jcupitt
commented
1 day ago Hello @afriebel85,
How many files are you stitching together? Windows has a hard limit of 2000 (I think). You might need to find a linux machine (or use WSL) if you are joining more than that.
You might also be hitting stack size limits. You are doing:
image = black(...)
for tile in many_tiles:
image = image.insert(tile, ...)So you are making a pipeline that's as deep as the number of tiles you are stitching. This will also fail for more than a few thousand tiles. You'd need to assemble in sections, then join with something like composite.
What are you doing with overlaps? You could do a feathered join, it might look nicer.
As your code stands, I think you'll write a float OME TIFF. Do you need all that precision? You'd save a lot of disc and CPU with an 8-bit image.
Other than that your code looks reasonable. I think I'd need to be able to run a copy here to understand what's going on in more detail. You'll need to make something you can send me that lets me reproduce the problem.
afriebel85
For my Akoya multiplex wholeslide sections I performed spectral unmixing with the Akoya InForm software which generated for a 8-channel scan 240 patches with float pixel precision resulting in a total of 166GB for this one scan. I now want to stitch these patches back together, and downcast the pixel precision to ushort. I started with the very nice script from Ajay Zalavadia, used the first 8 pages as they represent the 8 channels at highest magnification (see below) and added the downcasting to ushort (after multiplication with 10) in the interleaved_tile method. I tested the method on a smaller subset of 17 patches, and it took ~20min to complete. I checked the resulting ome.tif in QuPath and everything looked fine. I then tried to stitch the full set, however I got a crash after about 20 minutes:
I observed RAM usage, which shouldn't be a problem, it remains at ~3.5GB. Disk space isn't a problem as well with 1.3 TB available. I tried to diagnose the patches, in case there are faulty ones, but all can be read with tifffile and seem to have the exact same setup like so:
I am currently at a loss at what could cause this problem. What does the error message indicate?