Qupath 24bit images #21
Conversation
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Just to close the loop: I checked with fresh export from QuPath and everything work smoothly. Checked on small FOV as well as whole slide of ~11,000*11,000 pixels, with >70K cells. Many thanks for the support ! |
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I suggest also considering an implementation of Nimbus extension for QuPath, though I guess this will require some support from the QuPath team. The advantage I see is that it will allow to skip the export of the channel images, and to integrate Nimbus results into QuPath workflows. QuPath extensions for Stardist and Cellpose already break the image into overlapping tiles and resolve the results in the overlap regions. Stardist-QuPath extension process the tiles in parallel, Cellpose-QuPath extension does not. The challenge I expect is how to make use of the GPU / parallel processing. |
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Thanks for testing! I'll look into how I can make Nimbus available on Qupath, but I think it's not super straight forward unfortunately. |
Just a small fix to the other PR that handled the 24bit qupath segmentation maps. This one includes support for qupath seg maps that are either saved as channels first or channels last, according to the example data that ofra provided in #18. I'll merge without review, because the change is so small @ngreenwald.