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AIM - Guide Utilisateur

1. use the button or the shortcut key F12 and Youlez vous vraiment supprimer lafles ligneis de la table Aim Fen Liste Valeur Tab_4IM205_TYPE_ETUDE then confirm the deletion process ou Authors B Moutault amp C Chevalier Date 20 08 2012 Page 17 Version 1 5 1 1 Condition Conditions describes the framework within am20o var conomon pa which you have acquired your series of images un Panne Tanne aT Conditions enable you to keep a specific numerical DURE Dur e exploitation value for each study acquisition Fr quence Grossissement Heure r f rence Image r f rence The most common example is keeping the LUMI Luminosit M N oa magnification ratio in order to ensure traceability O en and or to use it during the image processing phase Nombre Cellule Par Ligne or the calculation phase to transpose measurements _ Een in pixels into millimeters SDEP Seuil d placement The table AIM200_VAR_ CONDITION contains a in A La ei 7 unique code and a label Reminder The rows highlighted in red indicate that the registered entry is already being used in a study and can no longer be deleted or modified 5 1 2 Result variables Result variables have two uses extracting measurements columns from results files predefining them by their labels calculating new result variables using a formula applied to a results table similar to the way in whi
2. Default enables you to select the executable file path by default as defined by the IT service of your company It is stipulated in table STD_IDENTIFIANT 6 5 Download Download enables you to open the ImageJ software website directly on the downloads page http rsbweb nih gov ij download html 6 6 Online support Online support enables you to open the ImageJ software website on the homepage http rsb info nih gov ij index html Online support for macros http rsb info nih gov ij developer macro functions html Authors B Moutault amp C Chevalier Page 35 Date 20 08 2012 Version 1 6 7 Close automatically CD Close automatically is an option for automatic closure of the image processing software when it s opened in the Analysis and Quick Processing windows Authors B Moutault amp C Chevalier Page 36 Date 20 08 2012 Version 1 Fast Processing Quick processing Menu CD Fast Procesing 7 1 Quick processing As its name suggests this window enables you to process a series of images quickly The study declaration and integration of results stages are bypassed although they can still be accessed if necessary File Study ME Fast Processing Processing Software Referential Options Module Window Help List of macros 31 A03_A_NOM_DESCRIPTION CHANGER Format MO STANDARD tous types dimage vers un type pr Load images CO
3. Page 47 Version 1 9 1 1 Consultation Using the Search criteria bar the list of studies can be filtered by study type name of study and by species code and label Search Criteria You can use the 4 hk When selecting a study in the main table it is possible to consult the list of materials in the details table in the Materials tab the list of acquisitions in the details table in the Acquisition tab the list of macros in the details table in the Macro tab 9 1 2 Create Modify To open the window to create a new study use the shortcut key F10 or click on the ki button i _ Similarly to modify a study select a row and use the shortcut key F11 or click on the a button Authors B Moutault amp C Chevalier Page 48 Date 20 08 2012 Version 1 te Modification of the study n 4 Type of study Exe nple Name Finesse des feuilles Establishment 0 3325 Groupe d Etude et de Contr le des Vari t s et de Brion SEV Person o 2413 RETAILLEAU Jean Michel ee DUS Species 40811 Carotte x T T Date of Receipt 24 10 2012 Addressing define default values Desired Date of Retum 1 Number of cells per Line by Zone Zone layout Mesurer la surface et le p rimetre des feuilles de carotte et calculer leur rapport De facon a exprimer la finesse des feuilles Indicate the study type
4. Download 35 6 6 Online support 35 6 7 Close automatically 36 7 Quick processing Menu 37 7 1 Quick processing 37 7 1 1 How to use this feature _ 37 7 1 2 Study 38 7 1 3 Images _ 38 7 1 4 Macros __ 39 7 1 5 Analysis __ 40 8 Macro Menu 41 8 1 Management of Macros 41 8 1 1 Consulting a macro _ 42 8 1 2 Create Modify a macro 42 8 1 3 Deletion 45 8 1 4 Import Export _ 45 9 Study Menu 4 9 1 Study declaration 47 9 1 1 Consultation 48 9 1 2 Create Modify _ 48 9 1 3 Deletion 49 9 1 4 Materials 50 9 1 5 Acquisition _ 51 9 1 6 Macro __ 53 9 2 Analysis 54 9 2 1 How to use this feature _ 54 9 2 2 Macros __ 39 9 2 3 Images _ 56 9 2 3 a How to use this feature 56 9 2 3 b Loading images __ 57 9 2 4 Files 58 9 2 5 Analyses__ 59 9 3 Integration 60 9 3 1 Processing history and results files _ 60 9 3 2 Display __ 61 9 3 3 Options __ 62 9 3 4 Integrate 64 9 4 Calculations 65 9 4 1 How to use this feature _ 65 9 5 Results 68 9 5 1 Display __ 68 9 5 2 Type of result __ 69 Authors B Moutault amp C Chevalier Page 4 Date 20 08 2012 Version 1 9 5 3 Clustering 9 5 4 Deletion 9 5 5 Graph ___ 10 Windows Menu 10 1 How to use this feature 11 Help Menu 11 1 How to use this feature 12 Freque
5. 5 5 2 Color Functions This option enables you to activate the Color button in the following windows Integration Calculation and Results 9 3 9 4 and 9 5 Authors B Moutault amp C Chevalier Page 31 Date 20 08 2012 Version 1 List of olor Active ar List of Lolors Inactive L Color Functions _ Color Functions In AIM windows when you click on the BE on a Sub menu appears Color lines RGB HSL Groups Colors Caption 5 5 3 Coloring the rows RGB HSL This feature enables you to color the rows in the results tables described by their plans for a better visual appreciation of the colors This is often achieved using the RGB color model but also by using Hue Saturation and Luminosity or directly by using a number from the AIM color gro TYPE_OBJET_NUM OBJECT_SERV R OBJECT_NUMBER Indicate the color reference OBJECT NAME IMAGE_NAME LINE COLUMN In order to ensure correspondence between the columns in ER Pixel_ results and reference plans dOuble Rusa 3 Pixel RHS click or use the arrows ae _AIM14_RESULT_CELLULE IMG _ 583 SCT NUM OBJECT_NAME a IMAGE NAME ALIMENT D_SF_3 5666_1 bmp D_SF_3 5666_1 bmp a 1 ol i F F mi cl b_SF_ 35666 1 bmp D_SF_35666_1
6. DED SEES I NOES EE C53_V_NOM_ESP Espece inconnue Betterave Orge Colza Toumesol Bl Laitue Tomate P cher Nectarinier Current DataBase C Mes Projets Aim Exe Base Current field ColTab_C53_V_NOM_ESP 5 6 1 Consultation The three tables are split into three tabs 5 6 2 Create Modify In order to add a new entry place the cursor on the last row and type in the entry field The codes used should be unique and the labels should be non zero Note for individuals the ACTIVE Y yes N no column enables the individual to be masked or displayed in the input windows The same applies for companies 5 6 3 Delete To delete an entry select it and click on the a button Note If an individual or company is no longer valid it is preferable to deactivate it rather than deleting it Authors B Moutault amp C Chevalier Page 34 Date 20 08 2012 Version 1 6 Processing Software Menu O Processing Software Open Application Path F Ge Detine By default Download F Online Help Automatically Close 6 1 Open Open enables you to launch the image processing software 6 2 Application path Application path enables you to consult the executable file path in grey as defined on your computer 6 3 Define Define enables you to select the executable item path and name of third party software 6 4 Default
7. GEVES Expertise amp Performance A I M User Guide Image Analysts Authors B Moutault amp C Chevalier Page 1 Date 20 08 2012 Version 1 AIM facilitates the processing of images using third party software ImageJ AIM enables you to establish a framework for your studies date client species device carry out processing operations and obtain results in one click archive the following in a database your Series of images your processing operations ImageJ macros your results files your individual measurements your clustered measurements grouped by variety image etc calculate new measurements for example convert pixels to millimeters cluster results by variety image series and to present them filtered in table format in the form of a graph for export into Excel AIM simplifies processing operations for users by encapsulating them automatic execution one click through the integration of history functions traceability rights management user or super user color management UPOV RHS and by displaying results in the form of a graph curve histogram AIM facilitates multi user multi workstation usage of the same project study as well as the sharing of processing operations ImageJ macros or results between partners bodies companies The field of imaging is becoming an increasingly integral part of our studies and professional projects on a daily basis Th
8. Date 20 08 2012 Version 1 Search Criteria You can filter the list of images Type f i displayed by using Search criteria select type of image I Initiale Inversee Yan Ue od This filter is very effective when P_yant m Tr Fun i i lodti e Coule using different types of images NBP ae Niveau de Gris color black amp white superimposed Superposee Couleur 9 2 3 b Loading images You have four options for loading images into acquisitions directories Select the acquisition then in the Images tab click on the Add button search for the images on your computer and confirm your selection Select the acquisition place cursor on the Images tab from your desktop Windows select the images and drag and drop them onto the AIM list Select one or more acquisitions S and click on the u button This method works if you have defined the loading directories in the Declaration window 9 1 5 AIM will load all the images it finds by acquisition even if the image had been previously uploaded E Click on and indicate the directory containing all your images A list will appear with the titles of the images the order of which can be changed 1f necessary E a You can select another directory and remove specific images Comment The fourth option is available when loading all your acquisitions The order of your acquisitions in this list is im
9. indexing options AIM uses the names of columns X and Y for the calculations If the names of the columns are different in your results file you can indicate this manually Indexing column name X Indexing column name Y aai You can also relaunch indexing manually using the ton Reminder the names of the images sent for processing by macro are modified by AIM AIM concatenates the image code making it possible once measurements are returned to know under which image and acquisition the measurements should be saved Caution When saving measurements the image code is important because it provides a link with the description of the material made in the study declaration If AIM cannot make that connection it will require you to enter a valid image code manually To do this AIM opens a text file Lecture txt containing the list of valid images and their codes Authors B Moutault amp C Chevalier Page 63 Date 20 08 2012 Version 1 Fichier Edition Format Affichage can not find the image code in the following label Here is the list of images 7 digit codes 1 that can be used to finish the display Orchide_Variety_415000003 Wf the results file r a a Please enter it manually example 9003746 een orchide_extract bmp 4000009 Tick wo orchide_v1 bm 4000010 orchide_v2 4000011 5 i i 4000012 10 oO o yo id bm 4000013 rchi 4000014 orchide_v6 4000015 9 3 4 Integrate I
10. 3 1 1 2 5 2 5 3 Zone 3is at the bottom left of the images 5 4 4 5 4 4 Delete To delete a layout and the zone details select it and click on the button or use the shortcut key F12 and then confirm the deletion Authors B Moutault amp C Chevalier Page 29 Date 20 08 2012 Version 1 re AIM Managing image processing and analysis Management of zone layout File Study Macra Fast Processing Processing Software Beferential Options Module Window BE Ie ME Ee eS Ha EN EE IE ele AIMO DISPOSITIF ZONE AD7_A_NOM hg A Pas N AD7_CL_DESCRIPTION Unique Double Care Ace En 16 zones Confirm deletion of the layout Square 2x2 COPY Thank you AIMO8_ZONE 4 miss 08 CRAO7_NUM_DISPO 2 fone 3is at the bottom left of the images 4 Current DataBase Ange_Adre User moutaultb Current field 5 4 5 Example A study is being carried out on the color of leaves from a dozen plant varieties A sample of some twenty or so leaves for each variety has been collected in the field Ex 1 A zone layout with zone is selected so that each scan shows only one plant variety This will make the operation easier A 1 zone layout has been created By LINE By COLUMN A zone layout with 4 zones 1s selected so that each scan contains 4 varieties or conversely so that a single variety may be spread out over 4 scans This feature ensures that a a failed scan does no
11. 3 1 4 Menu bar The menu bar and sub menus enable you to access the various windows of the software package by left clicking However you can use the keyboard by holding down the Alt key and pressing on the appropriate underlined letter at the same time ee File Study Macro Traitement Rapide Processing Software Beferential Options Module Window Help Comment Additional information on this menu bar is available further on in this Guide 3 2 Functions available in different windows 3 2 1 Exporting a table The icon can be found in the top right hand corner of all tables This icon provides you with the following options You can export the information contained in the window into various formats Excel Word Benjamin Benjamin Jean Michel Vincent E IAT Berard O Valerie Jean Michel FEE Select columns meee BE LEE S 2 4 En T o wi Eu Er m Oo Le Mi m j W Export table to Word Export table to XML Print D Charts Authors B Moutault amp C Chevalier Page 10 Date 20 08 2012 Version 1 You can select columns to display or hide or this can be done directly by right clicking on a column heading AD1_C_ETUDE SERV D NAKTUINEOUW le A01 C ETUDE Groupe d Etude et di le Groupe d Etude et di ily AD1 A NOM A205_A LIBELLE Cane Eee Etude Hortensia 3 2 2 Sorting and searching It is possible to sort columns by clic
12. 6 C COM A206_A_LIBELLE A206_A TEXTE 50 COUN Compte COUNT ECAT Ecarttype STDDEV MAXI Maximum MAX MEDI M diane MEDIAN MINI Minimum MIN MOYA Moyenne Anthm tique AMG NDEF Non defini AVG I then select the type of clustering required by zones and images That means I want to remove the cell feature in order to have only a single volume measurement per variety and time I confirm by clicking on the ln button I call up a display by selecting Image Zone I then locate the clustered averages for volume and time with a measurement per variety and per image AIM21 RESULT ZONE IMG 189 Volume Temps Fr OBJET OBJET NOM REPETITION AONE NO IMAGE NOM Moyenne 4 Moyenne 5 l Arthmetique Arthmetigue Non defini 4 1 Vanete_ 1 1 HG MB Mais 0902161545 1000 prg 11 7588 0 Won d fini 9 2 Vanete_ 1 HO MB Mais 0902161545 1000 prg 11 443 0 Non d fini 4 3 Vari t _3 1 EG MB Mais 0902161646 1000 pra 12 1913 0 Non d fini 3 4 Vanete_ 4 1 BD NB Mais 0902161545 1000 prg 11 3116 0 N on d fini 9 Wari t _1 1 ME Mais 0902161743 1001 pna 11 9045 2 Hon d fini 3 a Vanete_2 1 ME Mais 0902161743 1001 pna 6382 2 Hon d fini 9 3 Yarete_3 1 ME Mais 0902161 43 1001 png 2 Hon d fini 3 4 Vanete_4 1 ME Mais 0902161743 1001 pna 1828 2 Non d fini 9 1 Wari t _1 1 HG MB Mais 0902161943 1002 png 11 984 4 Non d fini 49 2 Vanete_2 1 HO MB
13. for which a processing result will be archived you are prompted to delete it 5 1 4 Statistical parameters AIM205 PARAM STAT W cC CO A206_A_LIBELLE AZ06_A_TEXTE_SG L NDEF undefined AVG a MOYA arithmetic mean AVG MINI Minimum MIN MEDI Median MEDIAN MAXI Maximum MAX ECAT standard deviation STDDEV This feature enables you to define a number of statistical parameters by specifying the SQL syntax required in order to cluster the results generated by AIM Note SQL syntax must be compatible with ORACLE for AIM use within GEVES and with HYPERFILESQL for EXTERNAL use Example STD MAX MIN COUNT AVG MEDIAN SUM VARIANCE 5 2 Experimental condition CD You must define the experimental conditions for each new AIM study This enables you to provide additional information during the automatized processing of data or calculations Authors B Moutault amp C Chevalier Page 21 Date 20 08 2012 Version 1 In general these conditions are identical within the same study type That is why experimental conditions are listed by type This window enables you to consult and manage conditions add modify delete AIM Managing image processing and analysis Management of experimental conditions l eo ee File Study Macro Fast Processing Processing Software Referential Options Module Window Help ME x ICE BIEN Ne Search Criteria You can use the Type SNES Phenotypi Name Species List of lists
14. thode simple seuil automatique ee nn 17 OUVRIR mage STANDARD ouvre dans le logiciel de traitement lesir EG ne teris TnT 50 091 AJUSTER Contraste STANDARD permet d ajuster automatiquement le cor run Colors foreground black background white sele 501050 7 DECOUPER Fornes manuel STANDARD permet de d couper une partie de limas Y z voir ou non les images 55 EDITER Film STANDARD Pr sente les images en stack film If 40 MESURER Pixel STANDARD Surface p rim tre largeur hauteur lon set BatchMode Vi_En_Cacher_Image 38 CHANGER Format STANDARD tous types d image vers un type pr cis H a a pe 39 INVERSER Couleur STANDARD tous types dimage vers un type pr cis ee ee ee ee Veen re BINARISER Manuel YAN Colza cotyl dons m thode simple seuil fixe _ M_En_Nombre_Fichier VI_Tab_lmages length 1 1 UBSEHEE EEE E aa m ss gt E S_ SCINE_ NE u Een View Text List of macros which it depends 0 List of macros that use 0 Current DataBase Ange Adre User moutaultb Curent field Ong_Liste_Macro Reminder A macro is a scripting language which enables you to automatize a sequence of actions Macros are saved under the file format TXT text The Image J software has a save function to record actions performed record which renders the process of writing macros more simple Authors B Moutault amp C Chevalier Page 41
15. 1 Exporting a table 10 3 2 2 Sorting and searching 11 3 2 3 Layout of columns in a table 12 3 2 4 Managing windows and tables 12 3 2 5 List of values _ 12 4 File Menu 14 4 1 Send a message 14 4 2 Application GEVES 15 4 3 Switch database GEVES 16 4 4 Change password GEVES 16 4 5 Screen shots 16 4 6 Quit 16 5 Referential Menu 17 5 1 List of values 17 5 1 1 Condition __ 18 5 1 2 Result variables_ 18 5 1 3 Type Image Object Study and File 20 5 1 4 Statistical parameters __ 21 5 2 Experimental condition 21 5 2 1 Consult __ 22 5 2 2 Create Modify_ 22 5 2 3 Delete __ 24 5 3 Medium and Source 25 5 3 1 Consult __ 25 5 3 2 Create Modify_ 25 5 3 3 Delete 26 5 4 Zone layout 27 5 4 1 Consultation 27 5 4 2 The concept of ZONES __ 21 5 4 3 Create Modify_ 28 5 4 4 Delete __ 29 5 4 5 Example 30 5 5 List of Colors 31 5 5 1 Consultation 31 Authors B Moutault amp C Chevalier Page 3 Date 20 08 2012 Version 1 5 5 2 Color Functions 31 5 5 3 Coloring the rows RGB HSL __ 32 5 5 4 Color Group Labels 33 5 6 Species Individual Company Non GEVES 34 5 6 1 Consultation 34 5 6 2 Create Modify_ 34 5 6 3 Delete _ 34 6 Processing Software Menu 35 6 1 Open 35 6 2 Application path 35 6 3 Define 35 6 4 Default 35 6 5
16. Date 20 08 2012 Version 1 8 1 1 Consulting a macro CD When selecting a macro in the main table you can consult the list of macros containing that macro in the details table The macro text in RTF will be shown in the right hand part of the window but cannot be modified here Using the gt View Text button you can open the macro in a text file the default program in this case is Bloc Notes without RTF formatting 8 1 2 Create Modify a macro To open the window to create a new macro use the shortcut key F10 or click on the hie button whic indicafes ihat the creator foro and the operation of fhe macro MACRO Fach AlM mace confains a pat HEADER which indieafes varables and valves easily undersfandahle by fe user Macro body Each AlM maco contains a pat BODY mich uses vanables of fhe AUTOMATIC HEADER and of ihe HEADER that checks the version and options of image processing software that fests the image ist Because FES emoty E musi update FW Tab_images eng 0 if Tab images gefhlelist W_ Sr Repsource whit Joaos on fhe image dst of fhe source directo V Str Aeosourvce fhat records images and results in the destination directory W_Sir_Aepdestina Fach AlM maco contains a pat OUTPUT that descnhes the elements fo record af fhe end af your analysis Likewise to modify a macro select a row and use the shortcut key F11 or click on the
17. Mais 0902161943 1002 png 11 719 4 lien d s A q ee Ce 1 Er ME Mais MANPIEIANI 1007 man 19 Ann A Example_2 We wish to measure the surface of leaves We have two varieties vl and v2 and our study contains two replications rl r2 We have three plants per variety replication pl p2 p3 and we use two leaves per plant fl f2 In our images we arrange the leaves in two zones so that each image contains two varieties Transposing these elements into AIM the varieties are the zones the replications are the acquisitions the plants are the images and the leaves are the cells Authors B Moutault amp C Chevalier Page 71 Date 20 08 2012 Version 1 AIM 14 Raw unclustered data AR AIM19 AIM19 Data clustered by Leaf OA na AIM21 Data clustered by Plant gaga IMAGE a gt Image Aim21 oo ca Cell Acquisition Aim13 AIM20 Data clustered by Replication aes ACQUISITION by Replication er OU Zon Aim20 rary ele AIM22 Data clustered by Variety MATERIAL Object Aim22 a 5 2 Authors B Moutault amp C Chevalier Page 72 Date 20 08 2012 Version 1 9 5 4 Deletion The deletion step is similar to the display step as you need to select the study the detail image material etc and the results type before clicking on and confirming your selection Caution the process does not involve cascade deletion If you delete the Aim14 results this actio
18. Processing Software Beterential Options Module Window Help DOO 8 SCO SOS e ms Search Criteria You can use the 17 ms Couleur os Photo Coloration NAKTUINBO UW MO UTAU LT 12 Couleur des Feuilles Exemple Groupe d Etude et di MOUTAULT rn amin Groupe d Etude et d MOUTAULT me 2 ACQUIS _ A_NOM A02_D_DATE SITIONS A4 A NOM A05_A NOM ADS A LOCALISA 14 Var_Extract 25 09 2012 Document PDF UPOV Var_1 2509 2012 Document PDF UPOV Var_2 25 09 2012 Document PDF UPOV List of ima ges N A2Z01_A_LIBELLE a ea Orchide_Varety_1 bmp Orchide_Variety_2 bmp rchide_Wariety_3 bmp Non Defini Non D fini Non Defini Non Defini Non Defini Non Defini Non Defini Non Defini D co om on ode LUE hi ca Curent DataBase Ange_Adre User moutaultb Current field ColTab_A13_A_NOM_FIC_IMAGE 1 10 15 44 P 9 2 1 How to use this feature Select the study to display the list of acquisitions and macros Select one or more acquisitions to display images and files Finally select the macros images and files to launch the analysis Authors B Moutault amp C Chevalier Page 54 Date 20 08 2012 Version 1 9 2 2 Macros You need to tick the macros you want to run during the next image processing operation AQ3_A DESCRIPTION YAN Colza cotyledons pivote cotyledons YAN Colza cotyledans methode simple se E PIVOTER be U BINARISER Manuel wy PIVOTER Coty do
19. TRAITER Pouvoir Couvrant v2 RE JMR calculer la surface d occupation des plante pois note 8 JPG RR N UE WS TRAITER Sclerotina sur colza cotyledon 201 yo BEN expression de la surface des necroses de TRAITER Sclerotina sur colza feuille 2013 yol BEN expression de la surface de la necrose sur TODAITED _ Calarntina mir anlaa fmia pann W m valeur du seuil pour la segmentation de 1 25 A masquer les images pendant le traitement 1 V_En_Creer_Image_Superposee 1 cr er des images Superpos es 1 ou non _Str_Nom_Result Pouvoir _Couvrant ds nom du fichier r sultat 7 1 2 Study Every time the window is opened a new study is automatically created under the heading Undefined with the name Quick processing which you can modify This enables you to save all the processing operations performed through the AIM application 7 1 3 Images To upload the list of images use the AP Load Dir button An options window will allow you to upload all the images contained in a directory You can also upload images by selecting them directly To modify the button option users must move from Directory to File then use the AP Add Fil button In order to remove one or more images from the list you must select it them and then click on the Renee button Authors B Moutault amp C Chevalier Page 38 Date 20 08 2012 Version 1 The
20. bmp D_SF_ 35666 1 bmp D_SF_3 5666_1 5mp D_SF_3 5666_1 bmp D_SF_3 5666_1 5mp D_SF_3 5666 71 bmp D_SF_3 5666_1 5mp EE lt 47 83393 0 207555 Ci Ci a a DM fm tw MN Let att etd ded ae ae a o Egi i m m ee mw eee 0 _AIM14_RESULT_CELLULE_IMG MaFOBJECT_NAMES Authors B Moutault amp C Chevalier Page 32 Date 20 08 2012 Version 1 5 5 4 Color Group Labels This feature enables you to name the colors of the rows of the results tables defined by group numbers for a better understanding of the measurements It also allows you to color rows 5 5 3 Adding color labels on Choose the column number of color group You simply need to indicate the column to establish the match containing the number of the color group Caption OBJECT_NUMBER OBJECT_NAME IMAGE_NAME LINE COLUMN Rouge Vert select the language in which you wish the l pu label to appear Pixel_ Feature enabling you to concatenate the label and its color code Feature enabling you to color the rows 39 35 AIM14 RESULT CELLULE IMG 583 sd before rs en ea T_NUMASBJECT_NAMES IMAGE_NAME Oe Cote
21. button enables you to select the complete list of images select unselect A pop up menu is available for this list of images Right click to call up the pop up menu Open enables you to open the first image selected Move up Move down enables you to change the order of the images in the list Save as enables you to choose a directory in which to save the selected images Upload Dir see above Add File see above Remove see above 7 1 4 Macros The list of macros is loaded automatically you can filter it with the aid of input fields Name Description Contact and Establishment Reminder Use the symbol to search the names which start with or contain the text entered Example to only see macros that contain the word process in their name type process and refresh the list exit the field Mme tete PES Me a ee Ze T ee ma MEL Eu tn List of macros 10 If A03_A_NOM_DESCRIPTION iB When you select a macro the ME Tu ei Bite TRAITER Champignon sur Feuille auto MO p text appears in the B R expression de la surface derhecroieenoe visualization field TRAITER Pouvoir Couvrant v2 RE JMR calculer la surface d occupation des plante It s poss ble to make temporary modifications TRAITER Finesse Feuille mm auto We Se eee Le These changes are saved until m the list 1s refreshed even if you Maco T
22. completed Setup completed Click Done to exit setup program MW Display ReadMe file M Launch program MF Display an icon on desktop W Display an icon in Start menu Srevious pie anne 3 Click on Finish 1 2 Automatic updates GEVES Once the AIM application has been networked updates will be installed automatically As soon as a new version is available an automatic update prompt will appear when the application is launched Mise jour automatique de 505 Une mise a jour de cette application est disponible Pour utiliser cette application cette mise a jour est obligatoire Utiliser la version install e Cuitter l application Informations sur la mise jour r Version actuelle de l application 11 012 Version de la mise jour 1 024 AN DEX Details WINDEV J Authors B Moutault amp C Chevalier Page 7 Date 20 08 2012 Version 1 2 Connection to AIM GEVES CD The password used to connect to the database 1s the same as that used for all Oracle databases Surname Initial of first name Note if you do not have an Oracle account contact our database administrator DBA christophe chevalier geves fr When you first connect to the database an information window will pop up and ask you to find your name in the address database Information Il n y pas de correspondance d etablie entre votre nom de connexion Oracle et votre identit dans
23. its name species establishment and person requesting the study the receipt and return dates and the number of replications for the objects materials varieties to be used in the study It is necessary to define the layout number of zones as well as the number of cells per row and per column if you know the indexing of your image series and the list of theoretical conditions A description field enables you to save comments and enter additional information The use of bold and underlined text 1s a reminder of the important fields that must be indicated 9 1 3 Deletion To delete a study select it and click on the button or use the shortcut key F12 then confirm the deletion Caution Studies selected for deletion should not have any images or processing operations attached to the acquisitions Authors B Moutault amp C Chevalier Page 49 Date 20 08 2012 Version 1 9 1 4 Materials This list enables you to declare the material to be studied The word material covers varieties batches of seeds or any other object to be studied species individuals galaxies Var_2501 CULT Var_ 2503 Var_berikumer Var_blanche a cal Var_bolera Var_de colmar b Var_soprano i co D bn de bo Fi Var_touchon Var_valor ca Click on the A Add button to create new rows You have default access to the label which 1s accompanied by a number incremented which is the highes
24. la base Adresse Vous allez d finir cette correspondance Recherche d un individu Liste des EDEN 1 167 GUITOUNI Tr de 46 656 30 2 E Seere nee If your name appears in the window select it and click on OK Should your name not appear search for it by clicking on Full list individuals If your name does not exist in the address database create a profile by going to Start Programs Adr Adr Authors B Moutault amp C Chevalier Page 8 Date 20 08 2012 Version 1 3 General overview CD 3 1 Main menu 3 1 1 Title bar amp AIM Managing image processing and analysis The title bar indicates the name of the software package and the active menu in square brackets 3 1 2 Toolbar The toolbar which appears in the start window remains available in all the main windows of the software package although certain buttons may sometimes be inactive in which case no action is possible and they may be greyed out The following functions are available Ce Le E Trennen m CE Gownewemy 5 ha senc for eny wingssesionenes M CBS Dee xesioncriens Omer RE CT E RECETTE TA meara ETES TE oem Ca feo CE Lino vas m em Authors B Moutault amp C Chevalier Page 9 Date 20 08 2012 Version 1 3 1 3 Status bar The status bar indicates the path of the database in line with the application the current connected user and the current field The date and time also appear on the right
25. manage the order of acquisitions with the CE CN EEE ons Changing the acquisition n 4 Ag For the study Etude Syngenta Mars 7009 Name Date 2510 20031 Support Cam 1 Source Banc_1 Images director Optional List of conditions 6 i A200_A_LIBELLE Grossissement Image r f rence Nombre Cellule Par Colonne Nombre Cellule Par Ligne Seuil d placement Materials of 20 Period for placement of material within the acquisition Enter the name date and medium used to acquire the images as well as the directory in which they are saved because when first launched AIM will load the images automatically The list of conditions is by default the same as that of the study but you can modify it by entering values and comments directly into the table Add and remove rows using the Ei j buttons The checkbox last column enables you to enter the conditions in the calculations window and is designed to describe as accurately as possible the image or images relating to this acquisition The list of materials works the same way The aim is to describe as accurately as possible the image or images and their zones relating to the acquisition so that your results can be directly linked to the materials objects varieties This list makes such a match possible For each row fill in the zone and replication as well as the set up period if you have time differences between see
26. or AIM errors Peat Relaunch the same processing operation yoo o Force the end of processing operation and retrieve the output files X Cd Force the end of processing operation and cancel the retrieval of the files AIM will indicate when a processing operation is ongoing by means of a flashing message SSS Analysis in p oe Caution the names of the images sent for processing by macro are slightly modified by AIM AIM concatenates the image code enabling the software package to know under which acquisition they need to be registered upon their return Authors B Moutault amp C Chevalier Page 59 Date 20 08 2012 Version 1 9 3 Integration CD This window enables you to consult and delete processing operations relating to the acquisitions with or without the results files It is possible to integrate these measurements into the database by choosing the result variables that are to be saved File Study Macro Fast Processing Processing Software Referential Options Module Window OO DE ET Search Criteria You can use the Groupe d Etude et RETAILLEAU su rs A Phase de test Grune d Ftude et di RETA LEAI dean aS Im A02_D_DATE_ACQUISITION m ee List results files and macros 1 history 1 E M A16_C_A_NOM_FIC_RESULT A12 D DATE TRAITEMENT NT TRAITER Pouvoir Couvrant v2 es File 6 Number of variables result already integrated for this treatment 0 and nu
27. or your AIRES the OUTPUT R NB Noiret Blanc To finish you need to enter data into the OUTPUT part which defines the elements that need to be recorded to end the processing operation images files output files There are three elements available Result file enables you to save all files measurements and others generated by the macro and the image processing software in the following table AIM16_FIC_RESULT_TRAITEMENT The files will appear in the Integrate window and will be available for integration into the database Image enables you to save all images segmented superimposed layered etc n the table AIM13_IMAGE The images will be available for new processing operations in the Analysis window File enables you to save all files traceability additional information in the table AIM25_FIC_DIVERS_DESC The files will be available for new processing operations in the Analysis window You can change the order of the outputs a and delete them Authors B Moutault amp C Chevalier Page 44 Date 20 08 2012 Version 1 Example for a macro that generates a number of results files in Excel format and binary black and white images with names ending in _NB the output section should be set up as follows Then click on the Save button to save the macro and click on the __ Close button to close the window 8 1 3 Deletion To delete a macro select it and c
28. ri hmn ee You modify the Match field as follows _1 for 2 To load use the button If you want to delete hide this part of the Load a directory window click on cars Comment by default the images added to acquisitions are undefined types We recommended that you specify the image type for better image management 9 2 4 Files You must select the files to be processed during the next processing operation List of Files ETUDE ESPECE Colza d hiver LAIM_Parametres Ini ACQUISITION NOM 11_08_03 Colza_1_ DATE 25 10 2012 SUPPORT Cam_4 Banc_1 REPERTOIRE CONDITION IFREG 7 en heure GROS 52 piel par 10 millimetres HREF 4 NCPC 10 NCPL 10 ISDIEP 0 3 This tab allows you to manage files and images see 9 2 2 and is equipped with an additional function Le SP Generate enables you to create a file automatically AIM_Parametres Ini which retraces information about the study and the acquisition Authors B Moutault amp C Chevalier Page 58 Date 20 08 2012 Version 1 9 2 5 Analyses to start the next processing operation having previously selected the macros images and files 1217335 In UT m This tab enables you to monitor processing operations to relaunch or halt a processing operation in case of macro user image processing software
29. the study record Example There are three varieties and two replications Six acquisitions are to be created The following options are available for the creation order Either by replication Or by material Variety_1 replication_1 Variety_1 replication _1 Variety_2 replication _1 Variety_1 replication _2 Variety_3 replication _1 Variety_2 replication _1 Variety_1 replication _2 Variety_2 replication _2 Variety_2 replication_2 Variety_3 replication _1 Variety_3 replication _2 Variety_3 replication _2 9 1 5 Acquisition Acquisitions are the directories of the study This concept is important as each acquisition will contain images measurement files processing history and study results Various data need to be entered for each acquisition such as the layout and description of materials their arrangement in the image series the conditions in which the images were acquired the image source the date they were acquired and a target directory for automatic image retrieval optional 9 2 2 b List of acquisitions 10 F ACQUIS ADZ_A_NOM 24 10 2012 Scanner 24 10 2012 Scanner Var_2503 24 10 2012 Var_berikumer 24 10 2012 Scanner Var_blanche a col 24 10 2012 Scanner Var_bolero 24 10 2012 Scanner Authors B Moutault amp C Chevalier Page 51 Date 20 08 2012 Version 1 To add modify or delete use the aa buttons To modify more than one acquisition use the CR You can also
30. 2012 Version 1 By default the application recalculates the axes boundaries as accurately as possible concatenates the labels of the various series columnA columnB columnC indicates the name of the study in the title places the key to the right of the graph retrieves the labels of the x and y axes as they are You can change certain features of this graph using the following options On the right hand side of the window the button is used to open and close the options panel Right click on the graph to open the contextual menu Title Graphique TEST 200010 K ais Temps Yi oyerne Anthrmetiogue Gridlines Y as Deme a oyenne Anthrnetigue Axes Style Min Y axis 0 es Zoom Max Y axis Oo wm Save As This enables you to change the axis labels and boundaries move the key save the graph or print it Print 51 x Germination de TEST 9000101 Vari t _1 HG D Vari t _2 HD Vari t 3 86 BE Vari t _4 BO 100 eee DE 90 F a r 60 50 40 1 Germee en Authors B Moutault amp C Chevalier Page 75 Date 20 08 2012 Version 1 10 Windows Menu D ai Mosaic EA Cascade lconize All El Restore All Align icons lel Close Al 10 1 How to use this feature This feature enables you to manage Aim windows with a single click I Tile Shows all open windows arranged symmetrically 2 Cascade Cascades
31. 9 Once integration into AIM is complete you will see Pouvoir_Couvrant xis Tel Covering Power peas field low 1 jpa 4 774 276 E01 155 peas field low_2 jpg TIG 524 peas field mean_1jpg 1125916 peas field mean_ Zjpg 1123557 peas field strong _1 jpg 201 543 peas field strong_ jpg Fr 201 459 Authors B Moutault amp C Chevalier Page 61 Date 20 08 2012 Version 1 9 3 3 Options One stage prior to integration into the database is the indexing of measurements This is done automatically with each display of results files File tab and takes into account the selected options Options tab Options Number of variables result already integrated for this treatment 0 and number of measuren Choose the type of indexing Simple Determined for each image with coordinates X Y Tracking Determined to the first image with coordinates X Y and follow up on the next images by distance calculation Incremented Assigned to each image by incrementation Manual Copied from the columns of the result file B Disabled The result file is not indexed to the display Indexing column name X Indexing column name r Restart indexation Indexing enables AIM to handle each of the different measurements in the results files on an individual basis enabling them to be registered in the database When images contain more than one object it is necessary to be able to distinguish between them AIM attribute
32. 9 key A window will open and you must select a value and validate The information will be added to the entry fields DHS 40770 Toumesol Lom J gose Filter the request Enter a letter for example m Species m Press F9 Select Mint and click on Ok Liste des esp ces 13 Type Code DHS 40 850 Mache DHS 43 150 Magnolia grandes fleurs Menthe DHS 43 524 Millet des oiseaux Authors B Moutault amp C Chevalier ge 12 Date 20 08 2012 sion 1 The information and the relevant code are added to the species field Note The symbol can also be used and is compatible with previous versions of GEVES applications GAD DHS VAT GED GEV Caution If the criteria you enter are too narrow the list of values will remain empty for example if the code begins with 9 Species 59 m Authors B Moutault amp C Chevalier Page 13 Date 20 08 2012 Version 1 4 File Menu Send message Application Change base Change password Screen capture Exit 4 1 Send a message In order to render the application more interactive AIM provides you with the possibility of managing a messaging system To access this system click on Send a message in the File menu When you first launch the application click on the Account button a The accounts g w wage Name of the account benjamin moutault Email address benjam
33. CRIPTION PLANNING Person 9 790 MOUTAULT Benjamin Phone DIET 7 Gone d Etude e et de Contr le des Vari t s et des Semences Les objets sont de couleurs fonc s sur un fond blanc r tro clair Ja Page 43 Version 1 Online Hel o m Comment it is important to be precise concerning labels as this will make searching easier and improve the readability and sorting of macros In the first tab labeled MACRO the macro is divided in 3 parts Header Vi_Str_Methode Huang autres valeurs possible Default the HEADER En Cacher Image 1 rendre le traitement cach 1 ou It is necessary to obtain the fixed values and parameters for the various commands used from your macros This information must be entered into the variables in order to clarify their use for users unfamiliar with the set up and to facilitate the temporary modification of macros while they are running Macro body ees j vertication version minimum IMAGE J et option standard gt es the BODY requires 1 442 Enter the macro process into this part taking care to use the variables in the HEADER and the AUTOMATIC HEADER This part enables you to format the text into RTF in order to increase the readability of the macro e g add colors to the comments TOIT zp ru F RES F i i creme Pata Fri j F F F St Aar c E ee ri Li i iat a ean es ie Sem oi aj fi A ECOT ar ie aid
34. DISPOSITIF_ZONE 4 C_NUM_DIS En 16 zones Triple AIMO8_ZONE 4 A0S_CRAQ7_NUM_DISPOS A08 C_ Current DataBase Ange_Adre User moutaultb Current field ColTab_AQ _A_NOM 1 15 55 52 5 4 1 Consultation Select a zone layout in the main table to see the description of the different zones in the details table 5 4 2 The concept of ZONES In image processing depending on the type of measurements used and the form of the objects being studied users have a wide range of layout options at their disposal The object can be displayed alone or in batches of hundreds of objects Objects may originate from the same population or from various populations population group batch material variety replication Each group has one defined space in the image series one zone Authors B Moutault amp C Chevalier Page 27 Date 20 08 2012 Version 1 In AIM you can manage several zones EN GE En EB 1 zone 2 zones 4 zones 16 zones Each zone represents one type of material and may contain one or more objects 1 zone layout with 10 objects per zone 4 zone layout with object per zone This image layout which arranges the objects by type of material and number of zones is called the zone layout and you must to enter it in AIM when declaring
35. Fa button or double click on the row Authors B Moutault amp C Chevalier Page 42 Date 20 08 2012 Version 1 amp Changing the macro n 9 36 m E Name BINARISER Simple Description STANDARD m thode simple seuil automatique PNG Online Help DESCRIPTION PLANNING Header W_Str Methode Huang VI_En_Cacher_Image 1 W_Bo_Imag_Superpose 0 Reminder Automatic Header Macro body fo ereeeeenenereeeeenereneeeeeneneenenennenee een meeten eee eee verification version minimum IMAGE J et option standard gt le fond est BLANC 2 terations 1 ET a Each AlM macro contains apat OUTPUT autres valeurs possible Default rendre le traitement cach 1 ou non 0 j creer des images couleur pour v rifier binarisation 1 ou non 0 Superpos e Couleur Noir et Blanc In addition to the macro text you can enter a sickle of information relating to the macro description Name Description Validity The person responsible for the macro Their e mail address Their telephone number Their company name And a mini macro user guide explaining its aim general function displaying the images expected on entry and those produced on exit explanations of certain variables Authors B Moutault amp C Chevalier Date 20 08 2012 BINARISER Simple yy Validity 7 Soo methode simple seuil a atique FNG DES
36. MPTER Celule STANDARD compte le nombre de cellules Choose a macro COMPTER Jeune Pousse a JMR comptage de jeunes pousses avec seuil fi 4 DECOUPER Formes manuel A Start analysis STANDARD permet de rate une partie de DECOUPER Vertical ou Horizontal auto BAG pemet de d couper les images automatiq DEFINIR l chelle Pixels Millim amp tres STANDARD Calcul du rapport Pixels Milimetre m D Aaiye ees U ENTETE VI_Str_Image_Format_Sortie bmp format de sortie des images JPG PNG TIF Vi _Decoupe 1 nombre d echantillons par image CORPS Be ____ 17 verfication version mini IMAGE antion standard fand RI ANC Current DataBase Ange_Adre User moutaultb Current field ColTab_A03_A_CONTACT_NOM 04 02 2014 17 06 32 You can also open this window with the button from the window MAIN 7 1 1 How to use this feature When the window opens AIM automatically launches a study All you need to do is to upload the images select a macro launch the analysis Authors B Moutault amp C Chevalier Page 37 Date 20 08 2012 Version 1 List of macros 31 a A03_A_NOM_DESCRIPTION aB A TRAITER Finesse Feuille mm auto RE JMR calculer la surface le p rimetre des plante ERICH pois note 5 JPG hl ee EN ee TRAITER Fleur scan 2 VE ec eee eG YAN mesurer la forme des fleurs scan Les p GU
37. Modify or remove codes for example Then if you want to run click OK ff heure limite d exploitation des zones i Vi_VarTab_Imag est un tableau de 0 par 6 cha nes J acquiimage zone VWi_VarTab_ one est un tableau de Opar 5 chaines acqui zone acqui VI_En_Id_Lig est un entier Ao En Mami cet on antiar 1TH Lok _ oma Otherwise the data will be calculated and recorded and the new results displayed 0 ee ae 0 113761 17401373 224 5 29395 8 030308 218 3 435963 Authors B Moutault amp C Chevalier Page 66 Date 20 08 2012 Version 1 You can relaunch the operation with new formulas which can be based on the new results Results Variables List of result variables with their type 28 OR A202 CL_FORMULE Incr mente chaque nom d image diff rent Rang Couleur RHS 73 valeur Rang de chaque couleur pour une image Color indicators are provided to help you SANS the result variables that have already been calculated the result variables that probably need to be calculated By default the list of result variables is limited to those which are of interest to you However Complete Li you can display the whole list using the tick box rs l Results can be exported to Excel using the Export button You can color the rows of the table using the Color button Automatically hide part of the calculation table columns Be Authors B Moutault amp C Ch
38. Module Window List of acquisitions 10 ADI_A_NOM Couleur des Fleurs Orchid es Test Couleurs RHS Traitement Rapide d une fleur 2012 Projet SCLEROVAR feuilles de colza Couleur des Feuilles Finesse des feuilles Etude Syngenta Mais 2009 M trologie des bancs COLZA Comparaison Couleur Appareil Photo Expression BioAgresseurs sur Feuille Denombrer des plantes jeunes Distinction de Grains Mars Mesure OCW sur Cotyl don Acquisition Help Exemple Phase de test D monstration Ext rieur Exemple SNES Ph notypage SNES Ph notypage Coloration Exemple Phase de test Exemple F ACQUIS Var_blanche a col Var_bolera Var_de colmar b Var_soprano Var_touchon Var_valor 24 10 2012 24 10 2012 24 10 2012 24 10 2012 24 10 2012 24 10 2012 24 10 2012 24 10 2012 24 10 2012 24 10 2012 IM Groupe d Etude et di MOUTAULT MOUTAULT CHEVALIER CETIOM MOUTAULT Groupe d Etude et d MOUTAULT Groupe d Etude et d RETAILLEAU DEMILLY Groupe d Etude et di DEMILLY NAKTUINBOUW MOUTAULT Groupe d Etude et di CADOT Groupe d Etude et di RETAILLEAU Groupe d Etude et di MURACCIOLE Groupe d Etude et di GUICHETEAU Gip Geves Jean Michel Didier Didier Benjamin Val rie Jean Michel Vincent Current DataBase Ange_Adre User moutaultb Authors B Moutault amp C Chevalier Date 20 08 2012 Current field
39. RAD Pook v change the macro tf A ENTETE JfHerrerenrenrenenren nennen ernennen ernennen enter WI_En_Seuil 115 jf valeur du seuil pour la segmentation de 1 25 I_En_Masquer_lmage 1 masquer les images pendant le traitement 1 t I_En_Creer_lmage_Superposee 1 cr er des images Superposses 1 ou non Vi_Str_Nom_ Result Pouvoir_Couvrant ds nom du fichier r sultat D E ff CORPS 2 Authors B Moutault amp C Chevalier Page 39 Date 20 08 2012 Version 1 7 1 5 Analysis When you have selected the images and the macro you need to launch the analysis by clicking on the button A stand by window appears Ow while the images are being processed by third party software If processing is not completed you must inform AIM that it is to be cancelled using the LA me button The AIM application detects when processing is completed and automatically brings up the images and results files provided in the Macro management window The new images will be uploaded to the list and the processing history updated You can view the results files using the button List the processing and results of acquisitions 2 M2_D_DATE_TRAITEMENTA A16_C_A_NOM_FIC_RE D 14 06 2012 15 28 16 Pouvoir _Couvrant xs zip a WP ol u 12 06 2012 15 05 38 Pouvoir_Counrant ds zip The Integration w ndow opens and you will be connected back to AIM in its normal functioni
40. a series of images using image processing software Analysis window AIM14 RESULT CELLULE IMG _ 7267 _ SBJE MS ORETNUSF OBJET NOM PS BNE_ NOM IMAGE NOM GNEMON Volume SF NDEF 9 1 Van t _1 1 HG NB_Mais_0902161545 1000 1 1 11 8861 13264 ES NDEF 3 1 Wan t _1 1 HG NE_Mais_ 0902161545 1000 1 2 11 690723053 0 NDEF 3 1 Van t _1 1 HG NE Mas 0902161345 1000 1 3 123190327472 0 NDEF 9 1 Ven te_1 1 HG NB_Mos 0802161545 1000 1 4 11 849133728 0 NDEF 3 1 Wan t _1 1 HG NE Mas 0902161545 1000 2 1 11 5429906162 0 I integrated these results into the database giving a total of over 7 000 measurements as I have several cells seeds per image and have around 50 or so images I have calculated a Time based on the frequency of images in my series I wish to cluster my results by variety and by time I select my study in the Result window and click on the This action opens the statistical parameters window I only select the Volume and Time result variables in the Var Result tab Param tres Statistique Mat riel 4 Aceton 1 Image PSO Trierer 1 Vai Rasuk 17 Param Stat 7 be c oons ATOZ A LIBELLE AS MORTAN A UNT TAN gt j FFC Authors B Moutault amp C Chevalier Page 70 Date 20 08 2012 Version 1 Then in the Param_Stat tab I choose to calculate an average Material 11 Acquisition 11 Image 11 Var Result 8 Parem_Stat 7
41. age Fiji FLY Outil de requ tage graphique Fly Speed Sql Query GAD Gestion Administrative des Dossiers GAIA Logiciel de distinction varietale GDN Gestion des d nominations GED Gestion des Essais Dhs GEV Gestion des Essais Vat GRT Gestion du R f rentiel Thalie GTD Gestion technique des dossiers GVA Gestion des varietes HYD Gestion des Ressources Humaines Hydromel IMJ Logiciel d analyse d image ImageJ LIM Outil de gestion de formulaires en ligne LimeSurvey NEP Gestion des Informations Biogeves Neper OLA Outil de d pot de formulaire d inscritption varietale en ligne On Line Application PAS Pathologie des Semences PHY Analyse Physique RRR Logiciel de statistique R SEM Gestion des Semences SIL SilverPeas Outil Collaboratif SIR Gestion de la saisie portable SOS Gestion centralis s des demandes d un service SYN Logiciel de synchronisation de r pertoire et ou d puration de r pertoire VAT Gestion des tudes VAT Utiliser les m mes identifiants En ES ea Authors B Moutault amp C Chevalier Page 15 Date 20 08 2012 Version 1 4 3 Switch database GEVES CD This submenu enables you to connect directly to another database without closing the amp Change database J a a a i application The prompt window displays a list of all available servers Those ending in Adre concern data from production sites and those ending in Copi al
42. all open windows 3 Iconize All Reduces all windows to icons 4 Restore All Enlarges all windows 5 Align icons Aligns the icons of reduced windows 6 Close all Closes all your windows After the separate line AIM listed open windows To switch from one to another with a simple click active inactive Authors B Moutault amp C Chevalier Page 76 Date 20 08 2012 Version 1 11 Help Menu amp User Manual Help on automatic functionality Modules Did you know 7 Data Dictionary Data model A Quern Dysfunction Suggestion 11 1 How to use this feature The Help menu enables you to find information on the AIM application You have access to the User manual Help with automatic functions Did you know Data Dictionary Data model Request Software issues Suggestions and About to obtain a response to your questions and problems User manual The AIM user guide n Pdf format Help with automatic functions _ Did you know Data dictionary description of AIM tables in Htm format or for Other applications Data model the graphic representation of AIM tables in Pdf format or for Other applications Query SQL text based on the tables n the application 99 Dysfunction Suggestion automatically opens the SOS application and a new rec
43. arious states color black and white The column entitled number of days archived enables you to define the time period during which an image will be stored before you are prompted to delete it AIMA04 TYPE _OBJET H cC CO VAR variety Undefined This feature enables you to describe the objects being studied type of material used AIM205_TYPE_ETUDE 205 C_CODEA A205 LIBELLE bject lesson germination phenotyping example evolution monitoring Authors B Moutault amp C Chevalier Page 20 Date 20 08 2012 Version 1 This feature enables you to describe studies for example by function type taking measurements counting examples or by user type seed sector plant varieties sector pests sector AIM207_TYPE FICHIER f7 C_ COF A207_A_LIBELLE B_JOUR_RED FRA Result file AIM 0 FRI Result file unintegrated 0 NDEF undefined 0 SFR without result file 0 This feature enables you to describe the results of image processing operations Essentially the processing operations produce a results file which is integrated into the database FRA type but they can also generate other types of files which are not destined to be integrated for example a report file FRI type There are also processes that do not generate any results files such as processes which modify the color of images The column relating to the number of days archived enables you to specify the length of time
44. bmp 1 16 222 158 223 0 3717 Vari t 11 Var Etract 0 Orchide_extract bmp 1 17 168 107 175 0 12391 Vari t 11 Var_Extract 0 Orchide_extract bmp 1 18 55 23 35 572055 _ en narrer ern a pers 14 02 2014 11 31 53 Curent DataBase Ange_Adre User moutaultb Current field Comment Most of the work is done at the level of the declaration of formulas 5 4 see 9 4 1 How to use this feature Display the results of a study acquisition or processing operation using the button Then click on the result variables button to open the window to select the Authors B Moutault amp C Chevalier Date 20 08 2012 Page 65 Version 1 B Resuts varabes Ce EE exe A202 CL FORMULE Incr mente chaque nom d image diff rent Rang Couleur RHS 73 valeur Rang de chaque couleur pour une image is The highlighted rows indicate the result variables Already calculated in RED Probably calculate in GREEN Complete List on Cese Select one or more rows and confirm your selection using the RS Comment formulas are based on other result variables information defined in the study declarative section or columns in the table If one formula is missing or contains an error the calculation stage will generate an error message CALCULATION potentially unfeasible Missing columns to calculate Dur e exploitation 19 Temps You can adapt the formula
45. ch spreadsheets Excel work AIM202 VAR_RESULTAT _ 76 ZZ on o CH AZUZ_A_LIBELLE SN ORAN AUNTS CALE O2 A LIB IMAGE A202 CL_FORMULE Champ Feuil 12 rapport E Rapport Champ Feuil 13 Finesse Feuille 13 rapport Surface des plantes P rim tre des plantes Longueur Courbe pixel E Curve_ Length 6 Largeur Courbe pixel E Curve_Width 16 image numero E Num_Image 17 Volume mm ff 43 acine Surface Pi M3 18 Distance r f Beart du centre dinerie par rapport une image de r fi 19 Temps ff Fr quence num ro d image 1 Surface des plantes P rim tre des plantes Enter 1 for the values of var_result POUR TOUTE LIGNE DE STABS Enter GROS forthe values of the condition GROS SRESS 9 4 Enter LIGNES forthe values of the column LIGNE FIN Enter RES forthe column calculated Enter STABS forthe table name Use the SNS EE EE buttons to manage the variables On the bottom left there is an overview of the formula for the selected row On the bottom right there is a reminder of the nomenclature that may be used in the formulas Authors B Moutault amp C Chevalier Page 18 Date 20 08 2012 Version 1 amp Create Modify variable results e n sl h ist NF FF Display Order The following elements are required in order to Caption Name of the variable results create a new variable Unit Specifies the unit of this variable Result Variable extracted o
46. ction Comments can also be inserted by starting the row with a double slash Another example involves a formula Unit which allows you to calculate the volume ee of an ovoid shape extracted of a measurement file calculated with a formula With the same surface variable 1 magnification MAGN and the following Windev functions root Formula u ae 4 3 root Area Pi 3 power and pi POUR TOUTE LIGNE DE STABS SRESS root 1 power MAGN 2 ValPI 3 ValPI 4 3 FIN Authors B Moutault amp C Chevalier Page 19 Date 20 08 2012 Version 1 Online Help htip doc posoft fr to learn about all Windev functions Enter 1 a a ee to refer to another result variable Enter GROS forthe values of the condition GROS a condition Enter LIGNE forthe values of the column LIGNE 4 a column contained in the calculations table Enter RESS forthe column calculated a column which will contain the result of the Enter STABS forthe table name formula the name of the calculations table See the Calculation window 9 4 for the list of columns present row image_name ZONE_NUM IMAGE_SERV IMAGE NUMBER IMAGE NAME 5 1 3 Type Image Object Study and File AIM201_TYPE IMAGE A201_A_LIBELLE Color 183 Black and white 130 NC Grayscal 366 0 NDEENN undefined This feature enables you to describe the images and their v
47. d lots for example Authors B Moutault amp C Chevalier Page 52 Date 20 08 2012 Version 1 9 1 6 Macro The list of macros 1s used to define those macros that will or that can be used in the study A03_A_DESCRIPTION OUVRIR Image STANDARD ouvre dans le logiciel de traitement les images s lectionn es CHANGER Format STANDARD tous types d image vers un type pr cis JPG PNG TIF E INVERSER Couleur STANDARD tous types d image vers un type pr cis JPG PNG TIF B COMPTER Cellule STANDARD compte le nombre de cellules EDITER Film STANDARD Pr sente les images en stack film Add or remove macros using the his BB buttons You can also modify their position order using the buttons to move up or down and update the order according to the filter applied using the Refresh order button The Guide button enables you to view the user guide for the selected macro Authors B Moutault amp C Chevalier Page 53 Date 20 08 2012 Version 1 9 2 Analysis O This window enables you to manage images files and perform analyses of the study You will find the main tables here Study and Acquisitions at the top and then in the details tables in four tabs tabs for macros images the files and the management of analyses this tab only appears during analysis File Study Macro Fast Processing
48. dary tables contained in the main windows There are three tabs available that enable you manage the different values for TYPES and VARIABLES for the AIM application _AIM Managing ima alata aoc amp File Study Macro Fast Processing Processing Software Referential Options Module Window Help E x Die eae OS eee AI e le A205_A LIBELLE Variable Result and Condition image Objet Etude and Stat Type Fle Type AIM201_TYPE_IMAGE AIM204_TYPE_OBJET 201_C_COD A201_A_LIBELLE IB_JoUR_REB 4_c_co A204_A_LIBELLE B Echelle 0 a Cultivar a Initiale Couleur 183 ESP Esp ce Initiale Invers e 183 Non defini Initiale Couleur Refaire 183 Lot Semence Modifi e Couleur 183 Serie Noir et Blanc 730 Vari t NC Niveau de Gris 366 Non Defini 0 Superposee Couleur 20 AIM205_TYPE_ETUDE AIM206_PARAM_STAT 05_C_COD A205_A_LIBELLE ___ B e ccor 4206 A LIBELLE A206_A_TEXTE_SQL 8 Coloration A COUN Compte COUNT 7 D monstration Ecarttype STDDEV Exemple Maximum MAX Ext rieur M diane MEDIAN NDEF Non defini Minimum MIN Moyenne Anthm tique AVG he NDEF Non d fini AVG AlM205 TrPE_ETUDE For each table MER A205 A LIBELLE CO COMPTER EY EVOLUTION suivi ME MESURER you can type the information directly into the final row or click on the oF button To modify information double click on a row to enter data To delete information select a row and TS TEST
49. e tools available on the market are frequently expensive and too specialized AIM will facilitate the processing of images performed using ImageJ software while offering significant flexibility with regard to the subjects studied plant medical spatial industrial Some examples of image processing performed using series of GEVES images Surface measurements height and width of grains back lit table corn 2009 Surface spread of fungus on leaves scanner wheat 2010 Surface measurements height and width of leaves scanner rape seed cotyledons 2010 Surface measurements height and width of flower petals scanner flax 2010 Ground coverage of plants camera in field peas 2011 Kinetics of seed imbibition and germination Jacobsen table multiple species 2011 Surface and perimeter measurements to define the thickness of leaves scanner carrot tops 2011 Quantification labeling of colors on leaves and flowers back lit table peas and orchids 2012 Authors B Moutault amp C Chevalier Page 2 Date 20 08 2012 Version 1 CONTENTS D Preface 2 CONTENTS 3 1 Software installation GEVES 6 1 1 Initial installation 6 1 2 Automatic updates GEVES 7 2 Connection to AIM GEVES 8 3 General overview 9 3 1 Main menu 9 3 1 1 Title bar 9 3 1 2 Toolbar __ 9 3 1 3 Status bar __ 10 3 1 4 Menu bar 10 3 2 Functions available in different windows 10 3 2
50. ems You can view the macro used for the processing operation gt View Macro You can view the results file in the format in which it was saved View Fle You can import your results file manually import should there be any modifications or corrections You can manage types of results files 5 1 3 4 Mody Type as well as the number of days for which they are saved pale When you select one or more processing histories AIM informs you of the number of result variables and measurements already integrated into the database Number of variables result already integrated for the treatments 3 and number of measurements 44 x 9 3 2 Display You must select a processing row that contains one or more result files Select file files place the cursor on the tab File and click on the button The format of the result file which comes from the image processing software ImageJ should be a Text file the extension is not important e g txt xls with the first row showing the column headings and separated by a tab See the example below Fichier Edition Format Affichage Label Area Plant Area covering Power peas field low_1 4007466 jpg 3774276 801155 21 peas field low_2 4007467 jpg 3774276 798524 peas field mean_114007468 jpg 3774276 1125916 peas field mean_2 4007469 pg 3774276 1123557 peas field strong 1 4007470 Pg 307200 201543 peas field strong _2 4007471 Jpg 307200 20145
51. equal to Couleur des Fleurs Orch Does not end with no Authors B Moutault amp C Chevalier Page 11 Date 20 08 2012 Version 1 3 2 3 Layout of columns in a table If the column layout is not suitable it is possible to move the columns simply by using drag and drop All column widths can be adjusted to suit the user In order to do this position the mouse cursor on the column dividers and move them to the right or the left while holding the left mouse button down When browsing the left hand part of the title of a column a padlock will appear You can set the columns to the left of the padlock by clicking This means that when you move the horizontal bar the left hand columns will not move anymore 3 2 4 Managing windows and tables The windows have splits horizontal or vertical split bars which allow you to modify the size of tables and other items Place the cursor over the split the cursor changes to a double arrow hold down left click and move the cursor In certain windows in AIM you will find search criteria in the upper left hand corner of the tables Select fields to filter the list Search Criteria ou can use the I M me IR You can use as a search criterion and the x button allows you to delete these criteria 3 2 5 List of values Certain entry fields allow you to call up a list of values Simply place the cursor over the entry field and press the F
52. evalier Page 67 Date 20 08 2012 Version 1 9 5 Results CD This window displays the results of a study raw calculated and clustered results It also makes it possible to cluster and delete data from the database Options Module Window Help NAKT UINBO Uw MO UTAULT Groupe d Etude et di MOUTAULT Groupe d Etude et d MOUTAULT Comparaison Couleur Appareil Photo Coloration Couleur des Feuilles Exemple A202 CL FORMULE numero determine la couleur UPOV groupe par les valeurs RWB Somme des Pel_ par Grp _Couleur_UPO V et par image num ro A detemine la couleur RHS groupe par les valeurs AVB H Somme des Pxel_ par Gr Couleur_RHS et par image Tpectreste Came Leid IMAGE NAME Nex Extract Var_Extract Var_Extract Var_Extract Var_Extract Var_Extract Var_Extract Var_Extract Var_Extract Var_Extract Var_Extract Var_Extract Var_Extract Var_Extract Var_Extract Var_Extract Var_Extract sede aka bmp Orchide_extract bmp Orchide_extract bmp Orchide_extract bmp Orchide_ extract bmp Orchide_extract bmp Orchide_extract bmp Orchide_extract bmp Orchide_ extract bmp Orchide_extract bmp Orchide_extract bmp Orchide_extract bmp Orchide_extract bmp Orchide_ extract bmp Orchide_
53. extract bmp Orchide_extract bmp Orchide_extract bmp Orchide_extract bmp 17 401373 6 030308 8 066875 3 213748 0 402226 0 633611 0 085321 5 94198 17 236826 22 075732 0 867428 0 623654 0 221428 0 282372 0627717 0 002031 0 036566 They 12 02 2014 11 41 11 9 5 1 Display Select your study the full details are displayed in the second part of the window There are six tabs describing the materials acquisitions images processing operations result variables and statistical parameters which are part of the study Everything is pre selected by default when you open the window or switch to another study You have the choice of de selecting or selecting one row or another from one tab or another in order to refine what is displayed or deleted Caution When you use the Next and Previous buttons to switch windows AIM pre selects the same study and the same acquisitions Authors B Moutault amp C Chevalier Page 68 Date 20 08 2012 Version 1 Other available filters include Type of results Cell Image Aim 14 E In column Results type Type of results The tick box In column governs the layout of the result variables Select the elements you wish to display then click on the button 9 5 2 Type of result Cell Image Aim14 raw and calculated results defining the cells zones images and acquisit
54. f a measurement file a unique number a value for the display order presentation of results ER a label Column Name for extraction the unit in which the variable expressed Title of the column in the resut files the variable type omg neuf the heading of the column or formula Caption Area Unit pixel If the variable is intended to contain measurements extracted RE VE from results files the column heading must be specific extracted of a measurement file For example to retrieve surface area measurements use the t heading Column Name for extraction Area 99 Area Caption Area mm Unit mm Result Variable U extracted of a measurement file calculated with a formula If the variable is intended to contain measurements calculated on the basis of a formula its wording needs to be edited For example in order to transpose surface measurements from pixels to millimetres the formula is area pixel Fomula magnification f Surface magnification POUR TOUTE LIGNE DE TABS SRESS 11 puissance MAGN 2 FIN E LIGNE DE STAES and EN must be added on either ade of the formula in order to apply the calculation to all the rows to be displayed You must replace pixel surface area with 1 which is the unique number of the variable magnification with MAGN which is the unique code for the condition squared with power 2 whichis a Windev fun
55. in moutault geves fr Main account El SMTP server address Smtp Geves Fr Click on the tabs to show New essages or Sent messages Attached files Authors B Moutault amp C Chevalier Page 14 Date 20 08 2012 Version 1 Functions of the different buttons gt Account Enables you to delete modify or create a new account see point 3 1 gt aa gt p Send Enables you to send a message gt ___New message Enables you to create a new message gt _ Modifier message Enables you to edit an existing message gt Delte Enables you to delete a message gt LPi Enables you to print a message Enables you to update data following any modifications or additions gt Qt Enables you to exit the messaging system 4 2 Application GEVES GEVES applications can be accessed directly through AIM without users having to re enter their identification details thanks to the option Use the same log in If the required application is not on your computer it will be installed automatically amp Liste des applications Loe ADR Gestion des Adresses AIM Gestion des traitements et d analyses dimages COM Gestion du syst me dinformation du service Communication DEM Demeter DHS Gestion des tude DHS DVP Gestion des tables de d veloppement FAC Facturation Sev FID Gesion des Fiches Descriptive FIJ Logiciel d analyse d im
56. ions in your study The following types are all results obtained from clustering operations A19 A21 A20 and A22 Cell Acquisition Aim19 defining cells zones and acquisitions In this case the image feature has been removed image series Zone Image Aim21 defining zones images and acquisitions In this case the cell feature has been removed Zone Acquisition Aim20 defining zones and acquisitions In this case the cell and image features have been removed Object Aim22 defining objects In this case everything has been removed and only objects are clustered 9 5 3 Clustering Select your study and click on the Authors B Moutault amp C Chevalier Page 69 Date 20 08 2012 Version 1 A Parameters Statistic TT Process 1 Ver Resut Parem_Stet 7 A206_ A TEXTE SQL MEDIAN MIN Moyenne Anthm tique oo different types of grouping a IMAGE ACQUISITION MATERIAL Le N ca Cell Acquisition Aim19 fone Image Aim21 one Acquisition Aim20 SF Object Aim2 A window will open and you will be able to select the material s acquisitions images and processing operations covered by the clustering function as well as the type types of Statistical parameters and clusters desired Then confirm using the Lied button Example_l For an overview of this clustering step we will look at the example of a study involving four varieties I have measured a Volume for
57. king on the column heading A205 _A_WBELLE is The symbol Le M indicates that the column 1s sortable The symbol Ascending ance indicates that the column is sortable and currently sorted in The symbol hd indicates that the column is sortable and currently sorted in Descending order The symbol L indicates that a value search can be performed in the column Date he IRAIN Tr 17707706 00 06 08 07 06 070706 070706 SS eM 25 4 B Daa Taa Left click on the magnifying glass and fill in the value Pr nom Demandeurs 07 0 _ Or right click to open the menu Search and Filter hristophe Hhristelle hristelle TE AD1_A_NOM sanr a ounen i Zu IND NAME YfND_FIRS 2012 Projet SCLEROVAR feuilles de colza in OUTAULT Benjamin 2013 Projet EURALIS feuilles de colza eurau mini 2013 SCLEROVAR Cotyledons amp Feuilles L Is equal to Comparaison Couleur Appareil Photo Delete the filter Starts with Couleur des Feuilles J Couleur des Fleurs Orchid es Is equal to 2012 Projet SCLEROVAR NE DRAP tic Ends with eee Is equal to 2013 Projet EURALIS f Contains D nombrer des plantes jeunes Distinction de Grains Mars Is equal to 2013 SCLEROVAR Cotyle Is different from Etude Hortensia Is equal to Comparaison Couleur Appar Does not start with Etude Syngenta Mais 009 mer Is equal to Couleur des Feuilles Does not contain Is
58. lect a list and use the shortcut key F11 or click on the button Adding a new list of theoretical Type of study Exterieur Name Count condition DUS Species 40500 Com Insert the type of study the title and species Click on the OK button to validate Note the species is optional but if it is stipulated by the user then this list of experimental conditions will only apply to that species Once the list has been created you must add remove conditions In the details table click on the hie button or on L Add Conditions to select new conditions multiple conditions may be selected List of lists of theoretical conditions 3 TSTE_COM ANS A LIBELLE 43 Conditions 2012 SNES Conditions 2013 SNES Conditions 2014 SNES PHE SNES Phe List of theoretical conditions 13 E B_LIS S00 CS AZ00_A_LIBELLE 4 N_VAL_CONDITS AID_A_REMARG 1 DELA D lai t0 t1 0 DURE Dur e exploitation FREQ Fr quence GROS Grossissement HREF Heure r f rence IREF Image r f rence LUMI Luminosit Caution when conditions are added they do not by default contain any values or comments It is up to you to provide that additional information by entering it directly into the details table List of theoretical conditions 13 ee LISTER DO Cra A200_A LIBELLE 2 D lai t0 t1 DURE Dur e e
59. lick on the button or use the shortcut key F12 and confirm the deletion MESURER Couleur des feuilles v2 moyenne BEN MESURER Niveau de Couleur AWB v2 BEN qu TRAITER Pouvoir Couvrant v2 JMR TRAITER Finesse Feuille mm auto JMR cal COMPTER Jeune Pousse JMR cons Confirm the deletion of the macro TRAITER Champignon sur Feuille JMR exp iss Thank you TRAITER Stipule JMR me SOUSTRAIRE Fond noir LPB uni MESURER Mm Surface Cotyledaons PATHO q DEFINIR l chelle Pixels Millim tres STANDA COMPTER Cellule STANDARD compre Tomo ve cernes INT mirr md oom E u 4 fi i i i al ET A TI 8 1 4 Import Export You can import or export macros into and out of the AIM application for example to facilitate the exchange of macros between users in different organizations and companies Each macro has a corresponding file a Word file doc Exporting macros Select the macros click on the p Epot button and indicate the destination directory Importing macros Click on the 7 impot button and select one or more Macro files Word files Caution if other Word documents are open they will be closed automatically Example to work out the expected AIM format for importing macros use the example file by pressing the button Authors B Moutault amp C Chevalier Page 45 Date 20 08 2012 Version 1 Below are 2 example files one empty and the other one a
60. low you to work on a copy of the database of one of the sites The copies are loaded from production data from a site following a simple request 4 4 Change password GEVES It is possibly to change passwords Meter as directly in AIM Base Oracle Ac ol Thalie Pas Phy Nouveau mot de passe Enter the new password and click on nee the OK button in order for the password to apply to all GEVES applications on all sites 4 5 Screen shots As the name suggests when you click on screen shot an image jpg 1s saved on your computer This image corresponds to what is displayed within the software package on the screen Question Une copie cran t r alis et sauvegard sous C Mes Projets Meteor ExeMet_Fen_Menu Jpg voulez vous la visualiser Then a window opens informing you of the location of the file image which has been generated and asking you 1f you wish to view the image 4 6 Quit This keeps your various settings for a future session and closes the AIM software package Authors B Moutault amp C Chevalier Page 16 Date 20 08 2012 Version 1 5 Referential Menu Hae Experimental condition 1 Medium and Source Zone Device Pot Colors Fae List of Colors Vi Color Functions E List of Values Species Individual Company 5 1 List of values This window allows you to manage information in the secon
61. lready filled out AIMI setion des macros F1 nom MERE IMR calouler la surface d occupation des plantes couleur verte par rapport au sol en champs if Seul pour bb Hinana ff rendre le traitement cache 1 ou nan 0 ff cr er des images Superpose fait pesant les zones JF taille piwel minimum des cellules mesurables FE nom de sorte du fichier de mesures N preise les nome d image avec into que resort A format de sorte des images A format de sorte des images tre de la colonne X fire de la colonne Pour utiliser ce fichier vo Si vous avez plusieurs me Merci bonne journ e u m Ce ES maTa mi CE oy F f ME La macro ten images de type coule mip 3 er dhomma ea ee ce er a N ee AAA A E J Authors B Moutault amp C Chevalier Page 46 Date 20 08 2012 Version 1 9 Study Menu 5 Declaration 0 Analysts te Integration a EF Calculs 2 Results 9 1 Study declaration Before processing images you need to define the operating environment This window enables you to create and manage the declarative aspect of studies which includes information such as the name of the study experimental conditions study materials varieties the number of replications usable macros acquisitions zone layout varieties on the images of the acquisitions etc File Study Macro Fast Processing Processing Software Referential Options
62. mber of measurements 0 Pouvoir_Couvrant xis 6 peas field low_1 jpg peas field low_2 jpg 798 524 peas field mean_1 jpg 1125 916 peas field mean_2 jpa 1 123 557 peas field strong_1 jpg 201 543 peas field strong_2 jpg 201 459 vr DataBase Ange_Adre User moutaultb Current field Tab_Resultat 10 40 54 There are two main tables studies and acquisitions The details table contains the list of processing operations history results files and results 9 3 1 Processing history and results files List results files and macros 3 Processing history 3 neue A16_C_A_NOM_FIC_RESULT A12_D DATE TRAITEMENT 45 20 11 2012 17 15 00 s zip BINARISER Simple BINARISER Simple 20 11 2012 17 09 32 20 11 2012 17 05 10 Each time an analysis is launched AIM records the date of execution Linked to each date you have either one or more result files no files if the macro does not generate any processing canceled if the analysis was halted manually Authors B Moutault amp C Chevalier Page 60 Date 20 08 2012 Version 1 You can delete this history using the TE vuitton Be careful as each deletion involves the cascade deletion of the attached results files as well as the measurements in the database calculations and clustered items You can delete results files using the Date button this does not involve cascade deletion of basic measurements calculations and clustered it
63. n Couleur des Feuilles Exemple Groupe d Etude et d MOUTAULT cal amin _DATE_ACQU B 3 Var_1 25 09 2012 Document PDF UPOW 4 Im 2 List the proces a g and Es n 2T TRAI SRAD MA STE LA LS ES ri er i 0 Orchide_extract bmp 1 ri a l 0 016294 Vari t 11 apa 0 Orchide_extract bmp 1 2 209 217 211 0 1137E Vari t 11 Var Etract 0 Orchide_extract bmp 1 3 219 199 205 1 03806 Vari t 11 Var_Extract 0 Orchide_extract bmp 1 4 221 203 224 5 2939 Vari t 11 Var Etract 0 Orchide_extract bmp 1 5 211 204 218 3 4859 Vari t 11 Var Etract 0 Orchide_extract bmp 1 6 36 19 26 2 34632 Vari t 11 Var_Extract 0 Orchide_extract bmp 1 7 151 106 111 0 45056 Vari t 11 Var_Extract 0 Orchide_extract bmp 1 8 212 217 220 0 40222 Variete 11 Var_Extract 0 Orchide_extract bmp 1 9 220 156 203 0 27345 Vari t 11 Var_Extract 0 Orchide_extract bmp 1 10 137 35 115 2 2284 Vari t 11 Var_Extract 0 Orchide_extract bmp 1 11 297 218 210 0 08532 Vari t 11 Var Extract 0 Orchide_extract bmp 1 12 149 38 135 0 5708 Vari t 11 Var Etract 0 Orchide_extract bmp 1 13 185 79 177 0 30674 Vari t 11 Var_Extract 0 Orchide_extract bmp 1 14 210 160 218 0 2295 Vari t 11 Var Etract 0 Orchide_extract bmp 1 15 178 70 160 0 84506 Vari t 11 Var_Extract 0 Orchide_extract
64. n the File tab you can integrate the results columns of your choice To do this click on the button and a window will open to allow you to select result variables for integration Results Variable valeur Bleu xX Fxel_ The result variables have been defined to match the column headings in ImageJ often in English Select one or more rows and confirm by clicking on Lok A message window will warn you that the result variables have been saved and will inform you of the number of rows that have been integrated re Recording 2844 results in 00 m 28 s 362 milli i Rouge Vert Bleu Pixel_ Authors B Moutault amp C Chevalier Page 64 Date 20 08 2012 Version 1 9 4 Calculations CD This window enables you to launch pre defined calculations for variables previously recorded in the form of a spreadsheet within which a formula may be applied This method can be used to carry out pixels millimeters conversions for example File Study Macro GEOEEBBEBISTLEEEIFE TS Em Fast Processing Processing Software Referential Options Module Window Help Search Criteria You can use tl x Tye gt Name Comparaison Couleur Appareil Photo Coloration NAKTUINBOUW MOUTAULT Benjami
65. n will not delete clustered data in Aim22 You have to perform the operation for each result type Comment However relaunching the clustering function automatically enables you to delete previous clusters in the destination table 9 5 5 Graph This is a feature that enables you to view AIM application data To do that you need to display and select all or part of the results see 9 5 1 particular attention should be paid to the selection order and then click on the button Choose the columns for graphic Caption ME Caption OBJECT_NUMBER OBJECT NAME 3 IMAGE_NAME z LINE COLUMN Temps Germ e Caption Caption A selection window opens with a list of usable column labels on the left side of the window Column table You must select the series one or more columns Series table the x value column X axis table and the y axis value one column Y axis table Use the amp and amp buttons to move the column labels Authors B Moutault amp C Chevalier Page 73 Date 20 08 2012 Version 1 TYPE_OBJET_NOM OBJET_SERW OBJET_NUM REPETITION IMAGE_NOM 90 a Li j h S 70 i lt D F Vari t _1 HG D variete_2 HD 40 Vari t _3 BG a U variste_4 BD 30 a D a 10 STSNSSSRARSTSORRESRERSEESS Temps Moyenne Arithmetique Authors B Moutault amp C Chevalier Page 74 Date 20 08
66. ng mode AIM 9 3 Authors B Moutault amp C Chevalier Page 40 Date 20 08 2012 Version 1 8 Macro Menu I ES Managing 8 1 Management of Macros In the AIM application images are processed with the aid of external software third party for example Image J selected by GEVES for its community and freeware character AIM runs Image J with the help of macros that can be managed from this window da Eile Study Macro Fast Processing Processing Software Reterential Options Module Window Help ME x ITALIE Search Criteria You can use the View Ay rer tice compre wer years pon a A DESCRIPTIONS or mr i 2 ere SU _ TRAITER Champignon sur Feuille JMR expression de la surface de la necrose sur la feu M_St_ Methode Huang T ai TRAITER Stipule JMR mesures longueurs et largeurs de la feuille de l e IVI_En_Cacher_lmage 1 Af rend SOUSTRAIRE Fond noir LPB uniformise le fond de limage en noir en partant VM_Bo_lmag_Superpose 0 if cree MESURER Mm Surface Cotyledons PATHO mesures surface cotyl don en mm sur table I 50 086 DEFINIR l chelle Pixels Millim tres STANDARD Calcul du rapport Pixels Milimetres f f CORPS 49 COMPTER Cellule STANDARD compte le nombre de cellules f j MESURER GEVES Analyse_Objet STANDARD mesures GEVES Analyse_ Objet sur gre IFF velica venin miim IMAGE Jea option standar BINARISER Simple STANDARD m
67. ns BINARI YAN Colza coty dons m thode simple se MESURER Mm n image YAN mesures OLAV largeur longueur sur c Macro PIVOTER Cotyl dons ORIGINAL fy ENTETE ff Vi_En_Seuil_ Segmentation 217 Vi_Str_Taille_Mini 900 _Cacher_Image 1 pour l tape de segm j taille minimum de sele rendre le traitement im fe 4 CORPS ff Le A verfication version mini IMAGE J option standard fond BLANC annee i run Options iterations 1 count 1 an foreground black background white selection yellow m voir ou non les images The l st of macros s displayed when a study s selected Whenever you select a study the macros list 1s updated macros are in their initial form When you select a macro its rich text content RTF is displayed on the right side You can modify it temporarily to suit the needs of upcoming processing operations For example if the macro has a header section it is easy to adapt some of the values without permanently changing the macro in the database of the application s macros Any changes are stored temporarily even if you modify the macro Until you refresh the display list by selecting a study or by switching windows for example The purpose of the macros tab is to inform AIM of the processing operations you have selected and their running order List of valid macros 4 Inactive PIVOTER Cotyledo
68. ns Aie f BINARISER a First Second Authors B Moutault amp C Chevalier Date 20 08 2012 A03_A DESCRIPTION YAN Colza cotyledons pivote cotyledons TAN Colza REISE a ae Se Page 55 Version 1 9 2 3 Images You must select the images to be processed during the next processing operation Images List ofimages 3 ie A13_A_NOM_FIC_IMAGE yanC0001_1 jpg P_yanC0001_1 jpg INB_P_yanC0001_1 png The list of images is displayed updated when you select one or more acquisitions The images are saved by acquisition meaning that the link to the declarative section in the previous window can be maintained Caution when uploading images take care to select the correct acquisitions 9 2 3 a How to use this feature The images tab contains the list of images a search bar and various action buttons and displays the images in the right hand section Le To ad Add images using Windows selection feature Le m Date Delete selected rows 4 Modify Type Modify image type as LS Refresh Order Update the order in line with the current filter in place name Le Open Open the image with your default software e g Picasa eo im Change the order of the images in the list Save the selected images to disk s Delete search criteria F l Le Display redisplay the image list Le Select unselect all images Authors B Moutault amp C Chevalier Page 56
69. ntly asked questions Authors B Moutault amp C Chevalier Date 20 08 2012 69 73 76 76 77 77 79 Page 5 Version 1 1 Software installation GEVES 1 1 Initial installation Depending on the site you are using for example the Magneraud site double click on the file INSTALL EXE file in the directory Z Windev AIM then follow the installation assistant s prompts clicking on Next at each stage as Setup wizard Welcome to setup wizard This program will install software on your workstation Tip end all current Windows applications before launching setup Application will be installed in following directory IL Program Files Gaia Advanced Cancel DRE vIAU Setup wizard A Directory C Program Files Gaia not found Do pou want to create it 1 Click Yes The installation assistant will then display a summary of the installation process EL Setup wizard Setup summary Setup will start now Selected options Setup will be done in directory C Program Files Gaia Selected setup mode complete Run automatic data modification Click Previous to modify options Click Next to continue lt Previous 2 A message will indicate the end of the installation process as well as prompting you to create icons and launch the program Authors B Moutault amp C Chevalier Page 6 Date 20 08 2012 Version 1 ih Setup wizard x Setup
70. of theoretical conditions 3 F S TS hs A09_A_LIBELLE i ESS C53 V_NOM_ESF af Tay A205_A_LIBELLE Conditions 2012 SNES Espece inconnue PHE SNES Ph notpage Conditions 013 SNES D Espece inconnue PHEHSNES Ph notypage Conditions 2014 SNES Espece inconnue PHE SNES Phenotypage of EE conditions _LISTEA O CA Ca m D_A_LIBE N N_VAL_CONDITA A10_A_REMARQUE gt DELA D lai t0 t1 1 hours a 2 DURE Dur e exploitation 60 minutes FM 2 FREG Frequence 120 minutes T 2 GROS Grossissement 80 pixels E 2 HREF Heure r f rence 4 hours 2 IREF Image r f rence 0 2 LUMI Luminosit 0 E 2 NCPE Nombre Cellule Par Colonne 5 T 2 NCPL Nombre Cellule Par Ligne 5 FM 2 RADM Radicule Minimum Longueur 1 millimiters FM SEMO Semence morte 0 F 2 SDEP Seuil d placement 3 millimiters E 2 TEMP Temp rature 20 experimantal condition E 5 2 1 Consult When the window opens the list is displayed according to the criteria entered in the search bar You should use the empty study type to display everything Once you have selected a list the details will appear in the second table 5 2 2 Create Modify To open the window to create a list of experimental conditions use the shortcut key F10 or click on the BB button Authors B Moutault amp C Chevalier Page 22 Date 20 08 2012 Version 1 Likewise to modify the experimental conditions se
71. on Authors B Moutault amp C Chevalier Page 24 Date 20 08 2012 Version 1 5 3 Medium and Source CD This window allows you to manage the medium and source for the images used in AIM You must select the medium source for each acquisition AIM Managing image processing and analysis Management of the Medi File Study Macro Fast Processing Module Window Help DEE Be Wiel Sa sia e eee sms r A05_A_REMARQUE E SNES module 1 Banc_2 SNES module 2 send by ESEO in 2011 CETIOM Paris Exterieur GEVES NAKTUINBOUW Sotaweg 22 Postbus 40 2370 AA Roelofa Exterieur UPOV Exterieur pa AD4 A NOM af VI D_DATE ACH Cam_1 04 02 2014 Current DataBase Ange_Adre User moutaulth Current field 15 45 13 5 3 1 Consult Select the source in the main table to see the various media linked to it in the detail table 5 3 2 Create Modify SOURCE To open the window to create a new source use the shortcut key F10 or click on on the oP button Authors B Moutault amp C Chevalier Page 25 Date 20 08 2012 Version 1 Likewise to modify a source select a row and use the shortcut key am NRA F11 or click on the a button cati Beaucouz Remark MR CHEVALIER Insert the name location a comment and the number of media you wish to define concerning this source Confirm by clicking on
72. ord About range of information on AIM including the version number and the email address for IT support Authors B Moutault amp C Chevalier Page 77 Date 20 08 2012 Version 1 Authors B Moutault amp C Chevalier Page 78 Date 20 08 2012 Version 1 12 Frequently asked questions CD Question My list of macros is empty incomplete in the Analysis window even though the macros have been declared properly at the study level study declaration window _ Answer Only active macros are visible in the Analysis window Return to the Macro Management window and validate the macros that you want to see and use in your study 6 1 2 zeuille Auteurs B Moutault amp C Chevalier Page 79 Date 01 10 2009 Version 1
73. portant sorted by date name etc or defined in the previous window 9 1 5 List of acquisitions 20 ei ACQUIS Images of directory C Users MOLITAU 1 Desktop Temp Name 2 A02_D_DATE ME 1 AQ2_A_ NOM s 16 05 2 E LOGOGEVESE amp P accro snes jpg Comespondence Be 16 05 2 E MinistereG Ptutelle jpg 1 fr 1 Var_1 r3 16 05 2 INRA bmp 1 m ba bis LEE Nouvelle image bitmap bmp ka ll Lan Nouvelle image bitmap 3 Copie bmp Var_2 12 16 0572 Nouvelle image bitmap 3 bmp JET tine D rl IE NR 1 z ar 4 Mm F Nouvelle image bitmap Copie bmp T Images will be loaded by matching the left and right hand lists acquisitions and images Authors B Moutault amp C Chevalier Page 57 Date 20 08 2012 Version 1 In the example below each acquisition will contain two images aCe ADGA NOM faq D_DATE_ACQUISIE Images du r p atene NOUS Eee Sees aka ae da 93 50995 ar 2501 25705 2012 Yar_2501_11 bmp Correspondance 3 50994 Var_2502 25 05 2012 Yar 2501 12 bmp 1 pou 1 9 50995 Var_2503 25 05 2012 Var 2502 r1 bmp 3 50996 War_berlikumer 25 05 2012 Yar_2502_12 bmp L I 50997 Var blanche acol 2570572012 Var_2503_r1 bmp 9 50998 Var bolero 25 05 2012 a 2503_12 bmp 9 50399 Var de colmar b 25 06 2012 Yar helikumer
74. s RHS gp Pixel_ _RHS a Rang Couleur RHS Bl 1 Var_1 D_SF_3 5666_1 bmp 1 1 746 0 241177 12 1 Var_1 D_SF_3 5666_1 bmp 1 2 726 2 915465 6 i 1 Var_1 D_SF_3 5666_1 bmp 1 3 590 0 506278 9 1 Var_1 D_SF_3 5666_1 bmp 1 4 T74 0 253462 11 1 Var_1 D_SF_3 5666_1 bmp 1 5 217 5 181109 5 1 Var_1 D_SF_3 5666_1 bmp 1 6 206 7 53275 3 1 Var_1 D_SF_3 5666_1 bmp 1 7 737 0 292258 10 1 Var_1 D_SF_3 5666_1 bmp 1 8 47 83393 1 1 Var_1 D_SF_3 5666_1 bmp 1 9 791 0 207555 13 1 Var_1 D_SF_3 5666_1 bmp 1 10 273 23 855216 u ee LOOK AIM14_RESULT_CELLULE IMG 583 _ after the I AL AUUE L OBJECT_NUMBER amp OBJECT_NAMES IMAGE_NAME A LINES COLUMN amp RHS omy Pixel_ _RHS Rang Couleur RHS Label RHS_op En Pale Yellowish Green 193D Yellowish white 155D Reminder Not all languages are available with regard to color classes Authors B Moutault amp C Chevalier Page 33 Date 20 08 2012 Version 1 5 6 Species Individual Company Non GEVES O This window enables you to manage the species individuals and companies used in the AIM application By default this window is hidden from GEVES users who benefit from centralized management of species individuals and companies amp AIM Managing image processing and analysis Management of list Local Values amp File Study Macro Fast Processing Processing Software Reterential Options Window Help EJE x
75. s the following values Row Column Zone to each measurement By default all images are subjected to incremental indexing as a part of which objects are numbered for 1 to N Example with four objects Simple indexing is carried out for each image based on the X and Y coordinates of the objects and the elements declared for the acquisition Column List of conditions D rs LA A200 LIBELLE Nombre Cellule Par Colonne Nombre Cellule Par Ligne Track indexing is carried out on the first image on the basis of the X and Y coordinates and the elements declared as above For subsequent images the calculation of the minimum distance is used Authors B Moutault amp C Chevalier Page 62 Date 20 08 2012 Version 1 The aim here is to maintain the same identifiers namely Row Column Zone for the objects and to track them throughout the whole series of images even if they have been displaced pa 1 pe Img_2 Img_3 Manual indexing is performed by copying the Row Column Zone values from the results file columns A window will pop up to ask what these columns are Select a column click on to define it as a row column or zone You can also double click The De activated indexing option enables you to take no action and simply to display the result file However you will not be able to integrate the measurements into the database For Simple and Track
76. studies See example 5 4 4 5 4 3 Create Modify f ee Adding a new layout sn Name LAYOUT Number of zones By LINE To open the window to create a zone layout use By COLUMN the shortcut key F10 or click on the oF button Description use the shortcut key F11 or click on the a button or simply double click ai zones By COLUMN Description You should insert the name and number of zones you wish to define for the layout It 1s also possible to add a description of the layout Confirm the selection by clicking on the OK button Authors B Moutault amp C Chevalier Page 28 Date 20 08 2012 Version 1 In order to add more specific information also insert the number of zones per row and per column These values will be used to integrate the results indexing see 9 3 3 For example for a layout with 4 zones AIM distinguishes between 2 by 2 squared 4 by 1 in a row and 1 by 4 in a column Caution When modifying the number of zones if you indicate a lower number the last zones defined will be automatically deleted See 5 4 4 ZONE Then you must fill in the zones that are created automatically at the same time as the layout number of zones To modify those zones use the shortcut key F11 or click on the Fa button or double click on the row TITLE column Perform the modification and exit the row AIMOS ZONE 4 A08 CRAO7 NUM DISPOSJAOS C NUM ZONES
77. t lead to the loss of all measurements for a variety A layout of 4 zones squared 2 by 2 Name Square 2x2 has been created Number of zones By LINE By COLUMN Authors B Moutault amp C Chevalier Page 30 Date 20 08 2012 Version 1 5 5 List of Colors CD This window enables you to consult the color classification schemes which are used as a repository in the AIM application amp AIM Managing image processing and analysis List of colors File Study Macro Fast Processing Processing Software Referential Options Module Window Help gt DER Er TE Search Criteria You can use the List of colors referenced in AIM 808 08 CLASS AT CODE_CO 2710_C_COD A212_A_LIBELLE 9_N_CODP9 9_N_CODPA 9_N_CODPA 9_N_CODEA 9_N_CODEA 9_N CODPAA_CODE_RVB_ A 2 as a D5B3E5 am ie hep oy CO ZE ee 2 Cm en 5 5 1 Consultation As with the other application windows a search bar enables you to filter the information to be displayed Search Criteria You can use the Choose the color classification scheme UPOV RHS or GEVES Specify a language French English German or Spanish You can also filter the colors referenced in AIM by Label or by Code The Coloring checkbox enables you to color the displayed rows Note Certain languages are not available for some color classes
78. t object number as well i men as the type of material used Double click on the row or on the button to modify the material Var_ 2502 CULT Cultivar Var_ 2503 CULT Cultivar Var_berikumer g Modification of study material Sax Var_blanche a col _ Var_bolero For the study Finesse des feuilles Var_de colmar b Var_soprano Material Caption Var_touchon Var_valor Serv amp Code Type of abject Ange_Adre User Ve de colmar O Click on the Delete button to delete the material You can manage the order of the materials you declare n the study using the buttons to move material up or down The _ Refresh order button reshuffles the order according to the filter in place The order is important when automatically creating acquisitions loading images automatically etc Authors B Moutault amp C Chevalier Page 50 Date 20 08 2012 Version 1 You can import data from an Excel file using the button while respecting the column order on the first page d A C D 1 TYPE OBJET SERV OBJET NUM OBJET LIBELLE 2 NDEF i 9 1 Vari t 1 3 NDEF i 9 2 Vari t 4 NDEF F 9 3 Vari te_ 3 5 NDEF 9 4 Vari t 4 6 NDEF d 9 5 Vari t 5 T NDEF i g 6 Vari t 6 To see an example file click on the button The DORE ton will automatically generate acquisitions in accordance with the material selected the order and the number of replications declared in
79. the OK button C oe oe j Number of mediums 3 Caution When modifying the number of media if you insert a lower number the last media defined will be automatically deleted See 5 3 3 MEDIUM Then you must indicate the media created automatically at the same time as the source number of media In order to modify the media use the shortcut key F11 or click on the Ex button or double click on the row window will open allowing you to change the name validity date resolution and comment UPFUY Exteneur NR CHEVALIER amp Modification of the medium n 4 CE nn O For medium 1 N R A Name Medium E 7 MEDIUM 31 C_CAMEAVRAD5_BA 8 Wine unit Apple unit as 5 3 3 Delete To delete a source and all corresponding media select the source Confirm the deletion of the source LN R A and click on the button or use the Thank you shortcut key F12 and then confirm the deletion Authors B Moutault amp C Chevalier Page 26 Date 20 08 2012 Version 1 5 4 Zone layout This window allows you to manage the zone layout used in AIM amp AIM Managing image processing and analysis Management of zone layout File Study Macro East Processing Processing Software Reterential Options Module Window Help AIMO7_
80. xploitation FREQ Fr quence GROS Grossissement HREF Heure r f rence IREF Image r f rence Authors B Moutault amp C Chevalier Page 23 Date 20 08 2012 Version 1 To remove conditions select them and use the shortcut key F12 or click on the ss button and confirm the deletion 5 2 3 Delete In order to delete a list of experimental conditions you must first of all clear the conditions contained therein List of lists of theoretical conditions 3 gt nes De une fSTE_COR Al WAT53_ ESA C53 V_NOM_ESP FT 3 Conditions 2012 SNES Espece inconnue PHE SNES Phe Conditions 2013 SNES spece inconnue a Pha Conditions 2014 SNES spece i PHE SNES Ph Management of experimental conditions Confirm the deletion of the theoretical condition Luminosit List of theoretical conditions 13 men And the next f_LISTEA N_ Cre A200_A_LIBE Thank you 2 DELA D lai t0 t1 DURE Dur e exploitation FREG Mi in HREF Heure reference IREF Image reference lm U NCPC Nombre Cellule Par Colonne You must select all the conditions and then confirm the deletion Then you can select the conditions list to be deleted by clicking on the button or using the shortcut key F12 and then confirming the deleti

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