Image null Qupath

Hey all,
I’m having some difficulty adding images to a Qupath project
(Qupath 0.2.0-m3)
I have a project open, go ‘add images’, ‘choose files’, select the relevant files, ‘import’
When the files import sometimes Qupath does not properly load the details, resulting in an image labeled as ‘image null’ instead of ‘MouseID10_section2’ in the image list
Is there any way to prevent this from occurring as I have 1000+ images to load like this and it is a frequent issue
(I am getting this issue even if I am only loading 8 images at a time in a fresh project)

Do you have any further details on the types of images or could provide a sample image? Is the problem consistent for a single image (every time you import that single image, it fails)?

QuPath relies on BioFormats or other readers to interpret the files, so frequently the problems that arise are due to the image type not being supported by one of the viewers.

There is also the possibility that it is related to this? I vaguely remembered it, but am not sure if it is the same as the issue you are seeing. This problem was seen in M3.

The Images are:
.tif files
size ranging from 662,000kb to 62,000kb
Multi channel (red, green, blue)

The ‘image null’ issue is inconsistent, one time it will be ID 4-6 another time it will be ID 9-11
Another thing I’ve noticed is that if I try and load many, lets say approx 20 images the image identification step will fail to identify all saying ‘loading 1/16’ sometimes and other times it will say ‘loading 1/20’

Also from what I can tell this is not the same issue as the other one you posted, I am not getting any error message or notification that loading has failed or otherwise been altered, and the images, if you click on the ‘image null’ in the image opens, but there is no ID attached, or any preview
They also (sometimes) load into the Image list out of order (ID 1,3,7,2,5,6)Capture

1 Like

My intuition is that this is some sort of memory-related error, possibly memory leak
My justification is that if I start a project, start opening images one by one until ‘image null’ starts appearing, then close Qupath and open Qupath again, then continue that project, I can skirt around the issue
Now I’ll have to do this over 1000 times, subdividing all the images into 40 projects (if it is memory leak that will hopefully help), but at least it works!

@petebankhead will likely have better ideas, but my default would be to at least try loading with only a single thread allowed. Or try M4.

This sounds to me exactly like the problem @Research_Associate linked to above - Image null Qupath - in which case I’ve described the cause on GitHub and fixed it in v0.2.0-m4.