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User guide - Noesis

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1. ma Eje EE oF les ojojejo le La Fremer TNPC User guide March 2011 Chapter 1 Generalities 4 The TNPC interface 1s split between the global information and seven tabs e Acquisition e Annotations e Shape analysis Expert mode e Live Expert mode e Apprenticeship of individual age Expert mode e Automatic estimation of individual age Expert mode e Automatic estimation of age structure Expert mode Figure 1 3 TNPC User Interface Reader Jean Work directory C Program Files Noesis TNPC5 Species Lemon sole Suffix seapesesessesogeogpegescoosoos a ay Sy i D E SM image_001 yw a Files Pe Database Ah Stage La Tnpes The global information are present whatever tab 1s selected It gathers general information asked at TNPC start up such as e Reader By default it is the name of the current Windows session e Work directory The directory where all the files you are working on are located e Species The species you are working on e Suffix This suffix can be chosen by the user to distinguish the files treated by TNPC and the others It is added to all the images generated by TNPC This is the only point that is not mandatory fremer TNPC User guide March 2011 Chapter 1 Generalities 5 Figure 1 4 Global information input Global information Reader Jean Sui Ean Work directory C Program FilesSNoesis s T NPCS images Y Species American sha Calibration no_
2. Figure 3 10 Autofocus parameters Z motion tab Ed Parameters os e Trajectory A Stage Microscope Autofocus Lens v Sd 1 Magnification A 1 Z mation Acquisition Interval Absolute y C Relative Z min A o0 Z max 0 Steps Criteria Pass 1 9 0 D 1 Pass 2 B 0 1 Do Fast 12 E Display A Save w Reset ES Setting Help a The number of the lens you are editing The number of the magnifier you are editing y Whether the upper and lower limits of the autofocus range are defined in absolute or relative coordinates If relative coordinates 1s selected a mean Z value 1s used in the pad center The lower limit when in absolute coordinates or the mean value when in relative coordinates Value is in motor steps The upper limit when in absolute coordinates or the delta value when in relative coordinates Value is in motor steps The number of motor steps between scans If the value is too large you risk missing the ideal point D The minimal score for each scan It must correspond to the number of pixels considered as clear cut by the criteria calculation algorithm When to stop searching for the best possible image by establishing a threshold of motor steps between the two best images If the steps are two small the autofocus takes longer than necessary if they are too large the final point will not be accurate In practice it should be
3. manual Please refer to it for more information Figure 5 7 Measure bar ela ic Sea Sat 7 ul mier PY Mremer TNPC User guide March 2011 Chapter 6 Live Expert Mode 51 Chapter 6 Live Expert Mode 6 1 Generalities The LIVE mode allows you to acquire and annotates images at the same time If the zone of interest is bigger than the image size TNPC will automatically create a mosaic image Figure 6 1 Live tab PEF Create radial Add GR markers Add CH markers Open radial Delete all radials and markers Change radials and markers colors Perform interpolation 0900000908 Validate the radials and markers positioning and launch the mosaic creation if needed The information stored are configured in settings Open settings Start image acquisition Name used for the different file saved image radial results 6 2 Settings To display the settings tabs you just have to click on 6 2 1 General The general settings allows you to parametrize the name and number of the image acquired Figure 6 2 General settings Generic name Image _ a Number of nest record E 1 Mremer TNPC User guide March 2011 Chapter 6 Live Expert Mode 32 Generic name used for the saves image radials results All the files will be named by this name followed by a number Number of the next otolith that will be stored All the files saved image radials resul
4. KA STAGE IW dos aad 29 320 Trajectory COMA SUELO nt AS SATA ATA AAA 29 Jale Trajectory SOLIS AA AA AAA AR 30 3 22 Mosd acous Uon IMPLOSTESS ta a a a 31 3 23 Semi ditomatic slice acquisito a A A A A AS darn ceatds 31 324 Mosaic Tidal CREALION al dades 32 31205 Acu SHON Il SCAMMEL SOL Ware cai ee he 34 3 26 Parametrizing otolith separation during scanner ACQUISITION oooococcnconcnnoncnncnnononnonnnnonnononnss 34 Fremer TNPC User guide March 2011 TNPC Vill Alo ANDON tab ads 36 A2 EN 37 A MORE Sc GINO S oc np sa 37 A POCO SS SELLOS ESA SARA AAA E 38 4 5 Use Smooth function Before red After blue ooooococcccccconccnnncnnnonnnoncnonononcnonnnononos 38 4 6 Use Detrend function Before red After blue 20 0 cece ccc cece cece ees eeeeeeeeeeeeenes 39 4 7 Use Demod function Before red After blue o oooooccocccnnccncccnnncnnnonononononononanonononnnos 39 4 8 Use TopHat function Before red After blue ooooocococcccononconcnncncononcononnoncnnonnononoo 40 4 9 IMerpolation s ctas td A T 40 4 10 Back calculation settings ssl adidas 41 AS E Ad E ae hea tele ec hiaas ties 42 AND WO parts adi deals 42 ad CH marker AAA A A A 43 4 14 The Result Viewer with an intensity profile 0 0 0 0 ccc cece cece eee ec ee ee ee enc ee eeeeeeeeeneeeenaenees 44 AJO CNPG toolbar in Result VIEWER iaa ii is 44 4 10 Growth pattern Result VIEWER rca o recado cla Tae 45 417 Nume
5. O02 44 66 068 1 12 14 16 16 2 22 24 26 28 3 32 34 36 38 4 42 44 46 46 5 52 54 56 58 6 plaice EC_2006_Q3_WT_5 X 4 00 Y 118 73 4 5 Numerical results The can also be used to build tables containing results about the growth and age and more precisely e the age the otolith s growth pattern e the position of the false rings or checks the back calculated fish length 1f the option is activated The calculations on the current image are added to those from the previous images of the session Once all the images have been analysed the table can be exported to Microsoft Excel Those data can also be stored in the database This option must be activated in the settings See Section 4 2 Settings Figure 4 17 Numerical results in Result Viewer Growth pattern Rings std 10 70 23358 1695639 278 9276 370 2313 433 4415 477 5883 v 4 gt Growth pattern Rings mooo E F_ S Mremer TNPC User guide March 2011 Chapter 5 Shape analysis Expert Mode 46 Chapter 5 Shape analysis Expert Mode 5 1 Generalities The SHAPE ANALYSIS section allows the user to make measurements on the representative shapes of the observed CS Automated functions can extract edges and calculate interesting values for the shape but you can use the length measurement toolbar for manual processing You can perform the shape analysis on the current image or successively to the d
6. please refer to your scanner manual G Note On a scanner acquisition you can acquire several slices at the same time Just bear in mind that the quality might be poorer than using motorized stage and microscope TNPC will split the otolith from the slices to get one otolith per image To get a good split dispose your slices like on a grid with some space between each slice Use your scanner software to select the area to acquire and launch the scan Once the scan is performed TNPC get it back Warning Acquisition might be limited by your computer RAM G Note The otolith detection is always performed from the top of the image If all the otoliths are at the same height the detection is made form right to left Mremer TNPC User guide March 2011 Chapter 3 Image acquisition 34 Figure 3 25 Acquisition in scanner software Preview Zoom EPSON Scan Mode y EPSON Sca n Professional Mode 7 m Settings Name Current Setting Save Delete Driginal Document Type Reflective a Document Source Document Table X Auto Exposure Type Photo v Deg mtia Progress Scanning lalo Time remaining less than a minute Target Size Original w 688 H 143 fin E Scale 100 Y Trimming Off On Adjustments oa Reset El EN B J Sean F 1 49 in 16512 x 3580 pixels 169 12 MB Help Configuration Close You have to tell TNPC
7. then the RefBlanc picture can be full white and the RefNoir image can be full black 3 5 2 Make a mosaic of a slice You might also want to make a mosaic of a slice and then get an image per otolith on the slice There is two way to proceed Either way you first need to have a trajectory created see Section 3 5 1 1 Build a trajectory The first way to proceed is automatic TNPC acquires the mosaic and then perform the otolith detection To launch the acquisition click on The second way to proceed is semi automatic Click on i to open the menu Click on Createf to launch the mosaic acquisition according to the trajectory you created Then when the mosaic have been acquired click on Segmentation to perform the otolith separation When all the otolith are segmented click on Validatef to perform all the processes that are configured see Section 3 3 2 Process Figure 3 23 Semi automatic slice acquisition Create the mosaic image El Ef Create j Otolith segmentation I Ajgmentatior Add Remove otolith Fai Pfiemove W validate Mremer TNPC User guide March 2011 Chapter 3 Image acquisition 32 Create the mosaic image Launch the otolith detection Add an otolith to the automatic detection Remove an otolith from the automatic detection Validate the detected otolith and perform the processes 3 5 3 Make a mosaic from two images If you do not ha
8. 3 2 2 1 Standard acquisition The first thing to check is that you can perform a standard acquisition This should always be fine but you need to check it first before trying the stage To know how to make a standard acquisition refer to Section 3 4 Standard acquisition Check that the image you acquired is the one you wanted If so you can try making your first mosaic image If not please configure again your microscope 3 2 2 2 Mosaic acquisition You will then check that your motorised stage is well configured by performing a mosaic image To know how to make a mosaic using a trajectory refer to Section 3 5 1 Make a mosaic from a trajectory Check that the image you acquired is the one you wanted If not please configure again your microscope and stage it this happens again refer to the troubleshooting section 3 2 2 3 Troubleshooting When your mosaic does not look like what you are expecting there are some basic operations you can do to try to fix things e If you have a specific software for your controller for example if you have a Zeiss controller You can try to switch axis one or several Mremer TNPC User guide March 2011 Chapter 3 Image acquisition 25 e You can try to rotate the camera of 180 e Check that the camera is perpendicular to the motorized stage e Check that the stage is not tilt You may want to use a spirit level e Take care of the zoom conversion between the comman
9. AS US O SS E O A A E A E E AS A a 5 SEST a ASA E E RUE 7 Pot ft fT Ff fF tf ft ft ft AS E a s Lf E IS SS A E E E A A AO PA SS i IAS lt lt RUIDO O HE IS A LA A E E ee EA Radiale_001 Si 0 00 Val 136 00 Age 0 Ready a e ai 4 4 1 Intensity profile shows the intensity profile of the selected radial if the option is selected see Section 4 2 Settings You can perform different actions using the TNPC toolbar Figure 4 15 TNPC toolbar in Result Viewer Add GR markers see Section 4 3 2 Position markers Add CH markers see Section 4 3 2 Position markers Put to 0 parts of the profile Interpolate markers between two points of the profile Do the selected processes see Section 4 2 3 Process Expert Mode Undo the selected processes 9 O 5 0 O Mremer TNPC User guide March 2011 Erase the growth pattern chart Chapter 4 Annotations 45 4 4 2 Growth pattern The RESULT VIEWER can also show the growth pattern associated to the current image interpretation It can help the user to evaluate its interpretation s pertinence The growth pattern can be erased using BI Figure 4 16 Growth pattern in Result Viewer iaa Result Viewer Growth pattern odao M File Edit View Tools Show Display 1DProcess Window oj laj xalal a ajejaj e ole ajaja kli cajon 5 Elle 910 es El kel eje wlx ilice 1
10. Help By zone ae By points Setting Shape Rectangle E Circle By points Scan mode C Knight Spiral Raster m Number of fields e Percent C Fixed Edge Overlapping Yes O No Autofocus Yes No Z motion C Plane amp Last point Radius of focus points 2 100 The shape should always be a RECTANGLE The scan mode should always be RASTER You should always put here or you can have holes in your mosaic Edges should always be overlapping Indicate if the focus is automatic or manual O 3 Do not change this parameter 5 1 2 Make the mosaic When you are back on the TNPC tab you can launch the mosaic acquisition by clicking on 24 You will see a blue table whose cells correspond to an image The stage will move and the images will be acquired one by one You can follow the process on the table a red cross appear on the cells that have been acquired Mremer TNPC User guide March 2011 Chapter 3 Image acquisition 31 Figure 3 22 Mosaic acquisition in progress Trajectory Tnpc_Live_Traj GI eg Area all fields 4 35228 mm Nb Fields 6 Warning In order to get the mosaic acquisition to perform correctly you need to have two images names RefBlanc and RefNoir loaded in TNPC The RefBlanc and RefNoir images are used to fix the lighting drifts If the acquisition system got no lightning defaults
11. Microsoft Excel To do so click on FILE gt IMPORT EXCEL FILE You will have to choose the file you want to import and the database you want to create If the columns exists in TNPC they will be filled with the data present in the database If columns do not exist in the database they will be added Figure 2 6 Create a database from an xls file Import an Excel file into a new Database TES Excel file to import C Program Files Noesiss a E E y Browse Path of the new database C Program Files Noesis TN PCSimages DbFromExcel mdb y Browse W Cancel Fremer TNPC User guide March 2011 Chapter 2 Databases 12 Warning This way you cannot add data to an existing database the import will create a new database 2 6 Add images You have three ways to add images to a database you can add the current image an image or a folder of images FILE gt ADD CURRENT IMAGE Will add the current image to the database The amp button at the bottom of the database tab will do the same FILE gt ADD IMAGE FILE Will add an image file to the database You will chose the file and click on Open FILE gt ADD A FOLDER Will add all the images of a folder to the database You will chose the folder and click on OK 2 Move a database with its images To move a database with its images you should open it in TNPC and then change the DEFAULT IMAGE DI
12. This will realise export and save operations If you are using a database as source it will also load the next image If you want to analyse an image that have already been analysed you can click on 21 This will load the stored radial and markers 4 4 Graphical results The intensity profile and the growth measures linked can be visualized and analysed in the RESULT VIEWER Use the RESULT VIEWER toolbar to analyse interactively with the intensity profile markers positioning automatic age calculation interpolation fremer TNPC User guide March 2011 Chapter 4 Annotations 44 Figure 4 14 The Result Viewer with an intensity profile Em File Edit View Tools Show Display 1DProcess Window E x olala jajaj al sleja el 21e ajajaj klausli caja 5 Elle 8 0 s Mel cr Jelet lx ecele 12 POP e O E OS ER EEES E E ES EE ERES CE E EA E ES E ES ES EE CE EEES EA E pia i D CeCe CC Cl ES E ft ft ft ft ft tf ft tf ft tf tt PA O E SO ES E A A PE E e e 4 HY N o o O ae ae see a 170 a se E N yy a ee Peele rN O E E 130 ESA PA ERES ER a Th pis pf _ Oc06oo c 6 oeeo 110 ol a a ae de EME EEE RAEE ES ee on E a Lt gt Pot ft fT tT hE mE op ee i ia ES a Fa a a PS Te E 0 A A S i pa
13. Visilog Visilog Adjust low and high levels in the Adjust low and high levels in the grey ramp below the image then grey ramp below the image then Ok Ok press press Figure 5 5 Edge detection result 5 3 2 Otolith analysis Several parameters can be calculated from the otolith and stored perimeter surface Fourier moments see Section 5 2 Settings for more information To perform the otolith analysis click on If you have not done the edge extraction before it will automatically be performed at this time see Section 5 3 1 Edge extraction for more information The calculation is run and then you got the result in the RESULT VIEWER Figure 5 6 Analysis result waa Result Viewer Analysis anl_plaice_iceland_2006_Q2_RL_WL_370 2 S Lil File Edit View Tools Format Window E x palal jajaj a elal el alel ajaja hli aal e 83 B E F 9 Nb objects 1 Mremer TNPC User guide March 2011 Chapter 5 Shape analysis Expert Mode 50 You can then either quit the RESULT VIEWER and validate your analysis or continue analysing the image 9 3 3 Measurements The MEASURE BAR features all the tools needed to manually measure everything in an image To display this toolbar you can click on VIEW MEASURE BAR or on We will not explain the buttons as they are in the Visilog 6
14. also acquire mosaics of slices and separate the otoliths If you got a scanner you can also acquire otoliths using it 3 2 Configure stage microscope and autofocus Before using the acquisition for the first time you have to initialize the stage controller Gf any the microscope and the autofocus by defining certain elements for each in the STAGE tab To access those settings you have to open the PARAMETERS window by clicking on Y A window with four tabs appear The first tab is about trajectory parameters do not focus on it first you have to configure you hardware 3 2 1 Initializing the stage controller Initializing the stage controller consist in establishing the communication between the controller and the physical parameters of the system To access those parameters select the STAGE tab 3 2 1 1 Controller settings You first have to set the configuration of the electro mechanical system type of stage COM port etc in the CONTROLLER SETTING window To access it select the number of controllers your controller type in the drop down list and click on Mremer TNPC User guide March 2011 Chapter 3 Image acquisition 15 Note If you do not find your controller in the drop down list please contact Noesis company Figure 3 1 Controller settings f Controller setting 5 Type STEREO_USB my v Motion C Enabled PY Disabled Serial Port Ey Control lt ves O Cno Cont
15. eee eeeneea ene enees 60 7 10 Automatic estimation of age structure estimation results oooooooccoconcnncncononnononnoncnnonnnnonos 61 Fremer TNPC User guide March 2011 TNPC 1X List of Examples 8 1 8 2 8 3 8 4 8 5 9 1 Dize 93 9 4 eae Sentence 10 translate nda dai 62 Sentence translated 1M Spanish iS 62 The AOG tanos c Ne a idas 62 The peste suert HS nia A a 62 Me Ass peces CEO lO A A A E aaa 63 Pee Bose Py A A E e O a OP re ey er 64 POE OTIS COMIC DAA AAA AS Sit eed cin ed AS NN 65 SO E CONTEO La II IIS ds 66 Edie dae MMle COment sio 67 Measures ale Te COMER erario 67 Fremer TNPC User guide March 2011 Chapter 1 Generalities 1 Chapter 1 Generalities 1 1 Introduction TNPC 5 is a dedicated software aimed to assist CS 7 interpretation financed by the French institute IFREMER Several years have been necessary to develop this software The project begun in 1994 with Herv Troadec s work then other people contributed to it such as Ronan Fablet H l ne de Pontual and Andr Ogor TNPC provides several features that will be explained in details in this documentation e Manage databases of images and associated data e Batch processes on CS images e Image acquisition with automatic stage scanners mosaics e Save predefined data radials intensity curves and user data for example age interpretation TNPC is based on the Visilog 6 platform Most of the features are Vi
16. for Automatic Estimation cccccceceececeeeeseeeeeeeneeees 63 Fremer TNPC User guide March 2011 TNPC vi Sida your own Code DOOK S erena a a ae aera eh es 63 IS 0 8 0 0 1 HIES MU ene eee 0 E a S a a ten Oren mne rete erat 64 9 1 Radials eraa Giles ys AAA AAA AAA 64 dos Marker LO IES NA NR cal 64 OSs RO eS PES TES AA AA A 65 OG RINGS POSITIONS ACTES Y ici 66 OD Snape Analysis da TES A ESAS AA A A AE A AAA A i 67 A Lto Cameras supported by T NPC rrenean e N tiatlentaestiaatereia nes 68 Ac Ae TBR ELS 94 Cameras ut ts 68 IO 0 hers e UE O RO O 68 SS A A A usenet anaenkecaeian joer Stee Meaatamnena antambea a vonae 69 As SPOT oidor weaage nada 69 AL Hamama U A ES A A A E A ao 69 AALS Ballmer OPON C od o A iS 69 AZ ES B Camela S eai a r E O idiss 69 Ie Al EE E T e E AS E AE dtd abe E A NE E AET 69 A G Ethernet Cameras sia 70 A anata aate tel lan cit cee ihe ae atanena cutie lon cut caemnaties 71 COSSA ri cda 72 Fremer TNPC User guide March 2011 TNPC vil List of Figures Lek Install acquisition board AVers o 3 12 Visos 0 MN and ENPCE WiIndGw a ie wees 3 LS ENEE US e eo 4 14 Global OMndaGOm APURE A EA 5 LES Globalno maton A A A A meee Ges 5 126 Cabrio MIO aeron a A a aT E anatakeuen 6 17s Entet new CaliDravlOn Namie A AS AA a A A 7 UO SERES COOIDAL rs iia 8 ZA The New database Window ta aid 9 la AMA DAS E VIN S rte ceano ad caco A a coseno aaa aaa cane anaes poten 9 Zas TM VIEW P
17. set you can define the stage parameters You got four tabs for the minimum position maximum position center position and motor parameters 3 2 1 2 1 Minimum position The minimum position defines the software based minimum stop positions in motor step sizes for the X Y Z and R axes Select an axis and enter a value in the field To be more precise or if you do not know what value to enter you can select the current position by clicking Get To automatically search for the minimum position click on Go To t Warning Do not use Go Tol if one of your axis has no mechanical stops that could damage your motorized stage and your microscope Figure 3 2 Minimum position tab Minimum Maximum Center Motor Psx 1 rn Psr Pam 2 Pos 5 0 2 Oce d Ao The X coordinate of the minimum position The R coordinate of the minimum position The Y coordinate of the minimum position The R2 coordinate second rotation of the minimum position The Z coordinate of the minimum position Button to acquire the actual position coordinates Button to automatically go to the minimum position on each axis Mremer TNPC User guide March 2011 Chapter 3 Image acquisition 17 3 2 1 2 2 Maximum position The maximum position defines the software based maximum stop positions in motor step sizes for the X Y Z and R axes Select an axis and enter a value in the field To be more precise or if y
18. the icon left right up or down Once the radial 1s at the desired position you can continue the radial drawing by clicking on the image at the desired point 6 3 3 Position markers You can add GR and CH markers to the radial Click on y to add GR markers or on y to add CH markers and then click on the image on the marker position To remove a marker simply double click on it 6 3 4 Interpolation Activate the interpolation by clicking on Choose the zone of interest by placing two markers at the beginning and at the end of the zone and click OK on the pop up window A new window should pop up just slide the two markers at the start and end of the zone where new markers should be computed Just validate the choice by clicking on OK in the window 6 3 5 Validation and exportation Once you have drawn your radial and positioned your markers you can validate and store the image by clicking on This will create the mosaic needed perform all the processes you set up and store the image radials results according to the settings Mremer TNPC User guide March 2011 Chapter 7 Automatic estimation Expert mode 55 Chapter 7 Automatic estimation Expert mode The automatic estimation is a process that needs an opened database You first need to open the database you want to work on 7 1 Apprenticeship of individual age 7 1 1 Generalities To perform an automatic estimation of age you will need
19. then will be redirected to the VIEW PROPERTIES window To simplify view creation you can also create a view by cloning the current view using VIEWS gt CLONE CURRENT VIEW You will be asked to enter a name for your new view and then will be redirected to the View Properties window You can modify the current view by clicking on VIEWS gt MODIFY CURRENT VIEW You will be redirected to the View Properties window You can delete the current view by clicking on VIEWS gt DELETE CURRENT VIEW You will be asked for a confirmation We have just seen than you can create several views and that operations are always done on the current view To change view you have to select the view you want in the view list on the top of the DATABASE tab Mremer TNPC User guide March 2011 Chapter 2 Databases 11 Figure 2 4 Database views list plaice_EC_20 myD atabase rr Read Only test_view 2 4 Display information and images from a database To display an image from a database you have to select it and then double click on its thumbnail It will load it as the current image Interpretations and analysis can be loaded by clicking on the appropriate fields Figure 2 5 Image thumbnail plaice iceland 2C testview myDatabase mdb Read Only 2 5 Import database from an xls file You can create a database from an xls file coming from a spreadsheet software such as OpenOffice Calc or
20. to have a codebook Either a codebook is present for the species you are studying and you will not need to perform this step or you might want TNPC to learn how to estimate age through the estimation you already made To set up the apprenticeship of individual age select the APPRENTICESHIP OF INDIVIDUAL AGE tab 7 1 2 Settings Before launching the apprenticeship you have to fill in some required settings 7 1 2 1 Global information The first thing to do is to select the species you want to study and its ICES l zone 1 International Council for the Exploration of the Sea Fremer TNPC User guide March 2011 Chapter 7 Automatic estimation Expert mode 56 Figure 7 1 Apprenticeship of individual age Global information Segmentaion Nucleus detection Radiales Global informations Age Species Plaice a ICES zone 7D Eastern Channel 2 Select here the species you are studying y Select here the ICES zone of the species you are studying 7 1 2 2 Age In this tab you have to select the field in database where you estimated the age the number of age classes and the age of the first class Figure 7 2 Apprenticeship of individual age Age Segmentalon Nucleus detection Radiales Global informations A EE Age field Agel A Number of age classes c T Age of the first class a 0 Select here the field where you estimated the age in Insert here the number of differe
21. to the Visilog 6 Stage Module documentation 3 2 1 4 1 Autofocus settings To open the autofocus settings window click on Setting Figure 3 9 Autofocus settings Color plan Motion Algorithm Transmission EY Criteria Algorithm standard User VBA Project No project EY hd Motion Ea Criteria Hamaca P Cancel Choose here the color plan on which to perform the autofocus If you have a color camera you will save time if the autofocus is performed on a single channel red green or blue or on a reduced part of the image This is particularly important if you are working in reflection mode because unlike of transmission mode you will always have an image no matter what is on the stage The motion default autofocus parameter corresponding to your hardware light source transmission or reflection The criteria algorithm used on each pass The default one is Standard If you want to change this parameter please refer to the Visilog 6 Stage Module documentation y Options to define your own autofocus algorithm If you want to define your own autofocus algorithm please refer to the Visilog 6 Stage Module documentation 3 2 1 4 2 Autofocus parameters This tab allows you to establish the criteria for autofocus calibration The parameters you select are defined each of the lens magnification combination fremer TNPC User guide March 2011 Chapter 3 Image acquisition 23
22. 42 43 54 54 Results Automatic estimation of age structure 60 61 Automatic estimation of individual age 58 59 Growth pattern 45 45 Intensity 44 44 Numerical 45 45 Installation 2 3 Stage microscope 14 25 L Launch Global information 4 5 Fremer TNPC User guide March 2011 Glossary Glossary 72 This glossary explains all the important notions involved in TNPC A AFISA Allometry Back calculation C Calcified Structure CS Mremer AFISA stands for Automatic FISh Ageing This is a European research project aimed to develop standardised systems to automatically age fish stocks Those systems should reduce fish ageing costs and harmonized methods between the different European laboratories You can see the AFISA website http ec europa eu research fp ssp afisa en htm for more information Allometry is the study of the relationship between size and shape It is a well known study particularly in statistical shape analysis for its theoretical developments as well as in biology for practical applications to the differential growth rates of the parts of a living organism s body The relationship between the two measured quantities is often expressed as a power law such as W a L gt With W the weight of the animal body L the length of the animal body a the intercept and b the slope growth coefficient of fish relative growth rate The derivation of growth hi
23. A ES 49 Je Measure MENIS ti ara 50 O Live Expert Model doanaren irns E ieee inees tico cacas atado ooo aaa oia aos 51 Gl Generalltles aire 51 A O Mente nana eae den cteetecemcatt 51 OZ E 01 e II mses arenes E aes E teen te aaeee OE S51 022e CRECES aore a A E EE A E TE 52 02 ACQUISITION a AE EA E AAE 52 OA EKDOR as a ali 53 0 23 Back calculation A A AAA A waht 53 3 OIOHt Hve annotato tran ts tidad 53 6 3 1 Start Mage ACGUISINIOM aia ad id ios 53 SR E picmtion nena aeencaams cane sapmeatastasa A 54 03 07 POSITION MIKELE ita 54 6 34 gt Imerpo lao iaa tada 54 6 3 5 Validation and eXportation 2 A AAA AAA Ad 54 7 AUtomatic estimation Expert mode ui la lios 55 Tel Apprenticeship of individual age saoririinaiii e ued ANAE NN E ANENE 55 dle tt AAA A EA AN 55 PAZ SEM led 55 ls Create the leamos TIe taa ias did 57 7 2 Automatic estimation of individual age cece cece cece eee e eee e eect eee e ee eneeaeneeeenaenees 58 Taza baane Ane THE ESTIMA A A AA 58 TPZ RESIS cepa Taran etal a eteneisnateiiun ae ennges E eens crea 58 7 3 Automatic estimation Of age stricture 2 0 cece cce cece a aa ai 59 Tooke Launch Te CSUN ATION 1 NA hal arch ASA A 59 Tv RESUS MGV EXPO rt conde a see addict 60 S Extend ENRE ur ied cee idaae eaiiea ese can aoeuedi cutee ase senso acces 62 Soe Translate NPC in VOU lan cuales td des 62 8 25 Nd Chane species avilable a A Shr otem ea tants 62 8 3 Change the available species
24. Get d ose e1 A Save A Rest 9 pS Setn 4 Hep 4 The number of the lens you are editing The number of the magnification you are editing The value of your lens The value of your magnifier Use a script to determine the field size The field size in motor steps S9000Uu00390 Use a calibration to determine the field size To know how to perform a calibration go to Section 1 4 Perform a calibration Geometric correction on the X axis Geometric correction on the Y axis Geometric correction on the Z axis Geometric correction on the rotation axis Light correction value If 1 1s selected the default value will be used Gain If 1 is selected the default value will be used 300030090909 Get the light correction parameters from the current values Offset If 1 is selected the default value will be used 3 2 1 4 Autofocus parameters Autofocus provides a clear and focused image by moving the microscope stage along the Z axis This presumes that the controller has a Z axis control and that it has been initialized Stable parameters such as the autofocus algorithms are in the AUTOFOCUS SETTING window While parameters subject to Mremer TNPC User guide March 2011 Chapter 3 Image acquisition 22 frequent modification such as those depending on the current objective or the current sample are in the AUTOFOCUS tab If you want to understand better how autofocus works please refer
25. MODEL and modify the equation using the variables and constants available and the standard operators 4 3 Position radials and markers 4 3 1 Position radials To create a radial click on al Right click on the center of the otolith the center of the circles On each right click you will end the segment and start the new one Continue until the end of the radial where you must double click to end the segment creation Click again on 4 to close the radial creation Figure 4 11 Simple radial i Note The segmented lines are automatically rescaled to the CS edge If you want not to you will need to change the Find edge property in the settings See Section 4 2 Settings for more information If the analysis cannot be realised along a simple trajectory you can draw several trajectories They will be linked according to their creation order Figure 4 12 Two parts radial Fremer TNPC User guide March 2011 Chapter 4 Annotations 43 4 3 2 Position markers To help interpretation of CS 2 types of markers can be used GR markers and CH markers To add GR markers click on To add CH markers click on You then just have to click on the radial where you want to place the marker To remove a marker just double click on it when its type is selected Figure 4 13 GR marker CH marker 4 3 3 Open Save radials When you have finished analyzing a radial you can validate it by clicking on Yd
26. RECTORY and DEFAULT VBA DIRECTORY in the DATABASE SETTINGS window You can open this window by clicking on OPTIONS gt SETTINGS Mremer TNPC User guide March 2011 Chapter 2 Databases 13 Figure 2 7 The database settings window Default Image Directory Default VBA Directory Jo photos pieces calciflesbatidroles rousse noires Y l Keep vba projects opened after running a macro New fields management Never Add O Always Add Ask question Thumbnail management Display All f Do not display W Ok d Cancel ie Help j 2 8 Modify a database images format It might be useful to change the images format so that people that do not have TNPC can read them To do so export the images using TOOLS EXPORT Choose here the new file format and select the parameters depending on the format Figure 2 8 The database exportation window Current database O Photos pieces calcities B audroies rousse nore 201 047 rime EE Export directory Q Image exportation Change the image format tif Guality 2 90 Y Export d w Cancel F Mremer TNPC User guide March 2011 Chapter 3 Image acquisition 14 Chapter 3 Image acquisition 3 1 Features You can acquire images using different ways You can acquire an image from a microscope connected to your computer If this microscope is equipped with a motorized stage you will be able to make mosaics from this microscope You can
27. Rz step M nica ry 0 Z step microns 9 0 The length in microns the plate moves on the X axis for each motor step The angle in degrees the plate rotates on the R axis for each motor step The length in microns the plate moves on the Y axis for each motor step The angle in degrees the plate rotates on the R2 axis second rotation for each motor step oOo 0 9 The length in microns the plate moves on the Z axis for each motor step 3 2 1 2 5 Saving parameters The previous steps are mandatory to initialize the stage controller Once you have completed them use Savel to save the configuration on the disk in the file plugins services stage stage cnf Use Reset to load a previously saved configuration 3 2 1 3 Microscope parameters Initializing the microscope consist in establishing its physical characteristics You can define settings for each lens such as the size of each field in motor steps or the range in motor steps for the autofocus Once those parameters have been defined moving the stage from one field to the next takes only a mouse click To open the microscope settings tab click on the MICROSCOPE tab G Note The stage module can remotely control revolving lenses and so change the lenses automatically if your microscope support this feature However you should have a look to the Visilog 6 Stage Module documentation page 2 23 for more details 3 2 1 3 1 Microscope settings To open the mi
28. Scientific Coordinator IREMER Institut Fisheries laboratory Sclerochronology centre LOGY gt ZW keli g mahe ifremer fr y A D zi D CENTRE O 55 O ra O Software Coordinator S bastien Fave Noesis noesis sfOnoesis fr User Guide Coordinator Jean Couteau Code Lutin couteau Ocodelutin com User guide TNPC User guide TNPC User guide Copyright O 2010 2011 Ifremer Code Lutin Jean Couteau Noesis SA Legal Notice License Creative Commons By SA You are free e to Share to copy distribute and transmit the work e to Remix to adapt the work Under the following conditions e Attribution You must attribute the work in the manner specified by the author or licensor but not in any way that suggests that they endorse you or your use of the work e Share Alike If you alter transform or build upon this work you may distribute the resulting work only under the same or similar license to this one With the understanding that e Waiver Any of the above conditions can be waived if you get permission from the copyright holder e Public Domain Where the work or any of its elements is in the public domain under applicable law that status is in no way affected by the license e Other Rights In no way are any of the following rights affected by the license e Your fair dealing or fair use rights or other applicable copyright exceptio
29. Y F1030 e JVC KY F75 A 1 3 SPOT e SPOT FLEX e SPOT Insight5 e SPOT RT3 A 1 4 Hamamatsu e Hamamatsu C4742 e Hamamatsu C8100 e Hamamatsu C8484 e Hamamatsu C9260 e Hamamatsu C9440 e Hamamatsu ARGUS20 e Hamamatsu C10600 A 1 5 Baumer Optronic e Baumer Optronic DWX e Baumer Optronic TXD A 2 USB Cameras All the cameras with a Microsoft Windows driver compatible with WDM are supported by TNPC Amongst the other cameras only the Lumenera cameras are supported A 2 1 Lumenera e Lumenera Infinity Mremer TNPC User guide 69 March 2011 Appendix A List of cameras supported by TNPC A 3 GigEthernet Cameras Only Baumer cameras are supported Mremer TNPC User guide 70 March 2011 Index 71 Index i Results Automatic A Age structure 60 61 Acquisition Individual age 58 59 Mosaics 28 32 Edge extraction 48 49 Scanner 32 34 Estimation numerical values 45 45 Standard 28 28 Growth pattern 45 45 Intensity profile 44 44 C Shape parameters 49 50 Calibration S Creation 6 7 Settings D Acquisition 25 28 Annotation 36 42 Database Annotation 36 36 Creation 9 10 Import 11 12 Apprenticeship of individual age 55 57 Autofocus 21 24 Controller 14 16 Live 51 53 Shape analysis 46 46 Microscope 19 21 sews 01 Shape analysis 46 48 Stage 16 19 E Estimation Automatic Age 58 58 Age structure 59 60 Markers 43 43 54 Radials
30. ainable development way ICES is the oldest intergovernmental organisation in the world concerned with marine and fisheries science It coordinates and promotes marine research on oceanography the marine environment the marine ecosystem and on living marine resources in the North Atlantic You can refer to the CES CIEM website indexfla asp for more information http www ices dk An image format is the way the image is stored Several formats exists with their pour and cons Five of them are available in TNPC e im Visilog image file Can be read only by people having Visilog or TNPC Now using the im6 file format with Visilog 6 e tif format allowing to store big bitmap images without loss Tif format is platform independent anyone can read it You can add a loss less compression LZW in TNPC preferences TOOLS SETTINGS OUTPUT IMAGE FORMAT gt TIFF gt COMPRESSION e jpg Format allowing to store image with compression and loss Can typically achieves 10 1 compression with little perceptible loss in image quality Platform independent format can be read by anyone TNPC User guide March 2011 Glossary Nucleus O Otolith R Radial Reader Result Viewer Ring S Sclerochronology Stage Mremer 74 e ppm pgm Format of images stored in plain ASCII text Files are stored without loss but can be bigger than with other formats Platform independ
31. ample Fremer TNPC User guide March 2011 9eqop QO IAOOO0QU9OOOSOSO Chapter 9 Export files 65 Length Weight Sex D Nb Distance Back calculated distance Y Edge Distance The image name The nucleus coordinates The edge coordinates at the profile level The profile start coordinates The profile end coordinates The LO point coordinates The pixel size Scale ratio between the image and the profile Parameters entered by the user from the database Parameters entered by the user from the database Parameters entered by the user from the database Marker s number Marker s distance from the nucleus Back calculated distance from the otolith center if the Length when captured have been given Edge s distance from the nucleus 9 3 Profiles pro files TNPC stores the grey levels of the pixels located on the radial and the markers position on a pro file They are CSV files located in the pro directory and are coded the following way Example 9 2 pro file content Image name 9 Xn Yn 9 xed Yed 3 AS YS D Xen Yen 8 XLO YLO O Calibration RadImaRatio 0 Species Catch zone 9 Catch date Sample 9 Length Weight Sex D PixelsNb D Mremer TNPC User guide March 2011 Chapter 9 Export files 66 Pixel Distance1 Distance2 P Check The image name The nucleus coordinates The edge coordinates at the profile level The profile start coordinates The profile end coordinates Th
32. arch 2011 Chapter 4 Annotations 38 900900 9 Store the rings positions in a xyd located in the xyd folder Store the interpretation in the database Store the estimated age in a datasheet in the graphic window Store the growth pattern in a datasheet in the graphic window Add remove one to the number of rings for age calculation or do nothing 4 2 3 Process Expert Mode On this tab you can manage all process settings which processes will be performed and what are their parameters Figure 4 4 Process settings Activate the SMOOTH function This function smooth the intensity profile to remove the high frequencies noise details from it This function got only one parameter the value of the thinnest ring width the default value is 5 The value is in pixels if there is no calibration in the calibration unit if it has been defined Figure 4 5 Use Smooth function Before red After blue 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 Show Hide the SMOOTH function parameter Activate the DETREND function This function removes the intensity profile trend It is defined by one parameter the largest growth ring width value by default 50 The value is in pixels if there is no calibration in the calibration unit if it has been defined Fremer TNPC User guide March 2011 Chapter 4 Annotations Figure 4 6 Use Detrend function Before
33. atabase images Figure 5 1 Shape analysis tab Acquisition Annotations Shape analysis Live i Source Database q gt o aa D te uu va EL p 9 The image source Previous image only when using database source Next image only when using database source Edge extraction Otolith analysis This will perform all the measures selected See Section 5 2 Settings Show hide the measures toolbar Validate analysis for this image go to next image when using database source Settings 990 009000 9 Name used for data export By default this is the image name 5 2 Settings The settings rules the shape analysis as it is there you can change the analysis that is made on the shape if the analysis is stored added in the database fremer TNPC User guide March 2011 Chapter 5 Shape analysis Expert Mode 47 Figure 5 2 Shape analysis settings Edge precision D 1 0 Measures groups Basic e PYS ave the contour 5 T WAYS ave the analysis 7 yAdd in the database Ey Export to ResullViewer Bel A P Mame of the parameters The edge precision y The group of measures to perform Modify measures groups cf Section 5 2 1 The measures groups Save the contour in a file located in the Ms r folder The contour file extension either seg or dat seg is a Noesis file format It contains information on the image and the associated data size typ
34. calib Y IY work in a database a Reset the acquisition Reset the stage Yo Ok Open the database module at TNPC startup Reset the acquisition at TNPC startup You must select this if your camera was not previously powered on Reset the communication with the motorized stage controller You must select this if your controller was not previously powered on Figure 1 5 Global information Reader Jean Work directory C Program Files oesi THPCS Species Lemon sole Suffix Note If you want to change global information you have to restart TNPC The ACQUISITION tab is used to acquire images from a camera and a microscope equipped with a motorised stage or a scanner and create mosaics Acquisition parameters can be changed from one session to another or from one image to another The image can be stored in the database as well as preferences To know how to perform acquisition go to Chapter 3 Image acquisition The ANNOTATIONS tab is used to set and store CS interpretation reading axis rings positions false rings and checks positions annotations You can also compute the otolith growth and fish length back calculation All the acquired information age CS interpretation growth patterns can be stored in the image database and exported in text or Excel format To know how to perform annotation go to Chapter 4 Annotations The SHAPE ANALYSIS tab provides an easy to use interface to
35. compute and record classical shape analysis methods surface Fourier parameters To know how to perform shape analysis goto Chapter 5 Shape analysis Expert Mode The LIVE tab provides a way to perform annotation and acquisition at the same time To know how to use the live mode go to Chapter 6 Live Expert Mode Mremer TNPC User guide March 2011 Chapter 1 Generalities 6 The APPRENTICESHIP OF INDIVIDUAL AGE tab provides ways to learn how to automatically estimate the age of a species from calcified structures whose age have been estimated by the reader To know how to use the apprenticeship of individual age go to Section 7 1 Apprenticeship of individual age The AUTOMATIC ESTIMATION OF INDIVIDUAL AGE tab allows you to automatically estimate individual age of calcified structures To know how to use the automatic estimation go to Section 7 2 Automatic estimation of individual age The AUTOMATIC ESTIMATION OF AGE STRUCTURE tab provides features to automatically estimate the age structure of a database To know how to use the automatic estimation of age structure go to Section 7 3 Automatic estimation of age structure 1 4 Perform a calibration The best way to perform a calibration 1s to put a micrometer or an object you know precisely the length on your stage and take a picture of 1t Then click on ZI to open the CALIBRATION window Figure 1 6 Calibration w
36. croscope settings window click on Setting button Mremer TNPC User guide March 2011 Chapter 3 Image acquisition 20 Figure 3 7 Microscope settings Number of lenses a El Number of magnification na 5 Project Marne Stereo usb Revolver Revolver Rotation Relative 8 Absolute Y Ok d Cancel Help j Number of different lenses on your microscope The number of magnification on your microscope Choose here the project corresponding to your controller If your controller is not present please contact Noesis Whether the lens change 1s manual or automatic When the lens change is automatic whether the revolver rotation is relative or absolute Once everything is set click OK and return to the MICROSCOPE PARAMETERS tab 3 2 1 3 2 Microscope parameters In this tab you can define for each lens magnification combination the lens field size autofocus steps and camera parameters Make sure that you have correctly selected the lens and magnification before entering its parameters fremer TNPC User guide March 2011 Chapter 3 Image acquisition 21 Figure 3 8 Microscope parameters eb Parameters Trajectory Ah Stage Microscope E Autofocus Num lens 7 amp 1 Num Magni ly B 1 Value y 1 Value 4 1 Field size X step 100 S O Scit Y step 100 Fn Caib 1 0 i DO 0 0 Dz Light mp 0 Gain 43 1 Py
37. ct the AUTOMATIC ESTIMATION OF INDIVIDUAL AGE Then you will have to fill in some parameters such as the source of data the species ICES zone and codebook to use and then launch the estimation clicking on Estimate Figure 7 7 Automatic estimation of individual age Automatic estimation of induvidual age Automatic 4 Source Curentimage y Species Place A rl ILES zone 7D Eastem Charnel y Codebook Plaice 7DEC y Neighbour number KNH a 5 w Estimate Tools developped by the Ifremer France 0 26 the Institute of Marne Research Norway and the Universitat Polit cnica de Catalunya Spain Select here the source Either the current image if you want to estimate a single image or the database if you want to estimate all your database Select here the species you are studying Select here the ICES zone of your species Select here the codebook to use You can use predetermined codebooks or the ones you created The Neighbor number parameter in the Nearest neighbor interpolation 9000o Launch the estimation 7 2 2 Results The estimation might take some time to complete Once it is finished you have the results in the RESULT VIEWER You can also find the results in the database in the field AUTOESTIMAGE Fremer TNPC User guide March 2011 Chapter 7 Automatic estimation Expert mode 59 Figure 7 8 Automatic estimation of individual age aa Result Viewer Esti
38. d and TNPC For example with a Zeiss stereomicroscope the zoom goes from 4 7x to 95x but in TNPC it goes from 0 75x to 15x Either calculate the right value for the zoom or select the right zoom with the command and hit Refresh TNPC will make the conversion for you Figure 3 12 Automatic zoom conversion SteREO Manager Refresh 3 3 Settings When you are on the TNPC screen on the ACQUISITION tab you can display hide the settings by clicking on There are four tabs for each settings section 3 3 1 Acquisition In this tab you can parametrize the acquisition by stating the generic name the base name of all the images acquired and the number of the next acquisition number that will follow the generic name To avoid noise and increase sharpness you can ask TNPC to make different images on the same point and store only one image that 1s an average of all the different images Figure 3 13 Acquisition parameters Acquisition tab Acquisition Process General Sharpness Generic name mae A Number of nest acquisition mE amp Average on m5 imadels The generic name used for acquisitions All image names will start by this name and will be followed by a number y The number of the next image acquired In this example the next image will be named image_1 Mremer TNPC User guide March 2011 Chapter 3 Image acquisition 26 Use an average on several images Z The number of imag
39. e raw data dat 1s a text format Save the analysis in a file located in Ms r folder Y The analysis file extension either a6 or dat a6 is a Noesis file format It contains information on the number and the coordinates of the segments dat 1s a text format f Add the contour and the analysis in the database Export the results of the analysis in the RESULT VIEWER performed You can show or hide the settings by clicking on 5 2 1 The measures groups The measures that are performed are defined in the settings You can chose the selected group using the list By default the selected group is BASICS If you want to know what measures will be performed by which group or modify a group click on That will open the MEASURES SELECTION window Mremer TNPC User guide March 2011 Chapter 5 Shape analysis Expert Mode 48 Figure 5 3 Measures Selection ii Measures Selection All measures Measures on segments r TNPC measures a 4 03 Basic A Area 3 BinBasics D AreaFraction H BinShape C BaryCenterX E 3 BoundingBox BaryCenterY H O FeretDiameters y C BinMom2x gt gt Fourrier 7 D BinMom2y z GreyMoments E BinMomsy ee 4 03 Intercepts Ra Bit _ Moments ss Pol Ox BoundingBoxDx a R spacial E abad nt s SizeDrientation v Description Add Group XX Delete Group 3 Close Help On the left part you got all the available measurement
40. e LO point coordinates The pixel size and the scale ratio between the image and the profile Parameters entered by the user from the database Parameters entered by the user from the database Parameters entered by the user from the database Number of pixels in the profile Grey level value of the pixel between 0 and 255 Distance from nucleus to the pixel Anamorphosed distance from nucleus to the pixel SAB OQAO OSOS OOSO9 gt lt qs z gt ex Presence or not of a marker 0 or 1 9 4 Rings positions xyd files TNPC stores the rings positions values in xyd files Those files contain the w and y position of the ring in the image and the distance from the radial start Example 9 3 xyd file content Version 500 No position 6 2 Ring9 3230 2260 41 6799240 Ring 411 202 99 899498 Ring 494 181 154 811142 Ring 607 238 214 195801 CheckRing 651 241 242 424835 Ring 676 243 258 464050 File format version The number of rings The type of ring here a real ring The X coordinate 9 O90 90 The Y coordinate fremer TNPC User guide March 2011 Chapter 9 Export files 67 9 The distance from the radial start to the ring A check ring 9 5 Shape Analysis dat files TNPC stores the shape analysis values in dat files You can export either the edge or the measures Those files contains the selected measures with for each measure their name and value Example 9 4 Edge dat file content X Y Index C
41. e possibilities in the settings toolbar Fremer TNPC User guide March 2011 Chapter 1 Generalities 8 Figure 1 8 Settings toolbar Create a new set of settings Load a set of settings Save the set of settings Save the set of settings under an other name The name of the set of settings used Fremer TNPC User guide March 2011 Chapter 2 Databases 9 Chapter 2 Databases 2 1 Introduction TNPC facilitates the creation and the analysis of CS otoliths scales image databases You can perform process on all the database including automatic exports of the data without any click or keyboard use To have a full description of the database functions please consult the Visilog 6 Database Module documentation 2 2 Create a database To create a database you have to go to the tab Click on gt NEW DATABASE You then have to select the directory in which the database will be stored its name and the default date Figure 2 1 The New database Window New database Directory C Program Files Noesis TNPC5 D atabase Y Name myDatabase Default date 12 08 2010 id WY Create j Cancel j The database has by default 9 fields Calibration Species Zone Date Sample Length Weight Sex Comment You can add other custom fields to do so refer to the Visilog 6 Database Module documentation You can visualize your database three different way forms by default list o
42. e with other people or for later use Figure 4 1 Annotations tab Acquisition Annotations Shape analysis Live Source Database a EJ ba xd H a Pr gil piice_EC_200_ 03 W1_501 ay The image source Previous image only when using database source Next image only when using database source Create radial Add a GR marker Growth Add a CH marker Check S 9090 GO0O00Q Open a radial If the image name is filled in cf the radial will directly open If not you will have to select the radial file manually Choose the radial colors Fusion image and annotations Validate analysis for this image go to next image when using database source Settings Create a radial with a rotation angle cf Section 4 2 Settings dd USOS 9 Name used for data export By default this is the image name 4 2 Settings You can display hide the settings by clicking on There are five tabs for each settings section 4 2 1 Profile This tab allows you to parametrize the profile used for all the age calculation and processes You can choose to visualize or not the intensity profile and the growth pattern modify the markers size the color channel used the neighbourhood to calculate the intensity profile reducing noise Mremer TNPC User guide March 2011 Chapter 4 Annotations Figure 4 2 Profile settings Interpolation Back calculation Profile Espot Process Marker w
43. ent format can be read by anyone The nucleus indicates the core or primordia of the otolith The nucleus is the formation center of the otolith the point from which all the radials start See Also Radial Otolith An otolith is a calcified structure of the inner ear of fishes This part grow with the fishes and growth rings appears on it making 1t the perfect piece to study to determine fish age See Also Sclerochronology Calcified Structure A radial is a line going from the nucleus of the otolith to the outer limit it might be segmented It is used to place markers in order to determine fishes age See Also Growth structure marker Check marker Nucleus Reading a calcified structure consist in interpreting its growth patterns A reader tries to interpret the marks recorded in a given structure The Result Viewer is a window allowing the user to see charts and tables and perform some calculations To open it click on TOOLS gt RESULT VIEWER The rings or bands are used for fish ageing Generally one ring is described by one light zone and one dark zone Sclerochronology is the science that studies living being by counting growth rings in their calcified structures otoliths scales skeletal tissue Its aim is to determine the age and the period and length of important events on a specimens life A stage is the part of a microscope where you put what want to study It can be fix or motorized In the ca
44. es on which to make an average if selected 3 3 2 Process In this tab you can specify a number of different processes to perform on the image to acquire in order to improve the image quality Note The process 1s performed on each image acquired when acquiring slides You can delete the spots reduce image size to get only the otolith configure the noise reduction and contrast enhancement algorithms Figure 3 14 Acquisition parameters Process tab Acquisition Process General Sharpness ds Delete the spots Facto C Ert C Manual 137 E Otolith registration Edge otolith distance LEJ SN Noise reduction E 5 0 gt contrast enhancement 40 3 0 Function that detects the calcified structure in the picture and to remove the background noise artefact It relies on the image binarisation from a grey level threshold This function will be efficient only is the observed object is contrasted compared to the background The spot deletion threshold configuration It can be automatic using a factorial or entropic analysis of the grey level histogram or manual and you need to state a value This function rotates the image so that the otolith main axis is horizontal It also crops the background to let a constant distance between the image and the otolith This function needs to have the Delete the spots function ran before The constant distance between the image and the otolith used in the ot
45. f thumbnails or table Figure 2 2 Database views Form Thumbnails Table Form Thumbnails Table Form Thumbnails Table Index fi Name plaice_EC_2006_03_WR_50 PathName ECplaice plaice_EC_2006_03_WR_50 Width 1280 Height 960 Type Unsigned char Calibration TIFF_calib_plaice_EC_2006 Species Alaska pollock sst lt s S Zone Date jeudi 12 ao t 2010 y Sample Length Po 0 Weight Poo 0 Sex tt Comment fremer TNPC User guide March 2011 Chapter 2 Databases 10 i Note The list of thumbnails visualisation might be unactivated To activate it go to OPTIONS gt SETTINGS and click on Display Alf on the THUMBNAIL MANAGEMENT section 2 3 Manage views Queries or views in the database can be written using a form or plain SQL in the window For more information about how to write queries please refer to the Visilog 6 Database Module documentation Figure 2 3 The View Properties window View Properties A Assistant SOL Query View Name SELECT a list of fields gt e FROM a view or a table ORDER BY a field Ascending Image v Index v A Descending WHERE optionnal logical condition on fields Name z PathN ame Width e AND Height Type OR Calibration Species x You can create a view from scratch by clicking on VIEWS gt NEW DATABASE VIEW You will be asked to enter a name for your view and
46. hain Ext chain Direction Label index 404 5 634 5 0 0 nl 1 Labell 1 Soleo Goole l 0 ll 1 Labell 2 lar O20 2 0 1 1 Labell 3 las Gaze a 0 1 Labell 4 blas Gloss A 0 1 Labell 5 364 50 6013 0 J 0 1 Labell 6 Soon Dew E 0 l 1 Labell 7 aolo GU 7 0 I Labell 8 Example 9 5 Measures dat file content Area NbHoles CroftonPerimeter BaryCenterX BaryCenterY 19600885 0 1 L244 36890 GAANG A627 0506 fremer TNPC User guide March 2011 Appendix A List of cameras supported by TNPC 68 Appendix A List of cameras supported by TNPC This appendice provide a list of camera supported by TNPC It was last updated the 9 march 2011 Some new camera might be supported since then If your camera works with TNPC and is not present in this list please tell us so that we can update this list A 1 IEEE1394 Cameras Cameras that respect the DCAM IIDC norm are well supported like Sony Hamamatsu Baumer and JVC Cameras not respecting those norms like Leica Nikon Olympus or Zeiss are not supported A 1 1 Sony e SONY CCM DS250 e SONY DFW V300 e SONY DFW V500 e SONY DFW VL500 e SONY XCD X700 e SONY XCD SX900 e SONY DFW X700 e SONY DFW SX900 e SONY XCD X710 e SONY XCD X710CR e SONY XCD SX910 e SONY XCD SX910CR e SONY DFW X710 e SONY DFW SX910 e SONY XCD V50 e SONY XCD VSOCR Mremer TNPC User guide March 2011 Appendix A List of cameras supported by TNPC e SONY XCD UI00CR A 1 2 JVC e JVC K
47. he angles of the radials that will be created for the automatic estimation Those angles must be separated by The more angles the longer the apprenticeship will be and the estimation after Select if you to use the Advection Diffusion algorithm This algorithm cleans the image y Angular sector around the radial y The size of the resampled profile The bigger the size is the longer the generation and later the estimation will be y The size of the profile The bigger the size is the longer the generation and the estimation will be 7 1 3 Create the learning file To create the learning file enter 1ts name and launch the apprenticeship Figure 7 6 Create the learning file Codebook myCodeBook w AporMlceshia fremer TNPC User guide March 2011 Chapter 7 Automatic estimation Expert mode 58 Insert here the name of the generated learning file the codebook This codebook will be available for this species in this ICES zone Launch the codebook generation The learning file the codebook will be stored in data Tnpc CodeBook in your TNPC installation directory This text file contains the parameters defined and the matrix used to auto estimate the age You can generate this file by hand without using TNPC but SciLab MatLab or other mathematical software 7 2 Automatic estimation of individual age 7 2 1 Launching the estimation To launch the estimation you will need to sele
48. he markers are positioned on the peaks or valleys extremum by default or on the end beginning or barycenter of those peaks or valleys fremer TNPC User guide March 2011 Chapter 4 Annotations Figure 4 8 Use TopHat function Before red After blue 40 A 0 5 10 15 20 25 30 35 40 45 50 55 60 65 m 75 80 85 90 95 100 105 110 115 120 125 Show Hide the TOPHAT function parameter The functions parameters 4 2 4 Interpolation Expert Mode This tab let you parametrize the interpolation function This function is used to interpolate the number of growth increments within unreadable areas You can choose between the density interpolation that relies on a mean frequency computed within the specified surrounding regions or the polynomial interpolation an implicit polynomial function whose zero crossings are the positions of the growth markers within the specified surrounding region Figure 4 9 Interpolation settings Profile Export Process P Interpolation Back calculation 4 Density 4 Polynomial Degree of the polynomial BE Activate the density interpolation Activate the polynomial interpolation The degree of the polynomial interpolation remer TNPC User guide March 2011 Chapter 4 Annotations 41 4 2 5 Back calculation This tab will allow you to activate or not and parametrize the fish s length back calculation To use the back calculati
49. how many slices there are on each row and each column of your grid Figure 3 26 Parametrizing otolith separation during scanner acquisition Number of objects by line Number of objects by column Background gt White o C Black bey ct Y 9 can J Number of slices per row y Number of slices per column The color of the background between slices white or black Launch the cut INPC will try to cut all the different otoliths to got one otolith per image Cancel the cut the acquired image will not be stored but will be kept as current image TNPC now split the acquired image into one image per otolith Mremer TNPC User guide March 2011 Chapter 3 Image acquisition 35 3 7 Current image processing Expert mode When you have images that have already been acquired but of poor quality you might want to use the acquisition processing tools to improve their quality To do so open the image you want to improve select the process parameters you want to apply on the acquisition settings cf Section 3 3 2 Process You can then click on and all the process you have set will be applied fremer TNPC User guide March 2011 Chapter 4 Annotations 36 Chapter 4 Annotations 4 1 Generalities The ANNOTATIONS section allows the user to interpret CS by creating radials positioning markers or calculate markers positions using grey levels curves The values can be saved to exchang
50. ht find an index at the end of this documentation This index specifies the pages where a specific topic is explained You might also use the table of contents 1 2 Installing TNPC Installing TNPC is quite easy You just have to launch the Setup exe file located on the installation CD ROM and follow the instructions The only choice you have to make is between the routine and expert interfaces following the use you will make of TNPC At the end of the installation process you can install TNPC documentation and your camera if needed Fremer TNPC User guide March 2011 Chapter 1 Generalities 3 Install acquisition board driver s TNPC 5 0 Setup Acquisition board installation Choice your board W dm camera T Matrox Meteor2 Std T Matrox Meteor2 Dig T Matrox Meteor2 Mc M Matrox Morphis 7 Baumer GApi InstallShield lt Back Next gt Cancel As said previously TNPC is built upon Visilog 6 platform Most of the user interface comes from Visilog 6 The only TNPC user interface is located on the right of the screen on the TNPC tab The other tabs contain features of the Visilog 6 platform Figure 1 2 Visilog 6 and TNPC Window File View Tools Vba Help olala slaa a ae Aala e aijaa 232 ZL I asda 3 x lo Reader Jean Work directory C Program Files Noesis TNPC5S Species Lemon sole Suffix 24m Be x 8
51. idth epi Minimal distance between markers 2u 3 Show profile A Show growth pattern Color channel Luminance Ey Radial Profile neighborhood Find edge a 5 5 Angular o j Rot 1 TE f Rectang pix D 1 37 The width of the markers y The minimal distance between markers A Activate the intensity profile visualisation y Activate the growth pattern visualisation Choose the color channel used red green blue or a balanced mean of the three colors the luminance Activate the edge detection when drawing radials by default the edge is detected Angle of rotation of the radial when pressing the gt button Activate the angular profile neighborhood The angle of the angular sector of the neighborhood Activate the rectangular box neighborhood The width of the rectangular box of the neighborhood in pixels 4 2 2 Export In this tab you can manage all the export settings Figure 4 3 Export settings Interpolation Back calculation Profle Export Process Save Profile 3 Age F Growth pattem 4 Ring positions 5 Add in the database Export 77 Age 5 Growth pattern Modify the age 06 Store the radial in a rad file located in the rad folder Store the estimated age 3 99909 Store the growth pattern in a iid located in the iid folder Fremer TNPC User guide Store the intensity profile in a pro file located in the pro folder M
52. in this selection Select here the field where the age you estimated is present Insert here the number of different age class Insert here the age of the first class All the ages before the first class will be identified as being of the first class For the last class it works the opposite way Parameter of the Nearest neighbor interpolation Parameter of the Nearest neighbor interpolation Check this box to estimate the individual age Check this box to estimate the age proportion Launch the estimation Once you have selected all the parameters you can launch the estimation by clicking on Estimate 7 3 2 Results and export The results of the estimation are showed in the RESULT VIEWER You can also find the estimation log in the file named est imateAgeProp log In this file you will see the input parameters as well as the results fremer TNPC User guide March 2011 Chapter 7 Automatic estimation Expert mode 61 Figure 7 10 Automatic estimation of age structure estimation results You have also the estimated age in the database on the column AutoEstimAge_2 Mremer TNPC User guide March 2011 Chapter 8 Extend TNPC 62 Chapter 8 Extend TNPC 8 1 Translate TNPC in your language If you want to use TNPC in your language but it is not present in the TNPC installation you can translate TNPC by yourself To do so copy the directory data Tnpc lang en and rename it for example in es if
53. indow Eii Calibration Curent Calibration Available Calibrations O g New 2 By Delete ls test Calibration iu test E Ets ch to image Selected calibration test Calibration 2422 Intensity H Y Z calibration properties Square pixels Unit um 9 Size in image Real size Origin image Real origin lt om ee 0 raged SAN ra Use the graphic tool to adjust the length on the image Create a new calibration Delete a calibration Create a new calibration from an existing one 9009 Attach the calibration to the current image Mremer TNPC User guide March 2011 Chapter 1 Generalities 7 The measure unit The length of the measure in pixels The real size of the measure in the unit defined Draw the measure on the current image Validate To create a new calibration click on New You will be asked to enter a name for your calibration Figure 1 7 Enter new calibration name Calibration est Calibration Cancel j Click on to display the measure bar on the picture Move it so that the distance measured is the one of the micrometer or the object Then in the CALIBRATION window you should see the length in pixels Put in front of it the real size and its unit 1 5 Settings management When you perform a lot of different otholith analysis you might need to change settings save them load old settings Each time you get settings you should have all thos
54. less than the depth of field The minimal score for each scan It must correspond to the number of pixels considered as clear cut by the criteria calculation algorithm Test the selected parameters Clear the output text see D Select the output mode Fast will just display the results Verbose will display a lot of information like the value used in the algorithms The autofocus calculation might take longer to proceed If checked the intermediary images are displayed in the viewer area to help you understand the operation of the algorithm D The output text Fremer TNPC User guide March 2011 Chapter 3 Image acquisition 24 Figure 3 11 Autofocus parameters Acquisition tab Z motion Acquisition Nb Images for averaging mn 1 Gradient threshold low 2 15 Gradient threshold high a 255 Threshold percentage reflexion my 1 Script Get The number of images used for averaging in each scan Low gradient threshold Used by the criteria calculation algorithm High gradient threshold Used by the criteria calculation algorithm O OOOO The percentage of the maximum criteria from which the first pass will stop when using a reflected source Use a script to adjust parameters Pand Y Get the actual values 3 2 2 Try the settings First Use This step might seem a bit tedious but it is necessary to ensure your microscope and motorised stage are well configured
55. mateAge CoJia File Edit View Tools Format Window Blasted lala a slez ope ajel kolli Gale Xd belie 910 ej a g y N F EstimateAge Ready A 7 3 Automatic estimation of age structure 7 3 1 Launch the estimation The automatic estimation of age structure consist in estimating quickly all the ages already estimated or not and adjusting the model using the already estimated ages The algorithm used for this estimation is the Nearest neighbor interpolation To perform the automatic estimation of age structure open the AUTOMATIC ESTIMATION OF AGE STRUCTURE tab fremer TNPC User guide March 2011 Chapter 7 Automatic estimation Expert mode 60 Figure 7 9 Automatic estimation of age structure window aaa Automatic estimation of age structure Apprenticest 4 gt Input selection for apprenticeship 5 pec lez one Sample Length a Aca T me Agel FingPositians Estimate age field Agel 2 Number of age class CEE Age of the first class Ig 5 Neighbour number kM la 5 Exponential factor kE sp O 2 Z E stimate the individual age amp Estimate the age proportion wv PE stimate Tools developped by the Ifremer France 0 5 the Institute of Marne Research Norway and the Universitat Polit cnica de Catalunya Spain o o 2 Select here the fields of the database you want to use for the apprenticeship An estimated age field must be
56. mulate The number of images and the digitized surface will be displayed Save the trajectory and name it The file will be saved in Tnpc Data Trajectory and will have a t rj extension Figure 3 20 Trajectory configuration Parameters lola kx Trajectory d Stage Microscope Autofocus ES Load A save Save as 2 imulate En jon i Help By zone Sep By points A Setting ClO OO Diet P1 Xy Bet P2 Xy Y Validate points Definition by fields number x1 0 x2 0 YI 0 Y2 0 of total nb of fields 100 Distance between 2 fields 2 x ME Distance between 2 fields 2 Y mu 9 Distance from last point A Search zone delta Z 1000 Fremer TNPC User guide March 2011 Chapter 3 Image acquisition 30 Save the trajectory Simulate the trajectory Get Point 1 coordinates Above you got the coordinates Get Point 2 coordinates Above you got the coordinates Validate the acquired points 0000090 Overlapping values The default values should be fine if you want to change those values please refer to the Visilog 6 Stage Module documentation Warning The settings must always be configured as stated below If you want to change those parameters please refer to theVisilog 6 Stage Module Documentation Figure 3 21 Trajectory settings Parameters T CES Trajectory fg Stage Microscope Autofocus LS Load j HA Save j Save as j j Simulate Q Cea
57. n be loaded by TNPC in order to be read again e The growth measures are stored in iid files They are CSV files that cannot be read by TNPC but by any text editor e The pro files store the intensity profile value They are CSV files that cannot be read by TNPC but by any text editor e The dat files store the shape analysis results or the otolith edge They are CSV files that cannot be read by TNPC but by any text editor e The rings positions are stored in xyd files They are CSV files that cannot be read by TNPC but by any text editor 9 1 Radials rad files Radials are saved in rad files in a rad directory They can be loaded using the button from the ANNOTATION tab To save a radial select the RADIAL checkbox from the EXPORT tab on the ANNOTATION parameters see Section 4 2 2 Export The save is done when the radial is created and validated by 2 By default the file created has the same name than the image except for the extension 9 2 Markers iid files The distances between the markers can be saved The files created are CSV files that got the same name than the images by default and the iid extension for Inter Incremental Distance They are saved in the iid directory and are coded the following way Example 9 1 iid file content Image name 9 Xn Yn 9 Xed Yed 9 XS YS 9 Xen Yen O XLO YL0 Calibration D RadImaRatio 9 Species Catch zone 9 Catch date S
58. nes corresponding to the useless species Example 8 4 The Species cfg file Version 500 mm Grey gurnard Mremer TNPC User guide March 2011 Chapter 8 Extend TNPC 63 Long finned gurnard oe ELO GUEnarOo Aspitrigla cuculus Red guenard Clupea harengus Atlantic herring 8 3 Change the available species for Automatic Estimation By default in the automatic estimation only Cod and Plaice are available and for only two ICES zone each You might want to add species and ICES zones To do so open the file data Tnpc lang yourLanguage Aea_Species cfg This file contains for each species the corresponding ICES zone and the prefix used for the default codebook name You just need to adapt this file to your needs adding species or ICES zone for a species by adding lines to this file or changing the prefix used Example 8 5 The Aea_Species cfg file Version 500 Coc 4 North Sea NScod Cod ZA North East Arctic NFACod Plaice 7D Eastern Channel ECplaice Plaice 5A Iceland ITCplaice 8 4 Add your own codebooks You can add your own codebooks by adding them in data Tnpc CodeBook They must be in the cbk format fremer TNPC User guide March 2011 Chapter 9 Export files 64 Chapter 9 Export files Several files can be created by TNPC e The radials files got the rad extension They store the appearance position and length of the radials They ca
59. ns and limitations e The author s moral rights e Rights other persons may have either in the work itself or in how the work is used such as publicity or privacy rights e Notice For any reuse or distribution you must make clear to others the license terms of this work The best way to do this is with a link to this web page http creativecommons org licenses by sa 3 0 The full text of the license can be found on the Creative Commons website http creativecommons org licenses by sa 3 0 legalcode TNPC iV Table of Contents IA 0 seo hae esac a O rine l rodu ON srir a want a omnes aeealos aeae eae ae nceanmeneea oman tate l Kanana AO a EE E E E T EE T ATIT 2 INPE US M ICE E A E 3 14 Pororo MEAR AAA AAA AAA At 6 LN SUING smana MEN ii cid 7 2e Databases AA A ASE A RAE a lames neevelones 9 2 Ae TOJU HON si AI Aa ias 9 Zi 2 remera dataDase iaa E 9 Z eN SN ONS Sree sti act A O Un A 10 2 4 Display information and images from a database cc cece eee ce eee eec ee eeceeeeeeneeeeneenes 11 23 import database tom and le ds 11 POAT IMA ES A A A II A A ua ERS 12 2d Move a database with IES IMACS a lo da leo aos 12 2 82 WModiy a database images TOrmal iria id 13 Se AIMASe AC QUISO eros ida raado alii ici 14 JA a DU E E T N eee ens oes 14 3 2 Configure stage Microscope and autofocus c ooccccccoccnconcnnoncnnoncononnoncnnonno nono nonnnnnananos 14 SoZ ls lintalizie the stase Contoller ada is bsos 14 3 2 e e Sen
60. nt age class D Insert here the age of the first class All the ages before the first class will be identified as being of the first class For the last class it works the opposite way 7 1 2 3 Segmentation Figure 7 3 Apprenticeship of individual age Segmentation Global informations Age Seamentaich Nucleus detection Radiales Segmentation threshold mp0 200 Radius separator kernel ley 10 Insert here the threshold used for segmentation You should not need to change the default value Insert here the radius separator kernel You should not need to change the default value Mremer TNPC User guide March 2011 Chapter 7 Automatic estimation Expert mode 57 7 1 2 4 Nucleus detection Figure 7 4 Apprenticeship of individual age Nucleus detection Global informations Age Segmentalon Nucleus detection Radiales Light Reflected a Method Centroid 2 Select here the type of light of your hardware between REFLECTED and TRANSMITTED Insert here the method used for nucleus detection between CENTROID MORPHOLOGICAL or EMPIRIC 7 1 2 5 Radials Figure 7 5 Apprenticeship of individual age Radials Global informations Age Segmentalor Nucleus detection Madiales Angles 0 30 180 A 2 Use the Advection Diffusion algorithm Angular sector fy 2 Size of the resampled profile my 64 Size of the profile Ge Insert here t
61. olith registration function This function reduce the noise in the image using a Gaussian filter parametrized by its variance Open the noise reduction parameter selection window This parameter value is expressed in function of the smallest growth rings width Using the bar you can move the parameter value The modification result is seen in real time on the window over the current image Figure 3 15 The noise reduction parameter adjustment Minimum growth increment fremer TNPC User guide March 2011 Chapter 3 Image acquisition 2 You can also manually state the noise reduction parameter a This function enhance the contrast mostly on the edges It relies on a Laplacian filter using a parameter Open the contrast enhancement parameter selection window Using the bar you can move the parameter value The modification result is seen in real time on the window over the current image Figure 3 16 The contrast enhancement parameter adjustment Adjustment of the parameter You can also manually state the contrast enhancement parameter 3 3 3 General In this tab you can parametrize how the image is stored its format its color channel if the calibration have to be inserted 1f the image have to be added to the database or 1f the image need to be stored in grey levels Figure 3 17 Acquisition parameters General tab Acquisition Process General Sharpness gt Insert
62. on function the field Length must exist in the database If it does not exist you have to create 1t or rename the according field Figure 4 10 Back calculation settings Profile Export Process COS SSS Cr SIL Poe or ee Se ee Interpolation Res Back calculation x Execute Back calculation Method Dahl Lea 2 Formula Ey Fish length ey 0 00 Allometry Slope A 1 00 Allometry Intercept fy 0 00 Activate the back calculation y The model used The formula used by the model User can modify the USER MODEL the others are not modifiable My The back calculated fish length The slope of the allometric relation The intercept of the allometric relation You can use the TNPC integrated models or create your own ones using 2 and The existing models are e The Dahl Lea model Li Si Lce Sc e The regression model Li a Si b e The SPH model Scale Proportional Hypothesis Li Lc b Si a Sc b a e The BPH model Body Proportional Hypothesis Li Lc b Si a Sc b a The variables used are e Li back calculated length of the fish e Si length between the marker and the radial origin The constants are e Lc fish s length when captured e Sc radial length e a allometric relation slope Mremer TNPC User guide March 2011 Chapter 4 Annotations 42 e b allometric relation intercept To build a new model select a USER
63. ou do not know what value to enter you can select the current position by clicking Geif Figure 3 3 Maximum position tab Minimum Maximum Center Motor Foss 100000 Pos A 2 Pos Y 100000 Posm2 O PosZ 100000 4 fe HH oTo The X coordinate of the maximum position The R coordinate of the maximum position The Y coordinate of the maximum position The R2 coordinate second rotation of the maximum position The Z coordinate of the maximum position Button to acquire the actual position coordinates Y Oo9O09090 V9 O Button to automatically go to the maximum position on each axis 3 2 1 2 3 Center position Center is an optional parameter that lets you establish the center of the X Y Z and R axes You can define as many centers as you like For instance if the stage contains multiple slides you can define a center for each Make sure that you have correctly selected the center index before entering its position For a single slide you can move the stage to a particular position and click Get Either way use Script to define a center serial Mremer TNPC User guide March 2011 Chapter 3 Image acquisition Figure 3 4 Center positions tab Minimum Maximum Center Motor Mb Flate a 1 Nur Plate Pos E 2500 Fos A ry 0 Pos Y 20 Por 0 Pos 7 0 47 Genf lt gt Scrip E 97 Oo9Q09090 D9 Q Button to define a center serial The number of plates on the s
64. re the estimated age Store the growth pattern in a iid file located in the iid folder Store the estimated age in a datasheet in the graphic window Store the growth pattern in a datasheet in the graphic window Add or remove one to the number of rings for age calculation o0 0000 6 2 5 Back calculation This tab is the exact same than for annotation Please refer to Section 4 2 5 Back calculation for more info 6 3 Otolith live annotation 6 3 1 Start image acquisition To start the acquisition click on The image coming from the camera will be displayed on the screen Y ou can then start the creation of the radial and add rings or false rings to it Mremer TNPC User guide March 2011 Chapter 6 Live Expert Mode 54 6 3 2 Create radials To start creating a radial click on You will see an icon enabling the motorized stage movements appear Figure 6 6 Motorized stage movements icon Warning Always use the motorized stage movements icon to move the stage If you use your controller joystick the radial creation will fail You can effectively start the radial creation by clicking on the image on the start point You can then select intermediate points by clicking on their location on the image If you need to move the stage it is advised to position a radial point near the image edge by double clicking on the it that will pause the radial drawing You can then move the motorized stage using
65. red After blue CONAN e A SSS tt ti ptt TTT ETT PE Ee eT AA Lol raras Lowy Let LA pt Beer tT TATA TM A IN HI We E ee eet ee ae ae O SS O S N 39 A A A A 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 Show Hide the DETREND function parameter Activate the demodulation function This function creates a demodulation of the intensity profile using an a priori growth model The intensity profile is seen as the result of the modulation of a periodic signal daily or yearly modulated by the fish s growth pattern To be used the DEMOD function needs to have the growth pattern values defined such as L which default value is 120 and K which default value is 0 2 for the Von Bertalanffy model and Lg and K for the exponential model The first model is available only if the back calculation function is activated see Section 4 2 5 Back calculation the exponential model is always available Figure 4 7 Use Demod function Before red After blue i 1 05 10 20 5 60 90 100 110 120 Show Hide the DEMOD function parameter Activate the TOPHAT function This function detects the relevant peaks by default or valleys of the intensity profile You need to set the minimum default 5 and maximum default 50 width of the structures to be detected and the threshold default value is 0 for the hat height T
66. rical results in Result Viewer ai 45 Snape analysis Aa sde la A las diles 46 La pe analysis Senasa dos 4 D gt Measures SElECTION NS AA A 48 DA Good threshold Bad threshold ur ea na E AEO A Ai 49 DOs dre d econ e SWE sal 49 SO ANY SIS TES UE aiia AE A E E 49 Ie WICASULC DA arie dt A N E sia tive tas late tisatudetouteanes 50 0 ENADO T ee ce en ee 51 O GCC hal eC ode aes 51 037 Checks Seine s s ean a a a ase rae hair a had ee ates 52 O74 ACUS GOs eos da iaa da 52 KPP SONES dd IA AS e AAA A 53 6 6 Motorized stage MOVeINENIS ICON loli E a alcios 54 7 1 Apprenticeship of individual age Global information oooccoccnconcnncncnncnconcnnoncononcnncnnoninnoos 56 72 Apprenticeship OF mdivid al AVE ACC dada 56 7 3 Apprenticeship of individual age Segmentation cc ccece eee ce eee e eee eeceeeeaeneeaeeseneeaeneeas 56 7 4 Apprenticeship of individual age Nucleus detection ccc cece ec eceec scence eee eeeeseneeaeneenes 57 7 5 Apprenticeship of individual age Radials oooooocccconcnconcnnononnoncnncncononnononnoncnncnnononnns 57 FOs Create the caras le IA AA AO 57 7 7 Automatic estimation of individual age ccc ccecc ec ece eee ee eee ee eee ee eae ee eases eens eneeaenseeeeaeneeas 58 7 8 Automatic estimation of individual age c ccc cee cece cence a a e eee ees eens a aaa 59 7 9 Automatic estimation of age structure window cccecc ee ce eee e cece nent eee e eee eee
67. rol Y Yes 5 C No Control Z Ye G No Control A C Ye No Control R2 C Ye Ed f No Home is 0 Yes No Speed eel 50 Speed home FO 1 Speed joy Hu 1 Acceleration Hp 0 Minimal Position Home C Negative Nb Z Ove Switch 0 Z parking position Current A Y Ok Cancel Help The type of your controller If you do not find your controller in this list please contact Noesis a Whether the controller is initialized or not You must choose disabled if you do not have a controller as in Demo mode or 1f it is not connected The port used If the X axis 1s controlled If the Y axis 1s controlled If the Z axis 1s controlled If the R axis 1s controlled 9909090 9 9 If the R2 axis is controlled second rotation Whether the Home position is the same as the reference position The movement speed The speed to go to the Home position The speed when using the joystick The stage acceleration Whether the minimal position is the Home position or the controller accepts negative values The number of electronic stops along the Z axis 9GQ 2e0 989880 OD If you want the Z axis to stop at a certain point when TNPC close Use this 1f you do not have electronic stops along the Z axis You can still use it if you got electronic stops fremer TNPC User guide March 2011 Chapter 3 Image acquisition 16 3 2 1 2 Stage parameters When your controller is
68. roperties WIACOW a ad 10 20 Database VIEWS USC o a 11 Ae AAA EE a tae pesca isa Adee taye ae cides E ta hd ae nna ed 11 20 Ereate asdatabase Tonm ANC LS TING la beats casa olor aaron cuales 11 Dele The database SEUINaS WNION viii E T 13 2 9 Ine database ExpOrtaoOm Window variado riada astra 13 Ss Controller ctas a is 15 2 MINIMU POSON LADY iia 16 Jos MAME POSION AD sai silos 17 5 4 COME POSITIONS TADA A AAA AE teens tae 18 3 5 Center seral script WIAOW sia A A A AAA A AE 18 KO MOTOT Gell het trade ol A ee Satna ta en A Suana cs teanen sean ne enema omental renee 19 Dia NMOTOS CONO SCINS A SA healed tween 20 S10 IVIICTOSCOPE Paramcters cr tea Gectes dis thot lade wits toute tania 21 TO AUTOLOCUS SENE Ss scada died id sai 22 3 10 Autofocus parameters Z motion tab ari seeadsediusne ta ssmadeatacance s 23 3 11 Autofocus parameters Acquisition tab ai A A Samlacas 24 3125 Ao mat o ZOOM CONVE ION aaa e 25 3 13 Acquisition parameters ACQUISITION tab ooooococcccocccconcnnoncnncncononcononnoncnnonnoncnnoncnnnnnanonos 25 3 14 Acquisition parameters Process tab 1 do lso 26 315 The noise red cton parameter adjustment lt onsi eia irei a NEE aN N E 26 3 16 The contrast enhancement parameter adjustment ooooocccoccnconcnnoncnnonconcnnoncnnoncononnnnnnnannnnonos 2i S17 Acquisition parameters General tab atada 21 3 18 Acquisition parameters Sharpness tab sssssssssesssseesssressssresssresssoresseressseresseressseres 28
69. s On the right you got a tree representing each group and the measures in each group To add a measure to a group select the group in the right part and the measure in the left part and click on 22 To remove a measure from a group select it in the right part and click on lt You can also add or delete groups 5 2 2 Other settings In addition to the measure group settings you have settings to save the contour and analysis or not export those values to the RESULT VIEWER and or the database You can also change the precision of the edge detection algorithm Like in all the tabs you can save those settings 5 3 Results 5 3 1 Edge extraction To obtain information about otoliths shape you have to extract the otolith edge first To access otolith s edge extraction you have to click on amp This function extract the background by applying thresholds on the picture before calculating a polygonal approximation of the edge This approximation uses precision parameters specified in the settings see Section 5 2 Settings for more information To perform a correct edge detection you have to adjust the thresholds in the grey levels bar under the picture Make sure all but only the otolith is in red some noise might still be in red it will be discarded by the polygonal approximation fremer TNPC User guide March 2011 Chapter 5 Shape analysis Expert Mode 49 Figure 5 4 Good threshold Bad threshold
70. s First Se S 24 A Se ee A NEEE N See enna Cn E Sire er een E S ere ter eer 25 Fess A CSONT A A E E E 25 VS POCS NA E A 26 o General rd tdi tata 2i 5 9 4 Sharpness EXPEC Mode k asii ias idos 28 IA Standard dC QUT SION srera earo a a E 28 0 Mosa cS AE XpPerlMOGe id 28 Jade Makea Mosaic roma tra CCO ro a a EI A E NEA 28 X2 Makea mMO C Ob MES a ES E eds weanigeam os 31 3 5 53 Make a Mosaic Trom tWO ImMades niii errie E ae ees 32 3 6 Image batches acquisition using scanner id bs 32 31 Cutrent mase processing Expert mode nestle 35 A AMO CALDOS e dd 36 Be Ne CMe A A E E 36 AS e ad el 36 A TOUS A A AA 36 BD EPONE lt peaien ce ena cena dete as maaan aoa eet E A ARR ar Aza Process EXP MOU a ia 38 4 2 4 Interpolation Expert Mode uni A A A ENE 40 AD Dd Baek calculation di atada ba 41 4 30 POSsiliOn Tadia and Markers arcilla 42 43l Position tadidls dd dl 42 Fremer TNPC User guide March 2011 TNPC V A POSIMOM MARES ds 43 Bids DCM SAV ada S PEO OP bie A hata 43 4 Grape abresults cd db decias 43 A als MENS POG EA EA A ASA 44 AZ ARO WI DALIA is A AA A a 45 A YoU CHICANO GUIS esse extrude a Shia a a A Antal apace etn Os Sy awesome caat 45 shape analysis EXPEC MOUC a O ANA a A aa 46 Dl General OS araa aa AE N 46 IA CANE a a I a A a eta ein cues 46 A The Measures SOUPS nn e a aai 47 IAN O o A E a A ued c tals elias 48 PR UIE senan er a A a Dnieper ena taeayeaes 48 Ie o A E E EA A AA 48 O ANALYSIS A E
71. se of motorized stages you can usually move the stage on the X and Y axis and sometimes on the Z axis too TNPC User guide March 2011
72. silog 6 features and you can find the appropriate documentation in the Visilog 6 documentation on the TNPC CD ROM We made the choice not to reproduce in this documentation all the Visilog 6 manual Warning All this documentation describe the expert version of TNPC The routine version being a simplification of it you can also use this documentation If you need something that is not present in the routine version you will need to install the expert version instead On this documentation graphical user interface elements are decorated to make them distinguishable Buttons are represented like that I am a button Other graphical elements such as window title tab title important words are displayed like that I AM A GRAPHICAL ELEMENT They might not look exactly the same on your screen Some terms are specific to halieutics or sclerochronology They are explained in the glossary at the end of this documentation The same way some terms are abbreviated in this documentation They are explained on the first occurrence and in the glossary If you do not know what something means you might find an explanation there 1 Traitement Num rique des Pi ces Calcifi es Numerical Treatment of Calcified Structures 2 Calcified Structures 3 IFREMER institute website http www ifremer fr anglais Fremer TNPC User guide March 2011 Chapter 1 Generalities 2 To help you find exactly the information you want you mig
73. story of individuals from measurements of increments within otoliths or calcified structures Correct application requires a model of the relationship between otoliths or calcified structures growth and fish somatic growth and assumptions about the constancy of increment deposition You can refer to Green BS and Mapstone BD and Carlos G and Begg GA Tropical Fish Otoliths Information for assessment management and ecology Springer Dordrecht pp 313 ISBN 978 1 4020 3582 1 2009 for more information A Calcified Structure or Calcified Piece is a part of living being made mostly of calcium carbonate such as coral reefs shellfishes or fishes otoliths It can usually be studied using sclerochronology See Also Sclerochronology Otolith TNPC User guide March 2011 Glossary Check marker CH marker Conseil International pour l Exploitation de la Mer CIEM G Growth structure marker GR marker H Halieutics International Council for the Exploration of the Sea ICES Image format Fremer A check or CH marker is used to identify false rings checks on a radial See Also Radial See International Council for the Exploration of the Sea A GR marker is used to identify growth structures on a radial See Also Radial Halieutics can be defined as The science of living aquatic resources running It tends to integrate new dimensions such as resource management or restoration in a sust
74. tage The number of the plate you are editing The X coordinate of the plate center position The R coordinate of the plate center position The Y coordinate of the plate center position The R2 coordinate second rotation of the plate center position The Z coordinate of the plate center position Button to acquire the actual position coordinates 18 If you want to use a script to define a center serial please refer to the Visilog 6 Stage module documentation page 1 12 Figure 3 5 Center serial script window Script EX Nb Center gt 8 Nb Center fY 4 Type center 6 ooo poon Select the first center Pos Xc1 12050 Pos Yc1 12050 PosZe1 15000 2 GetCl Select the last center Pos cN 47260 Pos YcN 47260 Pos ZcN 15004 2 GetCN w Ok Cancel Help 3 2 1 2 4 Motor parameters In the motor parameters tab you have to enter the step size for each motor Once these values are set the jog menu will automatically have distance steps available such as lum 10um etc By default the stage controller assumes that all measurements are in microns Once you have set all other measurements and calibrations for autofocus etc the measurement units are automatically updated Fremer TNPC User guide March 2011 Chapter 3 Image acquisition 19 Figure 3 6 Motor tab Minimum Maximum Center Motor step microns Dd 1 A step degrees 2 MI Y step microns 3 1
75. the calibration 2 Add in the database Color channel Green EY Images type mb ry r 5d Save the color images in grey levels Insert the calibration in each image Add the acquired image in the database The color channel to use when you got a color camera The image format For more info read mage format A 90 080 Whether to save the color images in grey levels fremer TNPC User guide March 2011 Chapter 3 Image acquisition 28 3 3 4 Sharpness Expert Mode Warning This tab 1s useful only 1f you got a stage with a motorized Z axis Figure 3 18 Acquisition parameters Sharpness tab Acquisition Process General Sharpness o Multiplan acquisition Number of acquisition ex 11 Interval pm a 1 0 Make a multi plane acquisition and calculate the best image The number of acquisition to perform around the current position for each image 9 The interval length on the Z axis between each acquisition 3 4 Standard acquisition The standard acquisition process consist in acquiring what the camera can see To acquire an image in standard mode click on The camera is now active and you can see what will be acquired in the main window A new icon is shown in the tab Click on it to freeze the image you want to acquire A window pops up If you choose yes all the processes you defines are then applied see Section 3 3 2 Process The resulting image is displayed in a pop up
76. ts will use this number 6 2 2 Checks The checks settings allow you to manage the interpolation function cf Section 4 2 4 Interpolation Expert Mode and the markers size configuration Figure 6 3 Checks settings Marker width 1 25 e Show growth pattern Type of Interpolation 65 Density A Polynomial Degree of the polynomial A 3 You can set here the marker size Show the growth pattern in the RESULT VIEWER after calculation Activate the density interpolation Activate the polynomial interpolation oOo 0 9 The degree of the polynomial interpolation 6 2 3 Acquisition The Acquisition settings allows you to choose the image type of the image acquired and some parameters about the acquisition Figure 6 4 Acquisition settings Create a mosaic a Inzert the calibration Images type im gt Allow the automatic creation of mosaic pictures Insert the calibration in the picture might be a mosaic y Choose the output format of the image 5 formats are available For more info read mage format Fremer TNPC User guide March 2011 Chapter 6 Live Expert Mode 53 6 2 4 Export In this tab you can manage all the export settings Figure 6 5 Export settings Save Export x Radial 5 Age 5 Growth pattern Export the age eS Export the growth pattern Modify the age O fr Store the radial in a rad file located in the rad folder Sto
77. ve a motorized stage you still can make mosaics using two images Open the interface clicking on You then have to choose the two images they need to already have been loaded in TNPC state how to perform the mosaic and then click on Create Figure 3 24 Mosaic manual creation naaa Image 1 d i Image 2 La bd Horizontal OL C vertical Overlapping percentage 4 20 0 Size of the search area 5 20 6 Create The first image The second image Make the mosaic horizontal or vertical The overlapping rate between the two images 9000 The tolerance in the direction normal to the displacement ie horizontally when you select a vertical mosaic Launch the mosaic creation 3 6 Image batches acquisition using scanner When you do not have camera and stage you can use scanners to acquire images Scanner can allow you to acquire either images batches that will then be separated or images alone Fremer TNPC User guide March 2011 Chapter 3 Image acquisition 33 Warning Take care about this acquisition mode as the precision might not be enough to make interpretations on the image after acquisition To perform a scanner acquisition click on A window will pop up allowing you to choose between the scanners installed on your computer Choose the scanner you want to use and click on Select G Note To be used in TNPC your scanner have to be installed on the computer first To do so
78. window while the main window still shows what the camera sees for the next acquisition 3 5 Mosaics Expert mode If the camera field does not cover the entire field of analysis image mosaics can be acquired automatically using the controlled stage 3 5 1 Make a mosaic from a trajectory 3 5 1 1 Build a trajectory To build a mosaic you first need to set a trajectory To do so go to the STAGE window Fremer TNPC User guide March 2011 Chapter 3 Image acquisition Figure 3 19 Stage window DD 1d A Jog 1 step Pos X 50 Pos Y 50 Lens y 1 Magnif 1 Type of coordinates Absolute Relative Field e All One Center CAN Current WBA Project x WBA Macro bos 29 At the beginning of the session initialize the motorized stage by clicking on Y The stage will move until it finds its origin value Activate the joystick by clicking on Click on to open the configuration window of the stage The trajectory will be calculated from a rectangle You have to give the two opposite points of the rectangle so that the trajectory can be computed Move the stage to the starting point P1 of the mosaic with the joystick then read P1 clicking on Get Pif Then move the stage to the ending point P2 and click on Get P2f The distance between 2 fields must be 98 on the X and Y axis In the tab the field EDGE OVERLAPPING must be ticked Visualize the trajectory by clicking on Si
79. you want to translate TNPC in Spanish In this copied directory open all the Lng files and translate all the sentences Each sentence is displayed like in Example 8 1 Sentence to translate The first part is a key the second part is the type of message the third part is the displayed sentence This is this third part that you need to translate Example 8 1 Sentence to translate frmAcqMosaique Caption Acquisition Mosaic Example 8 2 Sentence translated in Spanish LrmAcgqMosaique Caption Adquisici n Mosaico Once all your sentences are translated you have to change the language in the file data Tnpc AddLang cfg You can see the content of this file in Example 8 3 The AddLang cfgfile Between the empty quotes put you language code For example for Spanish put es Example 8 3 The AddLang cfg file Additional Language 8 2 Add Change species available If some species you want to study are not available in TNPC or if you only use some of the provided species you might want to add the missing species and remove the useless ones To do so open the file data Tnpc lang yourLanguage Species cfg After the first line stating the version of TNPC you have the list of species with one species per line Each line is compounded of two values between quotes The first one is the scientific name the second one is the common name You can add new species at the end of the file or remove the li

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