Threshold and Crashing

I recently started using qupath 0.2.3 and I’m having issues crashing when thresholding to count DAB positive pixels in my image (even on small areas). In the previous version I would make tiles and select all of them before running the positive pixel count command. This would run for a while but wouldn’t crash. Can tiling before running the thresholder on all annotations help prevent the crashing instead of running it on a large annotation?

Can you provide more details and exact information, please?

For example, I’m not sure from your post if you’re using the Positive pixel count or Create thresholder commands, and I don’t know which is the ‘previous’ version. I also don’t know how long it runs before crashing (in a single image, across images?), how much memory you have etc.

Finally, it’s not totally clear to me how you create tiles (or if this is necessary), and whether you delete any annotation used to define where the tiles are created.

All this information would be needed to be able to help further.

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Sorry about that. I was previously using version 0.1.2 and the positive pixel count command. I would create tiles with the Analyze → Tiles & superpixels → Create tiles and not delete the parent annotation. I would subsequently select all of the tiles before running the positive pixel count command on a single image and would see a progress bar.

Currently I’m using version 0.2.3 and the create thresholder command on a single image. I get the rainbow wheel spinning (using a mac) and see that qupath is no longer responding right away after clicking measure in the threshold command window.

I use 8GB of memory with both versions and was planning to increase it for 0.2.3 but the startup page for 0.2.3 states it can’t access the config file to change max memory.

I’m not sure how long you gave it, but it’s possible that it just needs more time.

I’d suggest making the Resolution value in the Create thresholder window low to begin to check it works at all. You can then increase the resolution to try to get a balance between acceptable computation time and detail.

You don’t need to create tiles when using Create thresholder, it should be able to handle larger regions directly (albeit perhaps taking a bit of time to do so, so best apply it to the smallest region that is sufficient rather than the entire image).

You can use View → Show memory monitor to check how memory use increases while it is running, which can help identify if that is the problem or not.

Unfortunately it seems QuPath can’t write this any more on a Mac. You can edit the config file yourself, see https://qupath.readthedocs.io/en/latest/docs/reference/faqs.html#set-max-memory

On a Mac, right-click on QuPath-0.2.3.app and choose Show Package Contents. You should find the file under Contents/app/QuPath-0.2.3.cfg.

Thanks! I’ll try those solutions. One additional question: would using images from an OMERO server make processes run slower compared to images imported from a hard drive?

I would generally say yes. Though if your OMERO server is local on the network and you have a 40Gbit LAN, you might not notice any difference. Image file size/resolution will also affect how noticeable the difference is.

Also might depend on load on the OMERO server, or the load on your hard drive. I have had things run VERY slowly on a local hard drive when… that local hard drive was also shared with other computers/users who could access that drive at the same time.

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