TissueSemgentation, colorTreshold

[mhoibo]

Hi,
I have been creating segmentations with both the new neural network based segmentation model and the color thresholding model, but I can't seem to be able to change the level/magnification of where to perform the color thresholding segmentation.

When I run the following line of code:
tissue_segmentation = fast.TissueSegmentation.create(magnification=X, useColorThresholdingMethod=True).connect(image_importer).runAndGetOutputData()

The output segmentation image is the same size regardless of which magnification I use (X), I see the same if I try to use the level argument.

When I use useColorThresholdingMethod=False, the size of the segmentation image is different when I change the magnification parameter.

Does anyone know why this happens, and how I can set the magnification level when running the color thresholding model?

Also, is it correct that the color thresholding segmentation performs its segmentations at x1.25 by default?

I am using the newest stable fast version (v4.10.0, installed today).

[smistad]

The color thresholding method (the old method) for tissue segmentation, never had a level or magnification parameter.
Thus this is only used with the new neural network method.
Color thresholding uses the highest level of the image pyramid.
See here: https://github.com/smistad/FAST/blob/master/source/FAST/Algorithms/TissueSegmentation/TissueSegmentation.cpp#L72

Maybe this should be changed? Why do you need to run in a specific magnification?

[mhoibo]

Ah, okay, I see, thank you for the quick answer.
It may not be necessary, but it was too see if there was a difference in segmentation performance at different magnifications, but maybe for the color thresholding it won't matter much?

[smistad]

Using a different level/magnification in color thresholding would definitely change the result. Both the output of the actual color thresholding will be different, and even more it will influence the morphology post processing step since a specific radius is used. The radius should then probably be adapted to the specific level/magnification

[mhoibo]

That makes sense, all of it. Thank you so much!