Can I start by saying I LOVE QuPath, it’s hands down my favourite image analysis software.
I have two recurring issues reading .CZI files from our Axioscan that I’m hoping someone might be able to help with?
Firstly, the label image always looks black, I gather that’s because it somehow ends up as a 16 bit image? I can export as png and adjust until visible but it’s not practical if you’re working with lots of images and need to quickly check what the slide label is. Is there a workaround? I tried Pete’s QuPath-extract_label script but it isn’t happy (v0.2.3 of QuPath, I can post the script and error if helpful?)
Secondly, CZI files with more than one scene import as separate scenes in the image list. Usually I put multiple tissues from one experiment onto a slide and would prefer QuPath not to split scenes, is there a way to specify the concatenate series option from BioFormats when opening CZIs so scenes stay together?