I am having a problem with the 3D version of the geodesic distance map of MorpholibJ. What I have is a 3D binary stack (~1600x1600x, 81 z levels) with a single white continuous mask on a black background and then another stack with similar dimensions where I have marked a single white dot as the marker. If this would work, I would import the 3D transformation to Imaris, where I could extract the distances of cells within the masked region to the marker position.
If I perform the 2D version of the transformation on one slice, it gives me exactly the result I want, but If I attempt the same with the whole stack using the 3D version, it just undergoes endless iterations. Things I have already tried are:
Thresholding both the marker and the mask image to make sure they are binary 8bit
Inverting the images (either produces a black stack with no map or endless iterations)
Making sure the continuous mask does not touch the edges of the image in xyz.
Resizing my stack (500x500px)
Test stack with a white cylinder in the middle (500x500x, 50 slices)
Independent versions of Fiji on separate computers
If on the other hand, I perform the 3D Chamfer distance map on my own stack on MorphoLibJ, it works with no problem. I am really starting to think, is there something wrong with the plugin. I tested 3D geodesic distance transformation half a year ago and I remember that it worked then. Does anyone have any ideas?