119092129 812 00606 00169 00169 00012 02612 02325 01164 01003 00836 00409 00592 00719 7155 2 25 1 87 17 Index image NUMBER Image date and time of the acquisition of the image Sensor data 00606 60 6m 00169 angle x2 0012 internal UVP temperature 02612 26 12 battery Volt other CAN input if connected to sensors 755 number of small P G particle image 2 mean area pixels of these particles 25 mean grey leve
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