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CryoCore Toolwatch 2026-05-27

This note updates the May 15 toolwatch with cryo-EM and cryo-ET tools, preprints, repositories, and data-source posture checked on May 27, 2026.

It is a triage record, not approval to install, run, upload, download, or redistribute gated software, raw movies, particle stacks, maps, tomograms, model weights, private structures, license files, or unpublished data.

What Changed

Area Candidate Posture Source-backed signal CryoCore use
Raw SPA CryoSPARC v5.0.6 gated Public CryoSPARC site listed v5.0.6 as latest on May 5, 2026. Strong gated raw-processing route if license and runtime access are cleared.
Raw SPA CryoSPARC Tools v5.0.3 planned GitHub lists BSD-3-Clause and latest release v5.0.3 on May 4, 2026. Metadata export and scripting adapter when CryoSPARC access is already cleared.
Raw SPA Topaz 0.3.20 planned PyPI lists topaz-em 0.3.20 on May 11, 2026. Open particle-picking lane for raw SPA runs.
Raw SPA CryoFSL watch MIT repo uses SAM2 Hiera-Large weights for few-shot particle picking. Small picking run from annotated micrographs if checkpoint terms are recorded.
Raw SPA ParSeek watch May 11 bioRxiv preprint reports synthetic-data particle picking; no public code found in this scan. Track as a possible Topaz comparison, not a first run.
Heterogeneity Cas9 heterogeneous reconstruction benchmark watch May 7 and May 11 bioRxiv preprints report experimentally grounded labels and limited method classification accuracy. High-signal benchmark candidate if data access is bounded.
Heterogeneity CryoARC watch May 26 bioRxiv preprint and GPLv3 GitLab repo. Conformational-landscape method; dependency and data footprint must be pinned first.
Heterogeneity CryoHype watch CVPR 2026 project and GPLv3 repo. Compositional heterogeneity research lane, not a default runtime.
Heterogeneity CryoDECO watch GPLv3 repo uses Cryo-IEF priors and CryoSPARC particle inputs. Comparison lane after weight and CryoSPARC gates are cleared.
Heterogeneity CryoWizard gated MIT repo, academic-only README language, CryoSPARC automation. Automation reference only until CryoSPARC, model, and secret gates are explicit.
Heterogeneity DynaMight planned Nature Methods and package metadata describe BSD distribution. Planned RELION-linked deformation and motion lane.
Cryo-ET AreTomoLive planned Nature Methods paper published May 25, 2026. Live tilt-series preprocessing and denoising pattern for bounded public data.
Cryo-ET DenoisET planned MIT repo with pretrained models and AreTomoLive paper. Denoising lane; outputs are derived evidence.
Cryo-ET Easymode watch May 21 bioRxiv preprint, PyPI GPLv3 package, SBGrid package about 4.9 GB. Cellular feature segmentation; model-weight posture needs review.
Cryo-ET copick planned Current docs describe storage-agnostic cryoET project API, CZDP, Napari, ChimeraX, and MCP paths. Default project and annotation glue for bounded cellular cryoET workflows.
Cryo-ET MissAlignment watch May 2 preprint and May 13 v0.1.6 release. ML alignment-refinement comparison after AreTomo3 baseline.
Cryo-ET PP7 cryoET standard watch May 22 bioRxiv preprint proposes an in situ cryoET standard. Track for benchmark data availability.
Map to model ModelAngelo v1.0.17 planned May 18 release includes nucleotide postprocessing alignment fixes. First-pass builder for RNA/DNA/protein map-to-model runs.
Map to model CryoAtom2 v2.1.0 planned March 17 release, MIT, multi-GPU posture. Second builder for protein/RNA/DNA complexes.
Map to model CryoREAD gated Kihara nucleic-acid builder, GPLv3 plus commercial-contact language. RNA-specific builder if use context is cleared.
Map to model CryoNet.Refine watch ICLR 2026 code pushed May 20, MIT. Stretch refinement lane after reproducibility tests.
Map to model PhenixCraft watch May 6 arXiv method pattern, no runnable code found. Track as Phenix plus predicted-model idea, not a runtime.
Map to model StructAgent watch May 18 bioRxiv preprint and Apache-2.0 repo for agent-guided model building and validation. Orchestration reference; workflows should still run concrete cryo-EM tasks.
Validation wwPDB validation reports planned Public XML/PDF reports are available for released PDB entries. Default first validation source before local recompute.
Map enhancement EMReady2 watch Nature Communications paper published May 16, 2026. Derived-map lane only; never replaces original-map validation.
Calibration WebCalEM watch May 26 bioRxiv preprint. Pixel-size calibration signal; hosted upload needs review.
Dataset cryoPANDA watch May 3 preprint reports 37M annotated particles from 252 experiments. Future ML benchmark metadata, not a repo asset.

Promotion Notes

  • Promote DynaMight license posture to open BSD only with exact source and dependency capture in the runtime image.
  • Keep CryoARC on watch until OpenFold or AlphaFold parameters, MSA/database paths, and example data size are recorded.
  • Keep CryoDECO and CryoWizard gated by Cryo-IEF weight terms, CryoSPARC access, and secret-handling posture before any run.
  • Keep Easymode on watch until pretrained model terms, hashes, package sources, and package size are recorded.
  • Keep EMReady2 and DenoisET outputs at derived-evidence level unless original maps, weights, parameters, and independent validation are joined.
  • Keep CTFFIND5 planned/gated until exact Janelia source or binary terms are recorded.
  • Treat CryoSPARC and Phenix as runtime-gated even when adapters or public reports are planned.

Sources Checked