imageHTS: Package overview

In imageHTS: Analysis of high-throughput microscopy-based screens

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

Authors

Gregoire Pau, [e-mail], 2010

imageHTS documentation built on Nov. 8, 2020, 8:29 p.m.