Add SWC female template mode support to WHS SD rat atlas script #716
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- SWC Female Template mode (True): Uses SWC female rat template as reference, from GIN repository - Waxholm/NITRC mode (False): Original workflow using zip archives from NITRC - Refactor download functions, add `download_swc_template_file()` - Use `construct_meshes_from_annotation()` - Add reference stack normalization for SWC template mode (uint16 scaling) - Bump version to 3
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| ) | ||
| STRUCTURES_ILF_HASH = None | ||
| else: | ||
| ORIENTATION = "lpi" |
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Users are allowed to switch between modes using the swc_female_template flag
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Hi @viktorpm, I think it would be better for the code for this new atlas to be in it's own file. Although there's a lot of shared code with the "original" Waxholm, I think it would be easier to understand if they were seperated. |
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Description
What is this PR
Why is this PR needed?
To support generating the WHS SD rat atlas using the SWC female rat template as the reference image, in addition to the existing Waxholm/NITRC workflow.
What does this PR do?
swc_female_templateflag:construct_meshes_from_annotation()How has this PR been tested?
It was run interactively on an HPC node
Is this a breaking change?
no
Does this PR require an update to the documentation?
Likely
Checklist: