Counting fibres

Hi there,

I would like to have some suggestions on how could I do some automatic fibres count, from binary images (obtained previously on Ilastik).
The problem is that is difficult to isolate the fibres as an object, and I need to count only the fibres that cross a line (the above line of a Roi), like the figure below:
data-3.tif (1.8 MB)

It can be done in any software of image analysis…

Any ideas?

Thank you in advance.


I suggest to extract the ROI profile and then apply a peak detection. Each fiber crossing the ROI boundary will result in an intensity peak in the profile. I have no experience in ImageJ but these topics can be a start.

1 Like

Here’s what I get using the Freehand line selection tool (green line), the Plot profile tool (CTRL+K), and the (very convenient) BAR peak finder recommanded by @B0RJA

I increased the line thicknessto 10 to get rid of noise, but maybe you don’t need that.
It’s not automated, but you can record the operations to create a macro.