Image import failing for multiple images in project

Hi all!

I’ve been using QuPath now for a little over 18 months but new to the forum, hoping someone can help me!

I’ve been working with multiplex immunofluorescence images (scanned using the Vectra Polaris; unmixed using InForm; and stitched using a script in QuPath 0.2.2). The final result is some very large tif images to be imported into QuPath in batches of 20. Bearing in mind, these have completed the prior steps in the same batches at the same time.

The fun has started when approximately half the batch will import as normal into a project but an error message quickly appears and disappears for the rest. To the point I actually don’t know what the error message is, it disappears so quickly.

I’ve tried restitching the images, creating a new project and adding them one at a time and the failed images still won’t import.

I’ve also made sure I’ve enough RAM/ space on drives for saving, as I was working under the assumption that this was something to do with the size of the images as the script works on a batch basis and some of the images where completed successfully.

Has anyone encountered anything like this before?

Thanks in advance!
A

Hi @AoifeMc ,

Welcome to the forum :slight_smile:
You can check out the log with Ctrl + Shift + L then copy/paste it here, so we can have an idea of what kind of error messages appears.

Does it always happen with the same subset of images? Do they have something different from the other ones in the batch? I haven’t fully followed the batch thing, when you say batch do you mean a batch of unstitched images that are now one ‘stitched’ image? Or are they still a batch of stitched images that you try importing at the same time?

Hi @melvingelbard!

I’ll try my best to answer your questions:

Does it always happen with the same subset of images? Yes, it is always the same images.

Do they have something different from the other ones in the batch? They are all different tissue samples but they have undergone the exact same processing at every point.

I haven’t fully followed the batch thing, when you say batch do you mean a batch of unstitched images that are now one ‘stitched’ image? Sorry, I explained that badly. I started with 20 slides at staining and these continued through the same process together until I had 20 “stitched” images to be imported into 1 QuPath project.

Or are they still a batch of stitched images that you try importing at the same time? Yes, that’s exactly it!

@melvingelbard The error log is below:

INFO: Initializing type adapters
INFO: Bio-Formats version 6.5.1
INFO: Loaded extension Bio-Formats server options (Bio-Formats 6.5.1) (13 ms)
INFO: Loaded extension Experimental commands (1 ms)
INFO: Loaded extension Experimental commands (18 ms)
INFO: Loaded extension ImageJ extension (51 ms)
INFO: Loaded extension JPen extension (13 ms)
INFO: Loaded extension Rich script editor extension (176 ms)
INFO: Loaded extension SVG export commands (1 ms)
INFO: OpenSlide version 3.4.1
INFO: Performing update check…
INFO: Starting QuPath with parameters:
INFO: Project set to Project: trial-project
WARN: Unable to obtain full image format info for file:/P:/PMC/PMC%20PROJECTS/PMC%202024%20Pituitary%20Study/Pituitary%20cohort%20samples/MP1/Stitched%20unmixed%20images/Batch%201%2018%20MAY%202021/21-2024-0146%20MP1.ome.tif (class java.util.NoSuchElementException)
WARN: Temp memoization directory created at C:\Users\3054957\AppData\Local\Temp\qupath-memo-11897830999262844585
WARN: If you want to avoid this warning, either disable Bio-Formats memoization in the preferences or specify a directory to use
WARN: Exception adding Image null
ERROR: Import images: Failed to load one image.

Perhaps @Colt_Egelston will have had more hands on experience than I with this pipeline, but in some cases the stitching was at fault and needed to be redone, but alternatively, in some cases, there were visible artifacts in some images due to problems with tiles prior to stitching, probably at the InForm export phase. Your errors seem to be significantly more frequent than his, though, so it is possible this has something to do with computer hardware or network stability during the write/copy process.

The errors were, I think, more common with larger images, but if you consider that a larger image is more tiles, there is more chance for something to go wrong if there is a small percentage chance per tile of something going wrong.

Do the images work if you load them individually?
How large are the stitched images?
Have you tried loading the images from a local drive and not a network drive?

My experience has been that pulling large stitched images from network drives causes a little havoc.