general > Questions regarding using QuickMaskNL for batch processing rat brain samples
Jan 21, 2025  04:01 PM | Janine Reinert
Questions regarding using QuickMaskNL for batch processing rat brain samples

Hello everyone,

I've been using VisuAlign as part of the QUINT workflow to adjust slices registered to the Waxholm Space Atlas (using QuickNII 2.2. with v4 of the Waxholm Atlas).


This has been working but I've come across two issues now
1. for generation of hemibrain maps using QuickMaskNL, the reference coordinates supplied on the Nutil documentation (https://nutil.readthedocs.io/en/latest/Q...) appear to be for a mouse brain or at least not for v4 of the WHS atlas.
I've managed to generate roughly fitting maps through trial and error (coordinate string: 242 32.2 292.8 242 367.9 291.8 242 34.5 48.7) but I'd be grateful if anyone could explain what the coordinates actually signify and how they were determined in the first place so I might be able to replicate this for the WHS atlas

2. I have a large number of brains (> 100) that I've registered and now need to generate the hemibrain maps for. Is there any way to automate QuickMaskNL for this? Manually entering all the info for the location of the json files, etc. is cumbersom work I'd like to avoid if at all possible

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TitleAuthorDate
Questions regarding using QuickMaskNL for batch processing rat brain samples
Janine Reinert Jan 21, 2025
Gergely Csucs Jan 22, 2025
Janine Reinert Jan 28, 2025