Hi Diana @afonso,
I just downloaded your dataset and it looks like it’s connecting objects that aren’t connected, for example the four orange/red objects in the center:
However, when you draw a line through them
and use the tool
Image > Stacks > Dynamic Reslice, you’ll see that these object are connected in the third dimension:
When using this tool, you can also move that line and browse through your volume.
As a potential way out, you can temporarily eliminate touching areas by calling a Minimum filter (Menu
Process > Filter > Minimum, radius 10) on the binary image (also known as erosion in this context):
… then call Connected Components Labeling:
… followed by a Maximum filter (same radius):
You will also see that it cuts objects in places where it shouldn’t. Thus, it might make sense to play a bit with the
And last but not least: There might be no perfect method
Let us know if this helps!