imageHTS: Analysis of high-throughput microscopy-based screens

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.

Author
Gregoire Pau, Xian Zhang, Michael Boutros, Wolfgang Huber
Date of publication
None
Maintainer
Joseph Barry <joseph.barry@embl.de>
License
LGPL-2.1
Version
1.24.0

View on Bioconductor

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

Files in this package

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