Collection of mathematical morphology methods and plugins for ImageJ, created at 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: erosion & dilation, closing & opening, morphological gradient & laplacian, top-hat...
Morphological reconstruction, allowing fast detection of regional or extended extrema, removing of borders, or hole filling
Watershed segmentation + GUI, making it possible to segment 2D/3D images of cell tissues
2D/3D measurements: volume, surface area, inertia ellipse/ellipsoid...
Binary / label images utilities for removing or keeping largest connected component, perform size opening, fill holes, kill borders...
In ImageJ, download the latest released jar into the plugins folder.
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.