Developmental atlases implemented in QuickNII / VisuAlign

Neural-Systems-at-UIO / VisuAlign

Online manual: https://visualign.readthedocs.io

MIT License

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Developmental atlases implemented in QuickNII / VisuAlign #29

Open ingvildeb opened 5 months ago

ingvildeb commented 5 months ago

We are currently in the process of sharing developmental atlas templates and delineations on KG and would like to have these implemented in QuickNII and VisuAlign.

Nifti files are found here: Z:\HBP_Atlasing\Developmental_atlases\DeMBA_Developmental mouse brain atlas\DeMBA-v1\01_working-environment\01_Data\Volumes_for_tools

There are two segmentation volumes for each age (2017 and 2022 versions of Allen). I think it would be good to have both versions available (some people might want to use the 2017 version for comparability with existing data), but if we only do one it should be the 2022 version.

They should work with the same label file as used for adults.

Tevemadar commented 5 months ago

Test versions are available in NESYS_Tools\DeMBA-v1

QuickNII

separate batch files start P7...P28 (DeMBA_P7.bat, etc.)
provide template, segmentations from 2017 and 2022, both coupled with "rainbow" variants (5 views in total)
tested to the extent that each atlas seems to load correctly
if QuickNII.exe is started directly, it loads the P28 atlas at the moment (this behaviour can be changed).

VisuAlign

contains the 2022 segmentations only
not tested yet.

Tevemadar commented 4 months ago

I don't expect complications, but someone needs to actually test them. @ingvildeb @sharoncy @Majpuc

ingvildeb commented 4 months ago

Thank you so much for implementing @Tevemadar, I have done a quick check already and everything loads and looks good. But I will continue with more thorough use in the coming weeks as I will register a larger number of series!

sharoncy commented 4 months ago

Great that you've been able to do some testing @ingvildeb. In order to officially release the new versions of QuickNII/VisuAlign , we need some text describing the atlases, relevant citations, etc. The text will be inserted in the QuickNII GUI in the "About" part (accessed via the ?). It will also be used on NITRC. Would you be able to collect this info please? We can discuss further at our next SW dev meeting.

ingvildeb commented 4 months ago

Sounds good! After some more testing of the templates in registrations, we have realized that they have a slight tilt around the midline, which might be confusing for users in QuickNII (you'd have to set an angle to get a straight coronal cut). We are currently working to adjust this tilt and will get back to you with updated templates ASAP. Very sorry for the inconvenience!

In the meantime, I'll prepare the texts you ask about and will aim to have them ready for the Monday meeting.