Nutil keeps changing assigned colours

[AutomatedOlfactoryBehaviour]

Hello everyone,

I keep having issues with Nutil changing the colours assigned for quantification (both for the objects to be quantified and the custom maps).
This presents on multiple levels:

• the colours shown in the main GUI don't match the actual colours assigned (visible only when clicking on the respective colour)
• the colour used for object quantification changes after the quantification has already started (visible as slow processing speed and notes in the command line defining pixels out of range)

I can reproduce this with Nutil 1.1. as well as 0.8. with parameter files generated from scratch (here it happens sporadically with no real pattern) but every time with any previously generated *.nut parameter file that is loaded.

Is this a known bug because I'm using custom colours? Or maybe an issue with using the waxholm atlas?

The issue isn't just highly annoying but prevents any sort of batch processing making quantification very slow.
I'd appreciate an inputs in this

[sharoncy]

Hi @AutomatedOlfactoryBehaviour. I haven't seen this issue before, but I'd be happy to investigate for you. Please send this info to [email protected], stating it is for Sharon Yates about "Brain Atlases". I'll also need a test dataset, so great if you can attach an example segmentation, corresponding atlas map, your json file from QuickNII or VisuAlign, and your .nut file (press "save as" in Nutil to generate this file).

Here is some additional info which may be useful:

• You say "the colours shown in the main GUI don't match the actual colours assigned". If you are referring to the "object colour" selected in the GUI, then this is not meant to match the colours assigned in the output images. In the GUI, you specify the colour in the segmentation images that you want to quantify, and then Nutil automatically assigns default colours to the objects in the output images depending on the regions they belong to (https://nutil.readthedocs.io/en/latest/QuantifierReports.html). You can change these colours by using your own regions and assigning colours to them (custom regions).
• You say "the colour used for object quantification changes after the quantification has already started". Do you save the settings before starting Nutil (e.g. press "save as" before pressing "start")? I'm not sure if this will help, but you could give it a try.