Fix stain-for-reg fallback when spim_templates exists but has no matching stains#115
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Copilot wants to merge 2 commits intospim-templatesfrom
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Fix stain-for-reg fallback when spim_templates exists but has no matching stains#115Copilot wants to merge 2 commits intospim-templatesfrom
Copilot wants to merge 2 commits intospim-templatesfrom
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…tching stains Co-authored-by: akhanf <11492701+akhanf@users.noreply.github.com>
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[WIP] WIP Address feedback on accommodating new templates
Fix stain-for-reg fallback when spim_templates exists but has no matching stains
Mar 4, 2026
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When
spim_templateswas defined in the template config but none of its keys matched the available dataset stains,stain_for_regremainedNoneand the workflow raised aValueError— even though a valid registration stain existed inconfig["stains_for_reg"]. The fallback toconfig["stains_for_reg"]was unreachable in this case because it was in anelsebranch tied tospim_templates is None.Change
else:withif not use_spim_template:so theconfig["stains_for_reg"]fallback runs whenever SPIM-template matching fails, regardless of whetherspim_templateswas absent or simply had no overlap with the available stains.✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.