Update DynaCell dataset entry (NeurIPS 2026 E&D submission)#3130
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mattersoflight wants to merge 6 commits into
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Update DynaCell dataset entry (NeurIPS 2026 E&D submission)#3130mattersoflight wants to merge 6 commits into
mattersoflight wants to merge 6 commits into
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…schema fixes - Title now matches the paper: "DynaCell: an Evaluation Framework for Dynamic 3D Virtual Staining of Live Cells" (was "A Dynamic 3D Live-Cell Imaging Benchmark for Virtual Staining and Cell Profiling") - Full 15-author list (Kalinin, Zheng, Theodoro, Ivanov, Hirata-Miyasaki, Lee, Liu, Varra, Chandler, Pradeep, Liu, Leonetti, Arias, Huang, Mehta) - Biohub branding: ManagedBy URL, Contact, AuthorURLs all aligned to https://www.biohub.org/comp-micro (Computational Microscopy Group) - Documentation URL points to the VisCy applications/dynacell tree - iPSC component framed as v1.1 (Allen Institute Terms of Use) - Tags trimmed to entries that exist in tags.yaml (12 valid; image-based profiling replaces cell profiling) - License field collapsed to a clean CC BY 4.0 link; AICS terms covered in Description - Added RegistryEntryAdded / RegistryEntryLastModified per schema - pykwalify schema validation: PASS (validation.valid) Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Hi @mattersoflight checking in to see if your tutorial is ready for review so we can merge this PR. |
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Dataset
Name: DynaCell - an Evaluation Framework for Dynamic 3D Virtual Staining of Live Cells
Bucket:
s3://dynacell(regionus-west-2, public)Size: ~407 GB (379 GiB) across 42 objects; the v1 release ships 24 OZX-packed OME-Zarr stores covering A549 human lung adenocarcinoma cells imaged on the Mantis correlative label-free / light-sheet fluorescence microscope at Biohub. Four organelle markers (H2B, CAAX, SEC61B, TOMM20) × three perturbation conditions (mock, ZIKV, DENV) = 24 stores; 262 FOVs total.
License: CC BY 4.0 for the A549 component. The forthcoming v1.1 hiPSC component (derived from the Allen Institute hiPSC Single-cell Image Dataset, Viana et al., Nature 2023) will be redistributed under the Allen Institute Terms of Use; the description notes this distinction.
Croissant metadata: Published at
s3://dynacell/v1/metadata/croissant.jsonwith Responsible AI fields, per the NeurIPS Datasets & Benchmarks track requirement.Validation
pykwalify -d datasets/dynacell.yaml -s schema.yaml→INFO - validation.validtags.yamlDocumentation,AuthorURL, and project URLs return HTTP 200arn:aws:s3:::dynacell, regionus-west-2)Known follow-ups (not blocking this PR)
DocumentationURL points to a feature branch (modular-viscy-staging); this will move tomainonce the upstream VisCy PR merges.Publications.URLwill update to the OpenReview / arXiv DOI once the paper is publicly available (currently points to the code tree).