Changing the threshold used by Create Objects in pixel classification

[Austin_Edwards]

I have some nice images of kidney tissue, where the endothelial cells in the kidney tubules are labeled with GFP. I am trying to segment the tubule cross-sections using a pixel classifier -> create objects workflow.

Is there a way to threshold the output of the pixel classifier at something other than 0.5 in a binary classifier scenario? I want to leverage the fact that the classifier is less confident in the space between closely touching tubules to achieve better separation.

Thanks in advance for the help.

[Research_Associate (MicroscopyRA)]

Not an answer to your question, but have you tried using some of the additional Features that help find edges?

Pixel classification — QuPath 0.2.3 documentation

Gradient magnitude is listed for edges, for example.

[Austin_Edwards]

Playing around with those definitely help! I would still like to be able to change the object threshold, but this is a big help for sure. Thanks!