No separation between green and red fibers

[apena6]

The color deconvolution step does not seem to separate red and green staining in my PSR images. I did not get any errors when running the fiber quantification matlab code, but the output parameter sheet had the same values for red and green fibers. I used tiled 20x images as input, does the code require 40x images?

[shamikmascharak]

Hi, thanks for your message! I’m not sure what might be causing that, perhaps a version issue? I would try deleting the code package and re-downloading from GitHub. Also would update Matlab if it’s an older version.

On Thu, Sep 29, 2022 at 10:29 AM apena6 @.***> wrote:

The color deconvolution step does not seem to separate red and green staining in my PSR images. I did not get any errors when running the fiber quantification matlab code, but the output parameter sheet had the same values for red and green fibers. I used tiled 20x images as input, does the code require 40x images?

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[apena6]

Thank you for your response, I re-downloaded the code (& updated Matlab) and now I am using v3 of the m file. I know get an error on line 56 stored_norm_im{i} = Norm(stored_im{i},target_im,'RGBHist',verbose); with the error that there are too many input arguments.