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:Philippe Grosjean [aut, cre], Kevin Denis [aut], Guillaume Wacquet [aut]

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'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

141 exports 0.00 score 77 dependencies

Last updated 6 years agofrom:f1f6cebc1faae5f49087275c69b6c67037a20b0c

Exports:aboutZIacquireImgactiveLearningactiveLearningGUIaddClassaddItemsToTrainaddToTestaddToTrainaddVigsToTrainanalyzeClasscalcVarscalibcalibratecellComputecellCountcellModelcheckDirExistscheckEmptyDircheckFileExistscheckFirstLinecloseAssistantcloseZooImagecollectTraincompTraincontextSelectioncorrectErrorcountCellsGUIcreateThresholddropItemsToTraindropVarsecdeditDescriptionexitZIexportResultsextensionPatternfocusGraphfocusRforceDirCreategetDecgetTestgetTrainhasExtensionimageViewerimportFlowCAMimportImgisZimjpgListlistFilesExtlistObjectslistSamplesloadObjectsmakeClassmakeIdmakeTrainmakeZidmakeZidbmakeZidbFlowCAMmakeZIVignettesmodalAssistantnoExtensionoptInOutDecimalSepparseInipngListprepareTestprepareTrainprocessImgprocessSampleprocessSampleAllprocessSamplesprocessSamplesWithCellsreadFlowCAMctxreadFlowCAMlstrecoderemoveObjectssampleInfosaveObjectsselectFileselectGroupsselectListselectObjectstartPgmtemplatetrimStringunderscoreToSpaceunzipImgunzipImgAllvalidClassviewFrenchManualviewManualviewResultsvignettesClasszicCheckZIClasszidbDatReadzidbDrawVignettezidbLinkzidbListzidbMakezidbMakeAllzidbPlotNewzidbPlotPagezidbSampleReadzidbSummaryzidbToZidzidbToZidAllzidCleanzidCompresszidCompressAllzidDatMakezidDatReadZIDlgzidListzidToZidbzidToZidbAllzidUncompresszidUncompressAllzidVerifyzidVerifyAllZIEzieCompilezieCompileFlowCAMzieMakezimCreatezimDatListzimDatMakeFlowCAMzimDatMakeFlowCAMAllzimEditzimExtractAllzimListzimMakezimUpdateAllzimVerifyzipImgzipImgAllzipListzipNoteAddzipNoteGetzisCreatezisEditzisReadZIUI

Dependencies:base64encbslibcachemclassclicodetoolscommonmarkcrayoncrosstalkdata.tablediagramdigestDTe1071evaluatefastmapfilehashfontawesomefsfuturefuture.applyglobalsgluehighrhtmltoolshtmlwidgetshttpuvipredjpegjquerylibjsonliteKernSmoothknitrlaterlatticelavalazyevallifecyclelistenvmagrittrMASSMatrixmdamemoisemimemlearningnnetnumDerivparallellypngprodlimprogressrpromisesproxyR6randomForestrappdirsRcpprlangrmarkdownrpartrstudioapisassshapeshinysourcetoolsSQUAREMsurvivalsvDialogssvGUIsvMisctifftinytexwithrxfunxtableyaml

Readme and manuals

Help Manual

Help pageTopics
ZooImage: analysis of digital plankton imageszooimage-package zooimage
The ZooImage error correction (manual validation) toolsactiveLearning addItemsToTrain correctError dropItemsToTrain
Various file utility functions used by ZooImagecheckDirExists 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 ZooImagecreateThreshold imageViewer modalAssistant selectFile selectGroups selectList selectObject startPgm
Function to import data from the FlowCAMimportFlowCAM readFlowCAMctx readFlowCAMlst
Various utility functions used by ZooImageaddClass calcVars calibrate dropVars ecd getDec listSamples makeId makeZIVignettes parseIni sampleInfo trimString underscoreToSpace zipNoteAdd zipNoteGet
Check .zic files (ZooImage Categories)zicCheck
Create and manipulate 'ZIClass' objectsconfusion.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 ZooImageprint.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 metadataunzipImg 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' objectsaddToTest addToTrain cellCompute cellCount cellModel contextSelection getTest getTrain prepareTest prepareTrain recode recode.ZITest recode.ZITrain template template.default