These two algorithms do not search shortest paths over the same area. Algorithm: Path finding algorithm used to search for shortest paths.Several input parameters can be set in DiversePathsJ GUI (Figure 4). User-defined path extremities overlaid on an input image (appearing as blue crosses with labels "1" and "2"). Starting the plugin with less or more selected points will throw an error.įigure 3. DiversePathsJ requires exactly two selected points. By convention, "1" is used as source and "2" as target points. The two user-selected end-points are overlaid on the input image as blue crosses with labels "1" and "2". Point selection tool of ImageJ used to set path extremities.įigure 3 displays proper initial conditions for the diverse paths search. To set the second one, maintain the shift key pressed and click at the desired location on the image.įigure 2. The first point can be set by simply clicking on the image. This is done using the point tool from ImageJ highlighted in Figure 2. ImageJ plugin menu featuring ChromosomeJ.īefore or directly after launch but in any case before running the diverse shortest paths search, a start and an end points must be selected. The plugin can be started from the Plugins tab of the ImageJ menu (see Figure 1).įigure 1. The archive should be uncompressed, and the elements it contains should be placed into the jars folder of the plugins folder of ImageJ ( ImageJ/plugins/jars/). DiversePathsJ also requires some external libraries that have been regrouped in the following archive file. To install the plugin download the DiversePathsJ_.jar file and put it in the plugins folder of ImageJ ( ImageJ/plugins/). Users are strongly encouraged to send bug reports, comments, praise and love letters at DiversePathsJ support address.įiji users: DiversePathsJ is available through Fiji's built-in updater using as update site URL. ImageJ and Fiji are both open-source and free and do not take more than a couple of minutes to install. The software provided here is a plugin for ImageJ or Fiji,Ī general purpose image-processing and image-analysis package. The use and exploitation of this technology. In addition, you undertake to include a citation to the associated papers whenever you present or publish results that are based on it.ĮPFL makes no warranties of any kind on this software and shall in no event be liable for damages of any kind in connection with You'll be free to use this software for research purposes, but you must not transmit and distribute it without our consent. Note that the SDK depends on the libraries contained in the following archive file. jar library and can be instantiated as shown in this code snippet. It can thus be used alone or integrated as part of larger image analysis pipelines.įor developers, we also provide the core processing units of DiversePathsJ as an SDK, without any user interface elements. The plugin only requires the specification of the source and target locations and of the dynamic programming potential map in addition to data-independent parameters (number of desired shortest paths and minimum amount of desired diversity between paths). It is implemented to leaves a lot of freedom in the definition of path diversity, such as imposing a minimal Euclidean distance between paths, or enforcing that the different paths accumulate a certain amount of diversity. The present software relies on a modified dynamic programming algorithm for finding a collection of diverse shortest paths in images between user-defined source and target locations. Hamprecht, " Diverse M-Best Solutions by Dynamic Programming," Proceedings of the Thirty-Ninth German Conference on Pattern Recognition (GCPR'17), Basel BS, Swiss Confederation, September 13-15, 2017, in press. Unser, " DiversePathsJ: Diverse Shortest Paths for Bioimage Analysis," Bioinformatics, in press. It is not linked to a specific biological problem and can be applied to a large variety of images. This software implements a dynamic programming approach for the general task of finding diverse shortest paths between two end-points. Written by Virginie Uhlmann at the Biomedical Image Group (BIG), EPFL, Switzerland
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