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.
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morphological filtering: erosion & dilation, closing & opening, morphological gradient & laplacian, top-hat...
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morphological reconstruction, allowing fast detection of regional or extended extrema, removing of borders, or hole filling
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watershed segmentation + GUI, making it possible to segment 2D/3D images of cell tissues
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2D/3D measurements: 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 plugin for the user is available on the ImageJ Wiki, as well as on the Fiji Wiki.
The main source code directory is src/main/java/inra/ijpb.
You can browse the javadoc for more information about its API.