EBImage-package {EBImage} | R Documentation

## Package overview

### Description

`EBImage` is the 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 `ImageMagick` library for image I/O operations and for many image processing routines. Algorithms for image analysis are implemented natively including algorithms for feature extraction.

Image data are stored in objects of the class `Image`, which is derived as an S4 class from `array` and inherits all of its properties and methods.

The project page is http://www.ebi.ac.uk/~osklyar/EBImage

### Package content

Classes

- Class 'Image', its accessor method
- Class 'IndexedImage'
- Common generic methods for class 'Image'
- 'Image' object creation, copying and assertion
- Image read/write operations

Image processing

- Enhancing images and colors
- Image color manipulation
- Generate a tiled image from a stack
- Image and color channel thresholding
- Image transformation, rotation, resize etc.
- Noise removal, blurring and smoothing of images

Image analysis

- Distance map transform of binary images
- Morphological trasnsformations of binary images
- Segmentation and edge detection
- Voronoi-based segmentation on image manifolds
- Watershed transformation and watershed-based object detection

Feature extraction

- Extraction of Haralick texture features and co-occurance matrices (GLCM)
- Extraction of edge profiles and edge features
- Extraction of hull features
- Extraction of Zernike moments
- Extraction of image moments and moment invariants
- Combined feature extraction for objects in indexed images
- Object removal in indexed images
- Marking detected objects in indexed images
- Generate a stack of images for detected objects
- Matching objects in two indexed images

Tools

- Color and image color mode conversions
- Drawing primitives on images, annotation
- Interactive image display

### Authors

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

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

[Package EBImage version 2.2.0 Index]