I have released a few small tools for Matlab <-> IJ integration:
Selection_To_Indices and Indices_To_Selection are PlugInFilters. The first converts an ImageJ ROI to a vector of Matlab indices for the same image. The second converts a Matlab vector of indices to an ImageJ ROI.
They are best used through two matlab scripts I have included, roi_to_vector.m and vector_to_roi.m (though technically, the PlugInFilters could also be used standalone through the clipboard).
The principal disadvantage with vector_to_roi.m is that the Matlab vector is a point cloud, and consequently rendered as a polygon with as many lines as points when converted to an ROI. The problem of converting point cloud to polygon appears nontrivial, however if anyone knows of a plugin or other algorithm that does a good job converting point clouds to polygons, I will be happy to incorporate it in the next push.
Finally, I have also added openImage.m, a script which automatically opens a Matlab object of any dimensions >=2 in MIJ.
I have migrated my IJ Toolkit over to GitHub at the address:
https://github.com/ericbarnhill/barnhill_ij_toolkitThe .m scripts are in the matlab folder, the .jar is in the dist folder, and .java and .class files are in src and bin where expected.
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