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docs(dynacell): point code links at applications/dynacell on main - #538
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alxndrkalinin wants to merge 6 commits into
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alxndrkalinin wants to merge 6 commits into
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The DynaCell application is on main since #534, so the README clone instruction drops --branch dynacell-models, and the README, the two Hugging Face cards and the Space README link to tree/main/applications/dynacell instead of the frozen branch or the repository root. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015kuht3npKtb2o5E6h19xbA
contentUrl still named modular-viscy-staging, a branch the release never shipped from. It now names tree/main/applications/dynacell, the same URL the paper, datasheet and S3 Croissant use. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015kuht3npKtb2o5E6h19xbA
iohub moved from czbiohub-sf to the Biohub organisation. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015kuht3npKtb2o5E6h19xbA
VisCy moved from mehta-lab to Biohub on GitHub. The rest of the repository moves in a separate PR; these five files are the ones this PR already edits. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015kuht3npKtb2o5E6h19xbA
"Reviewer-accessible sample" was review-phase wording; the release and the paper now call it a demo subsample. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015kuht3npKtb2o5E6h19xbA
- dataUseCases: virtual staining is the intended task; representation learning moves to "possible but not validated", the use cases list what the paper validates, and the unsupported "organelle classification benchmarks" and "PCC, SSIM, and FID" claims go. - iPSC nucleus and membrane are the Allen DNA and membrane dye channels (ChannelNumber405 / ChannelNumber638 in the conversion), not H2B and CAAX; only SEC61B and TOMM20 are endogenous tags. - iPSC training split is 500 FOVs for nucleus, membrane and mitochondria and 423 for ER. - No A549 perturbation is held out; training includes ZIKV and DENV. - Phase is reconstructed from brightfield volumes, not multi-angle transmitted light. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015kuht3npKtb2o5E6h19xbA
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Now that #534 put the DynaCell application on
main, the remaining links into the frozendynacell-modelsbranch (and one into the never-releasedmodular-viscy-stagingbranch) move tohttps://github.com/mehta-lab/VisCy/tree/main/applications/dynacell.applications/dynacell/README.md: the clone step no longer passes--branch dynacell-models, and the Code link points at main.cards/checkpoints_README.md,cards/demo_data_README.md) and the Space README: the links point at main. The live cards and Space README are re-uploaded from these files after merge.croissant/builder.py: the code FileObjectcontentUrlchanges frommodular-viscy-stagingto main, matching the paper, datasheet and S3 Croissant.The paper (Overleaf), project website, open-data-registry entry and S3 README were updated the same way on 2026-11-04.
Tests:
pytest applications/dynacell/tests/test_croissant.py→ 17 passed.🤖 Generated with Claude Code
https://claude.ai/code/session_015kuht3npKtb2o5E6h19xbA