imageHTS {imageHTS} | R Documentation

## 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

### Authors

Gregoire Pau, gregoire.pau@embl.de, 2010

[Package imageHTS version 1.36.0 Index]