MorphoLibJ

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.

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