I would like to calculate number of hollow fibers

Dear All, I am a beginner with Fiji ImageJ and do encounter following issue. I do have some micro-CT images of an artificial lung. I would like to count the number of fibers in both the oxygenator and heat exchanger compartment. What I did till now is to change the image type in 8 bit and to change the threshold so that I see the fibers as black dots. However, when I try to count these dots I do not succeed. I hope that this question is an easy one for the power users of this forum. If interested I can send an example picture.
Thank you all for your help.


Do you mind sharing with us an original image file? Either attach it directly here or share a link via a file sharing site (such as Dropbox). That way we have a better idea of how to help you. Also include - step-by-step - the exact commands you ran in Fiji…

Dear Etarena, in attachment an upload of an example filetop_0334.tif (3.3 MB)
As you can see there are two compartments filled with hollow fibers (fibers in the outer compartment have a smaller diameter than those in the inner). The scale of the picture is 12.5 pixels/mm. I would like to count the number of fibers in each compartment
What I did first was image => type => 8 bit. Then I tried to adjust the threshold. However this creates mostly small squares which are not counted by the analyze particles command.
I do hope that a power user as yourself has some tips and tricks to do the counting.
Thank you for helping me out

Dear @Fiji69fds,

I think you can use tools like this one:

I use it often when I need to find circular particles, usually it works fine after some fine-tuning of the parameter.
Since it works in pixel units, maybe just remove the calibration from
Image->Properties menu
setting unit to pixel and values to 1.

Unfortunately, at the moment I haven’t not time to try parameters but I am quite confident you can find some good set of parameters for your images.

Hoping that helps,
Emanuele Martini

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Dear Emanuele, Thank you for your prompt reply. I activated the update site for particle Sizer (Biomed group and ParticleSizer). I also installed R as advised. Unfortunately, most likely because I miss experience, I am not succeeding is counting the fibers in either compartment. I have tried several settings but at no avail.
Thank you for your help.