Hi @petebankhead and hi all,
I’m trying to do pixel classification on H&E staining (whole slide) for GI cancer patients (~11 different slides), and I’m struggling with 2 problems.
- There is a big variance in the quality of the staining, from too much purple- hematoxylin to too much pink- eosin (hospital staining, I can’t fix the staining).
- I tried 2 things to improve it, but still, there is a big variance, I changed the color by (a) double click on the ‘need to be eosin’ area and define it as ‘eosin’ (under the tab Image), (b) estimate stain vector> Auto.
Do you have an idea of how to improve it more?
- I’m trying to do pixel classification and each time I add another annotation the computer gets stuck and QuPath is using all the CPU, and then it’s finishing the process and stuck again with the next annotation I add, a similar case to this issue- QuPath ver.5 using up 100% CPU when doing simple annotations on slides).
Briefly, since it’s the ‘whole slide’ case, with different areas (from tumor and stroma to normal structures…) and a big variance, I take 10-13 region (500 um which are ~1/9 500px), which end with training image of ~140 regions in size of 1.4 M, with ~900 annotations.
In the training parameter I have ANN; Resolution-Moderate; check for 2 channels, 3 scales, 5 selected features. BUT, I don’t think it’s related, since as I said before, it’s get stuck with the next annotation without activating the training.
I’m working with ver 0.2.2 and 0.2.3
The computer parameters are- 2*Intel Xeon E5-2690 CPU @ 2.6 GHz, 256GB of memory, Nvidia Quadro P5000, 16GB graphic card.
Any suggestion what should I do?
P.S QuPath is amazing! this program change and help us a lot in the way we are working, a lot of thanks!