Nutil crashes when segmenting images with large masks

[ingvildeb]

I'm running a set of segmentation images containing "masks" (big objects covering damaged parts of my sections) and Nutil keeps crashing. Sometimes it runs through, so I know everything is working fine when it runs, but it crashes ~2 out of 3 times.

Example dataset: Y:\Dopamine_receptors\Analysis\QUINT_analysis\D1R\P35\D1R_P35_M_E54\07_nutil\02_output_masks, .nut file in the parent folder.

The color of the masks (object color) is black, and so is the background of the image. I think the problem might be that it's assigning all black pixels of the background are assigned to "Clear label" and that this is somehow overloading it and making it crash. I already turned of the coordinate extraction as it took ~8 hours to run if I included them.

I have also attached an example image below

[sharoncy]

A reminder to look into this @leuat

[leuat]

Hi there! I'm unable to find your files @ingvildeb since I don't know where Y maps to - the files are not on the \win-evs server, it seems. Perhaps they're in your private space? If so, could you send me 1 slice + the .nut file?

also, are these example files the actual mask files, or .. segmentations?

[ingvildeb]

Sorry about that, the Y maps to the imb-neuroinf (\lagringshotell), you should have access to them there segmentation files with masks overlayed and the nut file in question:

Y:\Dopamine_receptors\Analysis\QUINT_analysis\D1R\P35\D1R_P35_M_E54\05_masked_segmentations

(but this is not a specific problem with this nut file, rather with the process of running nutil on the masks)

[Majpuc]

Do you still have this issue? We recommend to run Nutil locally and also have all files stored locally.

[ingvildeb]

This was not really solved but I kept running until I had all the data.