(This could be a result of the characteristics of the DAB absorbance.) Let’s see …Īfter converting your original images A and B to RGB stacks it can be seen that the strongest effect of the different staining itensity is visible in the green and blue channel. I assume that there is a more simple solution. I also would like to skip absorbance, stain vector, color deconvolution etc. Let’s do the QuPath processing in the next step. Since it is unclear to me what you want to measure exactly I would like to use ImageJ/Fiji first. In the following I have downsampled the images to half of their original size to reduced the negative effects of this patterns. This checkerboard patterns can be found all over both images and disturbing. Would it be possible to have access to the original images? This can be also seen if the aR|aG|aB absorbance values are displayed in a 3D viewer. This shows that the linear assumption is not valid.
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