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:
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Morphological filtering for 2D/3D and binary or grey level images: erosion & dilation, closing & opening, morphological gradient & Laplacian, top-hat...
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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...
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Watershed segmentation + GUI, making it possible to segment 2D/3D images of (for instance) cell tissues.
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2D/3D measurements: photometric (intensity) and morphometric measurements such as volume, surface area, inertia ellipse/ellipsoid...
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Binary / label images utilities for removing or keeping largest connected component, perform size opening, fill holes, kill borders...
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In ImageJ, download the latest released jar into the plugins folder.
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In Fiji, you just need to add the IJPB-plugins update site:
- Select Help > Update... from the Fiji menu to start the updater.
- Click on Manage update sites. This brings up a dialog where you can activate additional update sites.
- Activate the IJPB-plugins update site and close the dialog. Now you should see an additional jar file for download.
- Click Apply changes and restart Fiji.
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