imageHTS: Package overview
Description
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.
Package content
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
Miscellaneous functions.
- 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