imageHTS: Analysis of high-throughput microscopy-based screens
Version 1.26.0

imageHTS is an R package dedicated to the analysis of high-throughput microscopy-based screens. The package provides a modular and extensible framework to segment cells, extract quantitative cell features, predict cell types and browse screen data through web interfaces. Designed to operate in distributed environments, imageHTS provides a standardized access to remote data and facilitates the dissemination of high-throughput microscopy-based datasets.

Browse man pages Browse package API and functions Browse package files

AuthorGregoire Pau, Xian Zhang, Michael Boutros, Wolfgang Huber
Bioconductor views CellBasedAssays Preprocessing Software Visualization
Date of publicationNone
MaintainerJoseph Barry <joseph.barry@embl.de>
LicenseLGPL-2.1
Version1.26.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("imageHTS")

Man pages

collectCellFeatures: Collect cell features.
countObjects: Count the number of objects in a segmented image
extractFeatures: Extract features from segmented images.
fileHTS: Get access to screen data files
getImageConf: Get the imageHTS configuration
getUnames: Get well unique names
getWellFeatures: Get well metadata, features and annotation information
highlightSegmentation: Highlight segmented objects in an image
imageHTS: Package overview
installCellPicker: Set up imageHTS web modules
makeCellHTS: Segmentation of yeast cells and ring-shaped objects.
parseDCF: Parse a DCF file
parseImageConf: Instantiate an imageHTS object
popCellPicker: Pop up imageHTS web modules
prw2uname: Convert and parse well unique names
readLearnTS: Learn, classify and predict cell labels.
segmentATH: Segmentation and quantification of cells stained for DNA,...
segmentWells: Segment cells in well images
segmentYeastBF: Segmentation of yeast cells and ring-shaped objects.
summarizeWells: Summarize cell features
zprime: Compute the Z'-factor quality score

Functions

buildCellHTS Source code
collectCellFeatures Man page Source code
countObjects Man page Source code
displayHTS Source code
extractCells Source code
extractFeatures Man page Source code
fileHTS Man page Source code
getCellFtrsATH Man page Source code
getCoords Source code
getError Source code
getImageConf Man page Source code
getUnames Man page Source code
getWellFeatures Man page Source code
highlightSegmentation Man page Source code
imageHTS Man page
imageHTS-class Man page
installCellPicker Man page Source code
installWebQuery Man page Source code
make.crown Source code
makeCellHTS Man page Source code
msg Source code
parseDCF Man page Source code
parseImageConf Man page Source code
popCellPicker Man page Source code
popWebQuery Man page Source code
predictCellLabels Man page Source code
prw2uname Man page Source code
readHTS Man page Source code
readLearnTS Man page Source code
rowcol2well Man page Source code
segmentATH Man page Source code
segmentRing Man page Source code
segmentWells Man page Source code
segmentYeastBF Man page Source code
sortOrientedContour Source code
summarizeWells Man page Source code
uname2prw Man page Source code
well2rowcol Man page Source code
well2wellid Man page Source code
writeContours Source code
writeLabels Source code
writeThumbnail Source code
zprime Man page Source code

Files

.BBSoptions
CHANGES
DESCRIPTION
NAMESPACE
R
R/cellPicker.R
R/classification.R
R/configure.R
R/extractFeatures-methods.R
R/extractFeatures.R
R/imageHTS.R
R/makeCellHTS.R
R/quality.R
R/segmentation-segmentATH.R
R/segmentation-segmentYeastBF.R
R/segmentation.R
R/summarize.R
R/webQuery.R
TODO
build
build/vignette.rds
inst
inst/NEWS.Rd
inst/cellpicker
inst/cellpicker/cellpicker.html
inst/cellpicker/css
inst/cellpicker/css/cellpicker.css
inst/cellpicker/css/ie.css
inst/cellpicker/javascript
inst/cellpicker/javascript/cellpicker_functions.js
inst/cellpicker/javascript/next_image.js
inst/cellpicker/javascript/var_ini.js
inst/cellpicker/javascript/wz_jsgraphics.js
inst/cellpicker/javascript/wz_tooltip.js
inst/doc
inst/doc/imageHTS-introduction.R
inst/doc/imageHTS-introduction.Rnw
inst/doc/imageHTS-introduction.pdf
inst/submorph
inst/submorph/conf
inst/submorph/conf/annotation.txt
inst/submorph/conf/description.txt
inst/submorph/conf/featurepar.txt
inst/submorph/conf/imageconf.txt
inst/submorph/conf/plateconf.txt
inst/submorph/conf/screenlog.txt
inst/submorph/conf/segmentationpar.txt
inst/submorph/conf/trainingset.txt
inst/submorph/data
inst/submorph/data/classifier.rda
inst/submorph/data/profiles.tab
inst/submorph/source
inst/submorph/source/PK-10B-pl1
inst/submorph/source/PK-10B-pl1/Well-A003
inst/submorph/source/PK-10B-pl1/Well-A003/FITC.jpeg
inst/submorph/source/PK-10B-pl1/Well-A003/Hoechst.jpeg
inst/submorph/source/PK-10B-pl1/Well-A003/Tritc.jpeg
inst/submorph/source/PK-10B-pl1/Well-A005
inst/submorph/source/PK-10B-pl1/Well-A005/FITC.jpeg
inst/submorph/source/PK-10B-pl1/Well-A005/Hoechst.jpeg
inst/submorph/source/PK-10B-pl1/Well-A005/Tritc.jpeg
inst/submorph/source/PK-10B-pl1/Well-B003
inst/submorph/source/PK-10B-pl1/Well-B003/FITC.jpeg
inst/submorph/source/PK-10B-pl1/Well-B003/Hoechst.jpeg
inst/submorph/source/PK-10B-pl1/Well-B003/Tritc.jpeg
inst/submorph/source/PK-10B-pl1/Well-B005
inst/submorph/source/PK-10B-pl1/Well-B005/FITC.jpeg
inst/submorph/source/PK-10B-pl1/Well-B005/Hoechst.jpeg
inst/submorph/source/PK-10B-pl1/Well-B005/Tritc.jpeg
inst/submorph/source/PK-10B-pl1/Well-C003
inst/submorph/source/PK-10B-pl1/Well-C003/FITC.jpeg
inst/submorph/source/PK-10B-pl1/Well-C003/Hoechst.jpeg
inst/submorph/source/PK-10B-pl1/Well-C003/Tritc.jpeg
inst/submorph/source/PK-10B-pl1/Well-D003
inst/submorph/source/PK-10B-pl1/Well-D003/FITC.jpeg
inst/submorph/source/PK-10B-pl1/Well-D003/Hoechst.jpeg
inst/submorph/source/PK-10B-pl1/Well-D003/Tritc.jpeg
inst/submorph/source/PK-11B-pl1
inst/submorph/source/PK-11B-pl1/Well-A003
inst/submorph/source/PK-11B-pl1/Well-A003/FITC.jpeg
inst/submorph/source/PK-11B-pl1/Well-A003/Hoechst.jpeg
inst/submorph/source/PK-11B-pl1/Well-A003/Tritc.jpeg
inst/submorph/source/PK-11B-pl1/Well-A005
inst/submorph/source/PK-11B-pl1/Well-A005/FITC.jpeg
inst/submorph/source/PK-11B-pl1/Well-A005/Hoechst.jpeg
inst/submorph/source/PK-11B-pl1/Well-A005/Tritc.jpeg
inst/submorph/source/PK-11B-pl1/Well-B003
inst/submorph/source/PK-11B-pl1/Well-B003/FITC.jpeg
inst/submorph/source/PK-11B-pl1/Well-B003/Hoechst.jpeg
inst/submorph/source/PK-11B-pl1/Well-B003/Tritc.jpeg
inst/submorph/source/PK-11B-pl1/Well-B005
inst/submorph/source/PK-11B-pl1/Well-B005/FITC.jpeg
inst/submorph/source/PK-11B-pl1/Well-B005/Hoechst.jpeg
inst/submorph/source/PK-11B-pl1/Well-B005/Tritc.jpeg
inst/submorph/source/PK-11B-pl1/Well-C003
inst/submorph/source/PK-11B-pl1/Well-C003/FITC.jpeg
inst/submorph/source/PK-11B-pl1/Well-C003/Hoechst.jpeg
inst/submorph/source/PK-11B-pl1/Well-C003/Tritc.jpeg
inst/submorph/source/PK-11B-pl1/Well-D003
inst/submorph/source/PK-11B-pl1/Well-D003/FITC.jpeg
inst/submorph/source/PK-11B-pl1/Well-D003/Hoechst.jpeg
inst/submorph/source/PK-11B-pl1/Well-D003/Tritc.jpeg
inst/submorph/submorph.R
inst/webquery
inst/webquery/index.php
inst/yeast.jpeg
man
man/collectCellFeatures.Rd
man/countObjects.Rd
man/extractFeatures.Rd
man/fileHTS.Rd
man/getImageConf.Rd
man/getUnames.Rd
man/getWellFeatures.Rd
man/highlightSegmentation.Rd
man/imageHTS.Rd
man/installCellPicker.Rd
man/makeCellHTS.Rd
man/parseDCF.Rd
man/parseImageConf.Rd
man/popCellPicker.Rd
man/prw2uname.Rd
man/readLearnTS.Rd
man/segmentATH.Rd
man/segmentWells.Rd
man/segmentYeastBF.Rd
man/summarizeWells.Rd
man/zprime.Rd
vignettes
vignettes/cellpicker.jpeg
vignettes/imageHTS-introduction.Rnw
vignettes/imageHTS.bib
vignettes/webquery.jpeg
imageHTS documentation built on May 20, 2017, 9:20 p.m.