accommodate new templates from SPIMtemplates workflow#112
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uses spim_templates dict inside an exisitng template, with these ones as additional "channels" to the ABAv3 template, since they are generated from data that is already nonlinearly registered to ABAv3.. However the template does drift a bit and is also susceptible to initial registration error, so would be good to do this iteratively in FireANTS, e.g. correct the template to push towards the ABAv3..
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Pull request overview
This PR extends SPIMquant’s Snakemake workflow to optionally use stain-specific “SPIM templates” (generated from SPIMtemplates and already registered to ABAv3) as the registration reference, instead of always using the anatomical template.
Changes:
- Add
spim_templatesentries to the ABAv3 template config and select a registration stain from those when available. - Add a new import rule to fetch/copy the selected SPIM template channel into the local
tpl-{template}space. - Update template-path helpers so registration can reference either
anat.nii.gzor the selected stain template.
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 5 comments.
| File | Description |
|---|---|
spimquant/workflow/rules/import.smk |
Adds import_template_spim rule to import stain-specific SPIM template channels. |
spimquant/workflow/rules/common.smk |
Makes template path selection depend on whether a SPIM template is being used. |
spimquant/workflow/Snakefile |
Adds logic to detect and prefer SPIM templates when available. |
spimquant/config/snakebids.yml |
Adds ABAv3 spim_templates URLs for YoPro and Iba1. |
Contributor
…tching stains Co-authored-by: akhanf <11492701+akhanf@users.noreply.github.com>
Fix stain-for-reg fallback when spim_templates exists but has no matching stains
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uses spim_templates dict inside an existing template, with these ones as additional "channels" to the ABAv3 template, since they are generated from data that is already nonlinearly registered to ABAv3..
Note: still working on optimal template estimation in SPIMtemplates, since the template does drift a bit and is also susceptible to initial registration error, so would be good to do this iteratively in FireANTS, e.g. correct the template to push towards the ABAv3.. Also this
doesn't have shape_avg enabled, andis greedy not SyN..