Large CZI image partially viewed at low resolution

Data Management
#1

Dear all,

I have been trying to load a few relatively large (12-15 GB) IF images in .czi format into the QuPath (v0.2.0-m6). When viewed at low resolution only part of the image is shown. When I zoom in the other parts that appeared black initially can be visualized. I have been trying to export it as a TIFF or other files (Pyramids) and have been unsuccessful. Also, I doubt that this is a memory issue (with 128GB) and persists across platforms (Mac and Linux).

I suspect that the problem is with the file itself. I would highly appreciate if anyone can instruct me of any workaround.

Here what I see at low zoom:

Screenshot%20from%202019-11-20%2023-01-54
Screenshot%20from%202019-11-20%2023-01-54956×513 299 KB

At higher zoom:

Screenshot%20from%202019-11-20%2023-02-18
Screenshot%20from%202019-11-20%2023-02-18938×655 926 KB

Many thanks,

Arash

#2

I am guessing the server is BioFormats, so adding the BioFormats tab, and mentioning @sebi06 in case he has any thoughts here.

There have been other examples of files where black areas showed up at certain zooms, but I think those problems were traced back to file corruption. I think they were on the forum though, so it might be worth looking.

Unrelated, but I think I can see your tiling from left to right, which doesn’t bode well for any kind of quantitative image analysis.

image
image939×658 932 KB