How to count closely spaced muscle fibers in a cross sectional image?

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Given this image:
I would like to:
-count the number of mucsle fibers
-calculate the area of each of the muscle fibers
-find the min/max diameter of each of the muscle fibers
My initial thought was to:
-reduce noise by using sobel filter or canny edge filter
-use circular hough transform to identify the muscle fibers
-create active contours
I got stuck on trying to implement the circular hough transform.
Any and all help is appreciated Thanks Mohammad
  1 Comment
Mohammad Aref
Mohammad Aref on 3 Jul 2013
Maybe I can count the muscle fibers using a manual cell counter
and then I can crop the image (imfreehand?) on one muscle fiber or a few muscle fibers that have clear divides between them. Then I can use something like this to calculate area and other parameters (<http://www.mathworks.com/help/images/examples/measuring-regions-in-grayscale-images.html?prodcode=IP&language=en>)
Are there any better, more automated ways to accomplish this? I need to count all the fibers, but do not need to find the areas or diameters on all the fibers.
Thanks again
Mohammad

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Accepted Answer

Image Analyst
Image Analyst on 3 Jul 2013
I'd use a manual counting system to get a count of the fibers - ask the users to click on a fiber with ginput(). Then I'd threshold to find the bright white pixels. You might have to clean up a little to get rid of any white things that appear inside a fiber. So now you know the area of the fibers (=area of image - area of white), and the count, so you can get the average area of the fiber set.
  2 Comments
Mohammad Aref
Mohammad Aref on 4 Jul 2013
Simple but intelligent. I'm trying this now. Any ideas on how to get rid of the white pixels inside the fiber?
Thank you very much for your time
Image Analyst
Image Analyst on 4 Jul 2013
Just threshold. Look at the color channels to see which one had good contrast. Then threshold:
whitePixels = redChannel > 200; % or whatever color or value you want.
The tricky part will be determining if the white is outside the fiber, or inside the fiber.

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