Hi Image.sc Qupath community,
I’m a graduate student who learned about using qupath for digital pathology from my university’s microscopy core, and I have been investing some time into learning the software during this CoV stay-at-home period.
As a new user, I have done my best to read up on some beginner friendly material for QuPath (including Pete’s youtube page, github documentation, and the very helpful “choose your own adventure” post on this forum).
The issue I am currently running into is that I while I am able to load some TIFF files of whole slide images, for some reason QuPath fails to load specific TIFF files at all. The following error message appears: “Import Images: Failed to load # images”. This occurs even if other images from the same scan/data-set load perfectly fine.
For other images, QuPath ends up not recognizing them as pyrimadal TIFF files and also fails to import them with an “Image null” error.
My question is whether these errors could be a result of the export format or other property of the file (like tile size or total file size).
I am very novice at computer coding languages, so I’m a bit lost as to how to generate scripts to re-format my files into proper open-slide/aperio image formats that QuPath seems to better natively support.
Any help with trouble shooting this error with file loading would be greatly appreciated. Also, if anyone can point to a good primer on using openslide or bioformat API to batch convert files, that would also be very helpful.
I am happy to provide any information that would help tease these issues apart.