Muscle Fiber Type Composition

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Hi all,

I am having some difficulties that I am hoping that you guys can help me with. I am taking 20x images of cross sections of muscles which underwent an immunohistochemical stain. This stain allowed for the distinction of four different muscle types: Type I (DAPI blue), Type IIa (Texas red), Type IIb (FITC green), and Type IIx are black. I am looking for an automated way to count the different fibers in an image. I have only found one macro that claimed to do this, but there seems to be an error in the code. Any suggestions? I am taking the images as ND.2 but converting them to TIF files. In ImageJ the pictures open as a stack, so the channels are easily split.

Thanks a ton!


Hello @mjshar02 and welcome to the ImageJ forum!

Can you post here a link to one of your images so we can better understand the problem and help you with it?


Here is an example of an image I took, the only difference is that the green and blue fibers shouldn’t be as speckled but more filled in. The black (not colored, but are dimly red from the original thresholding) fibers are the Type IIx fibers.


The article I found online used the macro in ImageJ that can be found under Supplementary Information in the following article: The only difference is that they did CY5 yellow instead of DAPI blue. However, the macro seems to have an error- I am not sure if it is within the original code, or if I am editing it incorrectly to access my files.


I see, can you post here the error you are getting?


The error said that a parenthesis was needed in line 34 [the line under FITC that states: for(i=0;i<list.length;i++)]. And there was an additional error saying that an image needed to be open to run the macro, which doesn’t make sense since the macro is designed to open folders containing the different images according to the color.


Sorry for the late answer, @mjshar02, what are you using to run the macro? Are you using Fiji or ImageJ?


I am using ImageJ to run the macro


OK, I see it now. Did you replace the folder names with your own?