Quantification of bald/necrotic areas

[Vasudeva Bhat]

Hi, I am new to QuPath and I was wondering if there was a way to quantify bald areas in H&E stained sections. I have attached images for your reference. I have many images to process and manual quantification is very tedious. Could someone help me with this?

Appreciate your suggestions!

[micros...@gmail.com]

Try selecting the area, SLIC superpixel segmentation, then Add intensity measurements (hematoxylin channel is probably the most useful). I also made use of the Haralick texture features at the bottom of the Add Intensity Measurements dialog to determine regions where either eosin or hematoxylin staining was very constant.

Useful links: https://groups.google.com/d/msg/qupath-users/sjTgDTEXu1Y/efR4YbtoAwAJ

https://groups.google.com/d/msg/qupath-users/gm0YYJxSriA/FE3hNBS3BAAJ

Visual example: https://github.com/qupath/qupath/issues/121

[Vasudeva Bhat]

Thank you very much. That was very helpful.