Package: zooimage 5.5.2
zooimage: Analysis of Numerical Plankton Images
A free (open source) solution for analyzing digital images of plankton. In combination with ImageJ, a free image analysis system, it processes digital images, measures individuals, trains for automatic classification of taxa, and finally, measures plankton samples (abundances, total and partial size spectra or biomasses, etc.).
Authors:
zooimage_5.5.2.tar.gz
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zooimage.pdf |zooimage.html✨
zooimage/json (API)
| # Install 'zooimage' in R: |
| install.packages('zooimage', repos = c('https://phgrosjean.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 6 years agofrom:f1f6cebc1f
Exports:aboutZIacquireImgactiveLearningactiveLearningGUIaddClassaddItemsToTrainaddToTestaddToTrainaddVigsToTrainanalyzeClasscalcVarscalibcalibratecellComputecellCountcellModelcheckDirExistscheckEmptyDircheckFileExistscheckFirstLinecloseAssistantcloseZooImagecollectTraincompTraincontextSelectioncorrectErrorcountCellsGUIcreateThresholddropItemsToTraindropVarsecdeditDescriptionexitZIexportResultsextensionPatternfocusGraphfocusRforceDirCreategetDecgetTestgetTrainhasExtensionimageViewerimportFlowCAMimportImgisZimjpgListlistFilesExtlistObjectslistSamplesloadObjectsmakeClassmakeIdmakeTrainmakeZidmakeZidbmakeZidbFlowCAMmakeZIVignettesmodalAssistantnoExtensionoptInOutDecimalSepparseInipngListprepareTestprepareTrainprocessImgprocessSampleprocessSampleAllprocessSamplesprocessSamplesWithCellsreadFlowCAMctxreadFlowCAMlstrecoderemoveObjectssampleInfosaveObjectsselectFileselectGroupsselectListselectObjectstartPgmtemplatetrimStringunderscoreToSpaceunzipImgunzipImgAllvalidClassviewFrenchManualviewManualviewResultsvignettesClasszicCheckZIClasszidbDatReadzidbDrawVignettezidbLinkzidbListzidbMakezidbMakeAllzidbPlotNewzidbPlotPagezidbSampleReadzidbSummaryzidbToZidzidbToZidAllzidCleanzidCompresszidCompressAllzidDatMakezidDatReadZIDlgzidListzidToZidbzidToZidbAllzidUncompresszidUncompressAllzidVerifyzidVerifyAllZIEzieCompilezieCompileFlowCAMzieMakezimCreatezimDatListzimDatMakeFlowCAMzimDatMakeFlowCAMAllzimEditzimExtractAllzimListzimMakezimUpdateAllzimVerifyzipImgzipImgAllzipListzipNoteAddzipNoteGetzisCreatezisEditzisReadZIUI
Dependencies:base64encbslibcachemclassclicodetoolscommonmarkcrayoncrosstalkdata.tablediagramdigestDTe1071evaluatefastmapfilehashfontawesomefsfuturefuture.applyglobalsgluehighrhtmltoolshtmlwidgetshttpuvipredjpegjquerylibjsonliteKernSmoothknitrlaterlatticelavalazyevallifecyclelistenvmagrittrMASSMatrixmdamemoisemimemlearningnnetnumDerivparallellypngprodlimprogressrpromisesproxyR6randomForestrappdirsRcpprlangrmarkdownrpartrstudioapisassshapeshinysourcetoolsSQUAREMsurvivalsvDialogssvGUIsvMisctifftinytexwithrxfunxtableyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ZooImage: analysis of digital plankton images | zooimage-package zooimage |
| The ZooImage error correction (manual validation) tools | activeLearning addItemsToTrain correctError dropItemsToTrain |
| Various file utility functions used by ZooImage | checkDirExists checkEmptyDir checkFileExists checkFirstLine extensionPattern forceDirCreate hasExtension jpgList listFilesExt noExtension pngList zidbList zidList zimDatList zimList zipList |
| The ZooImage GUI (Graphical User Interface) | aboutZI acquireImg activeLearningGUI addVigsToTrain analyzeClass calib closeAssistant closeZooImage collectTrain compTrain countCellsGUI editDescription exitZI exportResults focusGraph focusR importImg listObjects loadObjects makeClass makeTrain makeZid makeZidb makeZidbFlowCAM optInOutDecimalSep processImg processSamples processSamplesWithCells removeObjects saveObjects validClass viewFrenchManual viewManual viewResults vignettesClass ZIDlg ZIUI |
| Various GUI utility functions used by ZooImage | createThreshold imageViewer modalAssistant selectFile selectGroups selectList selectObject startPgm |
| Function to import data from the FlowCAM | importFlowCAM readFlowCAMctx readFlowCAMlst |
| Various utility functions used by ZooImage | addClass calcVars calibrate dropVars ecd getDec listSamples makeId makeZIVignettes parseIni sampleInfo trimString underscoreToSpace zipNoteAdd zipNoteGet |
| Check .zic files (ZooImage Categories) | zicCheck |
| Create and manipulate 'ZIClass' objects | confusion.ZIClass predict.ZIClass print.ZIClass summary.ZIClass ZIClass |
| Manage .zid files (ZooImage Data) | zidClean zidCompress zidCompressAll zidDatMake zidDatRead zidUncompress zidUncompressAll zidVerify zidVerifyAll |
| Manage .zidb files (ZooImage Databases) | zidbDatRead zidbDrawVignette zidbLink zidbMake zidbMakeAll zidbPlotNew zidbPlotPage zidbSampleRead zidbSummary zidbToZid zidbToZidAll zidToZidb zidToZidbAll |
| ZIE (ZooImage Extension) manipulate .zie files to add custom import, export, etc. routines to ZooImage | print.ZIE ZIE zieCompile zieCompileFlowCAM zieMake |
| Manipulate .zim files (ZooImage Metadata/Measurements) | isZim zimCreate zimDatMakeFlowCAM zimDatMakeFlowCAMAll zimEdit zimExtractAll zimMake zimUpdateAll zimVerify |
| Zip and unzip raw .tif images for ZooImage and embed metadata | unzipImg unzipImgAll zipImg zipImgAll |
| Various function to calculate results ('ZIRes' object) | print.ZIRes processSample processSampleAll rbind.ZIRes |
| Manipulate .zis files (ZooImage Samples description) | zisCreate zisEdit zisRead |
| Manipulate training and testsets 'ZITrain'/'ZITest' objects | addToTest addToTrain cellCompute cellCount cellModel contextSelection getTest getTrain prepareTest prepareTrain recode recode.ZITest recode.ZITrain template template.default |
