osifi / morpholibj

Collection of mathematical morphology methods and plugins for ImageJ

MorphoLibJ

MorphoLibJ is a collection of mathematical morphology methods and plugins for ImageJ, created at the INRA-IJPB Modeling and Digital Imaging lab.

The library implements several functionalities that were missing in the ImageJ software, and that were not or only partially covered by other plugins. Namely:

• Morphological filtering for 2D/3D and binary or grey level images: erosion & dilation, closing & opening, morphological gradient & Laplacian, top-hat...

• Morphological reconstruction, for 2D/3D and binary or grey level images, allowing fast detection of regional or extended extrema, removing of borders, hole filling, attribute filtering...

• Watershed segmentation + GUI, making it possible to segment 2D/3D images of (for instance) cell tissues.

• 2D/3D measurements: photometric (intensity) and morphometric measurements such as volume, surface area, inertia ellipse/ellipsoid...

• Binary / label images utilities for removing or keeping largest connected component, perform size opening, fill holes, kill borders...

Installation

• In ImageJ, download the latest released jar into the plugins folder.

• In Fiji, you just need to add the IJPB-plugins update site:

1. Select Help > Update... from the Fiji menu to start the updater.

2. Click on Manage update sites. This brings up a dialog where you can activate additional update sites.

3. Activate the IJPB-plugins update site and close the dialog. Now you should see an additional jar file for download.

4. Click Apply changes and restart Fiji.

Develop upon MorphoLibJ

If you develop plugins / applications based on MorphoLibJ, you can use add the following dependency in the maven project configuration file:

  <dependency>
    <groupId>fr.inra.ijpb</groupId>
    <artifactId>MorphoLibJ_</artifactId>
    <version>1.5.0</version>
  </dependency>

In case the last version of MorphoLibJ is not included in the maven repository, one workaround is to download the jar file of the last version, and to add it to the local maven repository. The following command may help (adapt version number as necessary):

mvn install:install-file -Dfile=MorphoLibJ_-1.5.0.jar -DgroupId=fr.inra.ijpb -DartifactId=MorphoLibJ_ -Dversion=1.5.0 -Dpackaging=jar -DgeneratePom=true

Documentation

A more detailed presentation of the library and its plugins is available on the ImageJ/Fiji Wiki.

We have as well a User Manual in pdf format.

The main source code directory is src/main/java/inra/ijpb.

You can browse the javadoc for more information about its API.

Citation

Please note that MorphoLibJ is based on a publication. If you use it successfully for your research please be so kind to cite our work:

• David Legland, Ignacio Arganda-Carreras, Philippe Andrey; MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ. Bioinformatics 2016; 32 (22): 3532-3534. doi: 10.1093/bioinformatics/btw413