The principle of morphological dilation is to test for each point of the plane, if the structuring element centered on this point intersects the structure of interest (see figure below). The most basic morphological filters are the morphological dilation and the morphological erosion. The original idea was to define a methodology to describe shapes by using another shape as test probe (Serra, 1982 1). Linear structuring element of various orientations may also be used to assess local orientation of the structures. Common structuring element include squares, discrete disks and octogons. Morphological filters are defined according to a structuring element of a given size and shape. They are local filters, in the sense that they consider the neighborhood of each pixel/voxel. Morphological filters are very common filters that can be combined together to provide a large variety of solutions. MorphoLibJ’s code repository has its own DOI. If you use it successfully for your research please be so kind to cite our work: Please note that MorphoLibJ is based on a publication. You can browse the javadoc for more information about its API. The main source code directory is on GitHub under src/main/java/inra/ijpb. Click Apply changes and restart ImageJ.Įach released version of MorphoLibJ comes with a User Manual in PDF format.Now you should see an additional jar file for download. Activate the IJPB-plugins update site and close the dialog.This brings up a dialog where you can activate additional update sites. Select Help › Update… from the menu to start the updater.In ImageJ2 (including Fiji), you just need to add the IJPB-plugins site to your list of update sites:.In ImageJ 1.x, download the latest released jar into the plugins folder.Watershed segmentation + GUI, making it possible to segment 2D/3D images of (for instance) cell tissues.ĢD/3D measurements: photometric (intensity) and morphometric measurements such as volume, surface area, inertia ellipse/ellipsoid…īinary / label images utilities for removing or keeping largest connected component, perform size opening, fill holes, kill borders… 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… Morphological filtering for 2D/3D and binary or grey level images: erosion & dilation, closing & opening, morphological gradient & Laplacian, top-hat… The library implements several functionalities that were missing in ImageJ, and that were not or only partially covered by other plugins. MorphoLibJ is a collection of mathematical morphology methods and plugins for ImageJ, created at INRA-IJPB Modeling and Digital Imaging lab. If you’d like to help, check out the how to help guide! This is helpful when dealing with noisy data where the magic wans will occasionally find the outline around a patch of above threshold noise instead of finding the desired object.ĭeusto University Bilbao P.A.S.The content of this page has not been vetted since shifting away from MediaWiki. It also provides a very nice little feature that has the program to compare the size of the current outline with the previous outline and to jog the ‘Vertical’ value or ‘Horizontal’ value in order to find the full outline again. The plugin provides navigation buttons for scanning through the stack (>). It will apply cuts defined by ‘First Slice’ and ‘Last Slice’. The application, will process an entire stack with specified starting frame and ending frame, using the magic wand outline to clear inside, and clear outside and then draw a line with graylevel=255. With ‘View ROI =>’ we can view the different ROIs in the same slice. We can create more than 1 region (maximum 4) by slice or image using ‘More ROIs’. To capture the values, we select the point in the image with ImageJ´s point selector, and push the ‘Take Point’ button. It could be very useful to reconstruct a 3D image of an organ composed of various regions with the plugin ‘Volume Viewer’ for example or other 3D reconstruction application. Generated regions (ROIs) are saved for each slice, so we can process the lungs from an image stack for example, or other organs. Restarting ImageJ will add a "Cell Outliner" command to the Plugins menu or a submenu of the Plugins menu.Īpplies the magic wand with a specified threshold and at a specified point or points (X and Y values) on the images or slices from a stack. Won't work on single images - a work around is to simply add an empty frame into the image.ĭownload Multi_Cell_Outliner.java to the plugins folder, or subfolder, and compile and run using Plugins/Compile and Run. Koldo Latxiondo (koldo2k at ) from Deusto University – P.A.S.Groupīased on the original Cell_Outliner plugin
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