![]() ![]() See the GNU General Public License for more details. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. This program is free software you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation ( ). Bertrand’s Topological Watershed site, with papers, lecture slides and source code. All source codes are publicly available as Maven project (see the GitHub repository). For a fast integration of our plugins you can use our update site. Serge Beucher’s site, with graphic descriptions and animations of the watershed algorithms. The CMP-BIA tools is a package for ImageJ/Fiji which will perform image segmentation and registration.Classic Watershed, plugin implementing the original watershed algorithm to segment 2D/3D grayscale images. If you are installing ImageJ on Windows, we strongly recommend that you store your ImageJ.app directory somewhere in your user space (e.g., 'C:Usersyour nameImageJ.app') rather than in 'C:Program Files' or other system-wide directory.If you move ImageJ.Morphological Segmentation, a plugin with a graphical user interface to segment 2D/3D images based on morphological operations and the watershed algorithm.Interactive Marker-controlled Watershed, same idea as this plugin but with user-defined seed points.David Legland, Ignacio Arganda-Carreras, Philippe Andrey MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ.Soille, P., “Morphological Image Analysis: Principles and Applications”, Springer-Verlag, 1999, pp.“Morphological segmentation.” Journal of visual communication and image representation 1.1 (1990): 21-46. By following these installation steps, you will be installing as well the rest of plugins in the suite. Note: Marker-controlled Watershed is only one of the plugins included in the MorphoLibJ suite. You should now find the plugin under the sub-menu Plugins › MorphoLibJ › Segmentation. Now you should see an additional jar file for download. This brings up a dialog where you can activate additional update sites.ģ) Activate the IJPB-plugins update site and close the dialog. To install it, you just need to add the IJPB-plugins update site:ġ) Select Help › Update… from the Fiji menu to start the updater.Ģ) Click on Manage update sites. The Marker-controlled Watershed plugin is part of the MorphoLibJ library. Labeled image containing the catchment basins and (optionally) watershed lines (dams).Įxample of marker-controlled watershed segmentation on nucleus of Arabidopsis thaliana (image courtesy of Kaori Sakai and Javier Arpon, INRA-Versailles) Installation.Use diagonal connectivity: select to allow the flooding in diagonal directions.Calculate dams: select to enable the calculation of watershed lines.Binary markers: select to specify that markers are binary and need to be labeled.Set to “None” to run the method on the whole input image. The Mask image: a binary image of the same dimensions as input and marker which can be used to restrict the areas of application of the algorithm.They correspond usually to the local minima of the input image, but they can be set arbitrarily.Īnd it can optionally admit a third image: The Marker image: an image of the same dimensions as the input containing the seed points or markers as connected regions of voxels, each of them with a different label.The Input image: a 2D or 3D grayscale image to flood, usually the gradient of an image. ![]() Marker-controlled Watershed needs at least two images to run: (2012), " Fiji: an open-source platform for biological-image analysis", Nature methods 9(7): 676-682, PMID 22743772, doi: 10.1038/nmeth.2019, ( on Google Scholar).Main dialog of the Marker-controlled Watershed plugin If you'd like to share an idea or project, please share them with the community. ![]()
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