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 screen data, facilitating the dissemination of high-throughput microscopy-based screens.
The following function instantiates the imageHTS object.
parseImageConf: instantiate an imageHTS object from a local or remote screen data repository
The following functions process, segment, quantify, summarize the well images.
segmentWells: segment cells in well images
extractFeatures: extract cell features from segmented images
readLearnTS: train a cell classifier
predictCellLabels: predict cell labels
summarizeWells: summarize cell populations
The following functions provides means to display and inspect the screen data.
installWebQuery: install the webQuery module
popWebQuery: pop the webQuery module
installCellPicker: install the cellPicker module
popCellPicker: pop the cellPicker module
segmentATH: segment cells stained for DNA, actin and tubulin
getCellFtrsATH: extract features from cells stained for DNA, actin and tubulin
The following functions give access to the screen data.
fileHTS: build the path to a screen data file
readHTS: read a screen data file
parseDCF: read a DCF configuration file
collectCellFeatures: collect cell features
getWellFeatures: get well metadata, features and annotation information
The following manipulate well unique names.
getUnames: get well unique names
prw2uname: convert a (plate, replicate, well) data frame in well unique names
uname2prw: convert well unique names in a (plate, replicate, well) data frame
rowcol2well: convert a (row, col) data frame in well names
well2rowcol: convert well names in a (row, col) data frame
well2wellid: convert well coordinates in numerical well identifiers
zprime: compute the Z'-factor quality score
highlightSegmentation: highlight segmented objects in an image
countObjects: count the number of objects in a segmented image
getImageConf: get the imageHTS configuration
Gregoire Pau, firstname.lastname@example.org, 2010
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