Bioimage Analysis / ImageJ plugin
MorphoLibJ
Apply mathematical morphology to clean masks, separate touching objects, and measure labeled structures in 2D or 3D.
Best fit
ImageJ users who need reproducible operations on binary masks or labeled volumes.
What you need
ImageJ or Fiji with the MorphoLibJ library and an image or label map in a supported form.
What to check
Structuring element size and connectivity assumptions can change counts and shapes. Record both when comparing samples.