So I understand the open-ness issues that make .mrxs files tricky, but I’m wondering if there is some best practice approach to get multi channel (4 in my case) mrxs data into QuPath. If I try to open it directly I’m seeing 3 of the 4 channels. (Ultimately I just need to use the dapi to guide per cell measurements of the other 3 channels)
I’ve tinkered with exporting the relevant (smallish, couple gig total) section of the slide from caseviewer to a tiled tiff and following the instructions here QuPath multiple channel in separate files - how to merge them? to combine the 4 channels. I haven’t quite gotten it to work for all 4, but given just for 2 channels it locked up for 20 min running the script and once have the image in it qpath is unresponsive I have doubts about it. (I was trying with milestone 8)
If I manually combine those same images in fiji first into a 2gig tif everything works fine,tho the import is a little slow but i wonder if there is a smoother path, or indeed any path for bigger ROI?
A bit of a newbie to QuPath so might be something I’m missing but if anyone has an approach that is working for them I’d love to hear about it.