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Add deepcell types 2026-06-23 weights to registry#8

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rossbar wants to merge 4 commits into
vanvalenlab:mainfrom
rossbar:add-dct-2026-06-23
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Add deepcell types 2026-06-23 weights to registry#8
rossbar wants to merge 4 commits into
vanvalenlab:mainfrom
rossbar:add-dct-2026-06-23

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@rossbar

@rossbar rossbar commented Jun 30, 2026

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Okay here's the replacement for #5 !

@xuefei-wang can you confirm that the hash for this set of weights is the right one (i.e. the listed hash matches the md5sum of the weights that should be uploaded)

@rossbar rossbar added the enhancement New feature or request label Jun 30, 2026
…25-06-09

Stacked on vanvalenlab#8. Three changes to the deepcell-types asset registry:

1. Model: serve the vocab-bundled 2026 checkpoints and default to 2026-06-15.
   - 2026-06-15 (default) -> deepcell-types_2026-06-15_resmlp.pt, b819a7e0
   - 2026-06-23           -> deepcell-types_2026-06-23_resmlp_ptft.pt, 402e94c1
   These bundle ct2idx/canonical_channels so deepcell-types predict()'s
   vocab guard accepts them (the un-bundled 067f558b in vanvalenlab#8 fails it). This
   matches deepcell-types _model_registry (PR xuefei-wang/deepcell-types#70).

2. Baselines: add a deepcell-types-baselines section + download helper for
   the comparison baselines (cellsighter, maps [+ _stats], xgboost [+ .remap]),
   hashes matching the 2026-06-30 retrains in deepcell-types #74. Each baseline
   maps to a list of assets to carry companion files. Nimbus is omitted (its
   weights are distributed upstream via nimbus-inference, not re-hosted).

3. Drop the legacy 2025-06-09 CLIP entries: they are incompatible with the
   current deepcell-types code and have no deepcell-types consumers (both the
   old and new packages download via their own _auth, not deepcell_auth).

Assets must be uploaded to users.deepcell.org before merge.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_016oVttaRJScBzjoJDB8ZkpA
… conflicts

main advanced (torch-mesmer weights, vanvalenlab#7) after this branch was cut. Resolved
by keeping all of main's additions (torch-mesmer manifest section +
download_torch_mesmer_model + its __all__ entry) alongside the deepcell-types
changes on this branch:
- deepcell-types serves the bundled 2026 checkpoints, default 2026-06-15
- new deepcell-types-baselines section + download_deepcell_types_baseline
- legacy 2025-06-09 entries dropped

Also fixes a latent export bug: download_deepcell_types_baseline is now added
to __all__ (this branch predated main introducing __all__, so the function
would not have been re-exported via `from ._download import *`).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_016oVttaRJScBzjoJDB8ZkpA
@xuefei-wang

xuefei-wang commented Jul 12, 2026

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Heads-up @rossbar — I pushed two commits directly onto this PR's branch (add-dct-2026-06-23), to keep this in sync with the deepcell-types package release. Summary of what changed and why:

1. Serve the vocab-bundled 2026 checkpoints; default to 2026-06-15

  • 2026-06-15deepcell-types_2026-06-15_resmlp.pt (b819a7e0…) — paper headline
  • 2026-06-23deepcell-types_2026-06-23_resmlp_ptft.pt (402e94c1…) — SSL/pretrain-finetune arm

The original deepcell-types_2026-06-23.pt (067f558b…) is the un-bundled file: it lacks the bundled ct2idx/canonical_channels, so the deepcell-types package's predict() vocab guard rejects it. The bundled repackages carry that vocab (weights byte-identical, verified) and pass the guard. These now match the deepcell-types package registry (xuefei-wang/deepcell-types#70).

2. Add comparison baselines (deepcell-types-baselines + download_deepcell_types_baseline()) for cellsighter / maps(+_stats.npz) / xgboost(+.remap.json), hashes matching the 2026-06-30 retrains (xuefei-wang/deepcell-types#74). Each baseline maps to a list of assets so companion files travel together. Nimbus is intentionally omitted — its weights are distributed upstream (angelolab/Nimbus-Inference) and shouldn't be re-hosted here.

3. Dropped the legacy 2025-06-09 (×2) entries — legacy CLIP checkpoints, incompatible with current deepcell-types code, and with no deepcell-types consumers (both the old and new packages fetch via their own _auth, not deepcell_auth). If you'd rather keep them archived in the manifest, easy to restore.

Merge/conflict: I also merged current main in to resolve the conflict from the torch-mesmer addition (#7) — kept all of your torch-mesmer changes and added download_deepcell_types_baseline to __all__ (this branch predated main introducing __all__, so the new function wouldn't otherwise have been re-exported).

⚠️ Before merge: the new md5s require uploading the exact files to users.deepcell.org at the manifest keys — bundled models b819a7e0/402e94c1, and baselines cellsighter c5a105fb, maps 1ad5e30c + stats 1f462d0c, xgboost 9e51cf1a + remap fba1b0e7.

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