I have a binary image, already segmented, of a z=25 stack, of mitochondria. I’m looking at differences in shapes and volumes, and trying to quantify the in vivo range.
When using the FIJI pre-installed “3D Object Counter” plugin I get a very different result from when I use the plugin “Connected Components Labelling” from the MorphoLibJ collection. (3D Counter settings - size filter >10 voxels; MorphoLibJ settings - connectivity 6 and 16-bit result). It’s a binary image, with a voxel depth of 0.2663212, and pixel width/length of 0.0658941 microns.
P.eg, 3D Objects Counter retrieves 1137 objects while Connected Components Labelling retrieves 2109 objects. When I plot the Volumes retrieved by both, or the surface areas, the ranges are very different… A link for the image I’m using (25MB) is here https://mycore.cnrs.fr/index.php/s/5TFPhSwBPIA8y54 (not sure if I could upload the file here…) if you want to replicate my data.
Can someone help me understand the differences in both methods (if there should be any!) and what I might be doing wrong?