EBImage {EBImage} | R Documentation

## Package overview

### Description

`EBImage` is an image processing and analysis package for R. Its primary goal is to enable automated analysis of large sets of images such as those obtained in high throughput automated microscopy.

The package uses the `ImageMagick` library for image I/O operations and some image processing methods. The `GTK` library is used for displaying images using `display`.

`EBImage` relies on the `Image` object to store and process images but also works on multi-dimensional arrays.

### Package content

Image methods

- `Image`
- `as.Image`, `is.Image`
- `colorMode`, `imageData`
- `getNumberOfFrames`

Image I/O, display

- `readImage`, `writeImage`
- `display`, `animate`
- `image`

Spatial transform

- `resize`, `flip`, `flop`
- `rotate`, `translate`

Image segmentation, objects manipulation

- `thresh`, `bwlabel`
- `watershed`, `propagate`
- `ocontour`
- `paintObjects`, `rmObjects`, `reenumerate`

Image enhancement, filtering

- `normalize`
- `filter2`, `blur`, `gblur`
- `equalize`

Morphological operations

- `makeBrush`
- `erode`, `dilate`, `opening`, `closing`
- `distmap`
- `floodFill`, `fillHull`

Colorspace manipulation

- `rgbImage`, `channel`

Image stacking, combining, tiling

- `stackObjects`
- `combine`
- `tile`, `untile`

Drawing on images

- `drawfont`, `drawtext`

Features extraction

- `getFeatures`
- `hullFeatures`
- `edgeProfile`, `edgeFeatures`
- `moments`, `cmoments`, `smoments`, `rmoments`
- `haralickFeatures`, `haralickMatrix`
- `zernikeMoments`

Deprecated

- `frameDist`, `matchObjects`
- `stopIfNotImage`
- `morphKern`, `mkbox`, `mkball`
- `header`, `assert`
- `chooseImage`
- `resample`, `sharpen`, `umask`, `modulate`
- `negate`, `affinet`, `normalize2`, `noise`
- `mediansmooth`, `cgamma`, `enhance`, `denoise`
- `contrast`, `despeckle`, `edge`, `segment`
- `cthresh`, `athresh`
- `channelMix`

### Authors

Oleg Sklyar, osklyar@ebi.ac.uk, Copyright 2005-2007

Gregoire Pau, gpau@ebi.ac.uk

Wolfgang Huber, huber@ebi.ac.uk

Mike Smith, msmith@ebi.ac.uk

      European Bioinformatics Institute
      European Molecular Biology Laboratory
      Wellcome Trust Genome Campus
      Hinxton
      Cambridge CB10 1SD
      UK

The code of `propagate` is based on the `CellProfiler` with permission granted to distribute this particular part under LGPL, the corresponding copyright (Jones, Carpenter) applies.

The source code is released under `LGPL` (see the `LICENSE` file in the package root for the complete license wording). `ImageMagick` and `GTK` used from the package are distributed separately by the respective copyright holders.

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

See the GNU Lesser General Public License for more details. For LGPL license wording see http://www.gnu.org/licenses/lgpl.html

### Examples

      example(readImage)
      example(display)
      example(rotate)
      example(propagate)

[Package EBImage version 3.0.5 Index]