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Spotlight v2 segmentation-aware-loss - #535

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alxndrkalinin wants to merge 87 commits into

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dynacell-spotlight-v2-arms

Open

Spotlight v2 segmentation-aware-loss#535
alxndrkalinin wants to merge 87 commits into
mainfrom
dynacell-spotlight-v2-arms

Commits on Oct 26, 2026
- feat(viscy-utils): add the segmentation-aware and background losses
  
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- feat(viscy-utils): build foreground masks with CLAHE, median and Otsu
  
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- feat(viscy-utils): make prediction writes resumable, identified and write-once
  
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- feat(viscy-utils): guard every fit with checkpoint and health callbacks
  
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- fix(viscy-utils): keep SSIM finite under mixed precision; lazy exports
  
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- feat(viscy-data): slab-only and read-once predict, uint8 foreground masks
  
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- feat(viscy-models): per-axis CellDiff patches and mask-conditioning channels
  
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- perf(viscy-models): non-uniform ODE time grids for CellDiff sampling
  
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- feat(viscy-models): add the MorphEm feature extractor
  
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- feat(viscy-models): let the PatchGAN discriminator preserve the Z axis
  
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- feat(viscy-models): UNet3D downsample_z for FNet-2D; reject non-5D input
  
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- fix(viscy-transforms): stop BatchedRandAffined blanking singleton axes
  
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- perf(viscy-transforms): mark the sampled normalizers pointwise
  
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- test(viscy-transforms): make the Gaussian-noise statistics test deterministic
  
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- build: parallel test runs with pytest-xdist
  
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- test: register pytest markers at the root and make them strict
  
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- build: put the dynacell hf_demo on the pytest pythonpath
  
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- test(dynaclr): join annotations on the full fov_name
  
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- docs(cytoland): correct the Spotlight recipe comments
  
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- docs(cytoland): install the VCP tutorials' unpublished deps from GitHub
  
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- docs: cut CLAUDE.md content the code or global memory already states
  
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- ci: run the viscy-utils tests in their own job
  
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  69391a1
- ci(dynacell): run the launcher, engine and prediction-writer suites
  
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- build: re-lock against the ported packages and main's dynacell
  
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- feat(dynacell): DynaCell v1.1 benchmark configs from dynacell-models
  
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- feat(dynacell): DynaCell v1.1 application code from dynacell-models
  
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- build(dynacell): lock the dynacell eval, croissant and preprocess deps
  
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- test: drop the requires_data marker registration
  
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- ci(dynacell): run the release-path, provenance and watchdog suites
  
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- docs: add the runbook for jobs that hang while holding an allocation
  
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- refactor(dynacell): scope the grouped eval walk to registered model dirs
  
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- test(dynacell): drop the Spotlight leaf entries from the config guards
  
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- docs(dynacell): describe the 2D seed1 leaves without the Spotlight generator
  
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- docs(dynacell): drop the Spotlight eval generator from the generator lists
  
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- feat(dynacell): Spotlight v2 arm leaves, fit overlays and eval buckets
  
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- feat(dynacell): Spotlight v2 generators, fg-mask tools and segcons segmenter
  
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- feat(dynacell): register the Spotlight arms in the grouped eval generator
  
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- test(dynacell): guard the Spotlight leaves and arm names again
  
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- docs(dynacell): mark the 2D seed1 leaves as generated again
  
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- docs(dynacell): list the Spotlight eval generator among bucket writers
  
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- fix(viscy-utils): declare torchvision, which evaluation.metrics imports
  
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- ci(dynacell): keep main's batch-launcher test and the writer tests out
  
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  0da2de6
- refactor(viscy-utils): share the fit-callbacks lookup between CLI injectors
  
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  3b8fd66
- refactor(viscy-utils): drop MonitorHealthCheck's unused check_finite flag
  
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  149b5a9
- docs(viscy-utils): stop describing fg masks as built from Otsu thresholds
  
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- build: leave the hf_demo pytest path to the DynaCell PR
  
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- Merge the shared-packages gate fixes into the DynaCell branch
  
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- Merge the DynaCell branch's gate fixes into the Spotlight branch
  
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- fix(viscy-utils): guard a fit that sets no callbacks
  
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- docs(viscy-utils): say what the AMP skip counter actually counts
  
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- Merge the shared-packages Copilot fixes into the DynaCell branch
  
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Commits on Oct 27, 2026
- Merge the shared-packages Copilot fixes into the Spotlight branch
  
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- fix(viscy-utils): resolve viscy_utils.callbacks names lazily
  
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- Merge the lazy viscy_utils.callbacks exports into the DynaCell branch
  
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- Merge the lazy viscy_utils.callbacks exports into the Spotlight branch
  
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- docs(cytoland): install viscy-data from GitHub in the VCP tutorials
  
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- fix(viscy-utils): return an empty CLAHE result when the clip range is zero
  
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- fix(viscy-utils): keep a step-cadence leaf's last.ckpt on its step trigger
  
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- fix(dynacell): skip only PAPER_KEY-known arms in the grouped eval walk
  
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- docs(dynacell): say the instance-AP audit does not share the walk's arm skip
  
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- test(dynacell): carry the seg-consistency engine and focus-parity tests
  
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- Merge the shared-packages review fixes into the DynaCell branch
  
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- Merge the DynaCell branch's review fixes into the Spotlight branch
  
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  b663d7d
- fix(viscy-utils): take last.ckpt from every monitored checkpoint
  
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  0b1cb97
- refactor(dynacell): one model-dir acceptance rule for parse and walk filter
  
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- fix(dynacell): share the foreign-model skip between the walk and the audit
  
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- fix(dynacell): keep raising on campaign models the generator cannot parse
  
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- docs(dynacell): stop pointing at the Spotlight leaf generator from this branch
  
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- Merge the shared-packages save_last fix into the DynaCell branch
  
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  a04b3eb
- Merge the DynaCell branch's walk/audit fixes into the Spotlight branch
  
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  430f521
- fix(dynacell): parse the warmup-matched pix2pix2d stores in the grouped walk
  
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  97c30a1
- fix(dynacell): skip the listed checkpoint re-predicts in the grouped walk
  
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- fix(dynacell): name the P1 segcons replicate dirs as foreign in the walk
  
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  3fe7293
- fix(dynacell): list checkpoint re-predicts per organelle
  
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  a6ad266
- refactor(dynacell): one skip rule for the grouped walk and the audit
  
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- test(dynacell): guard the grouped registries against the walk crash class
  
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  3daaac5
- docs(dynacell): reflow the checkpoint re-predict comment
  
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  91b03e9
- Merge the grouped-walk live-tree fix into the Spotlight branch
  
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  3b07b0d
- fix(dynacell): keep the wmatch refit out of canonical and instance-AP leaves
  
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  8ebca43
- Merge the sibling-only wmatch exclusion into the Spotlight branch
  
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  09a3285
Commits on Oct 29, 2026
- docs(dynacell): retitle the paper and describe DynaCell as the broader framework
  
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- docs(dynacell): call the contribution the DynaCell evaluation suite
  
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Commits on Nov 2, 2026
- docs(dynacell): retitle to The DynaCell Evaluation Suite
  
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Commits on Nov 3, 2026
- Merge main (#533 squash) into dynacell-v1.1-application
  
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- chore(dynacell): delete finished one-shot tools
  
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Commits on Nov 4, 2026
- Merge #534's final commits into the Spotlight branch
  
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  904caba
- Merge main (#534 squash) into the Spotlight branch
  
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  a69fe49

Commits

Commits on Oct 26, 2026

Commits on Oct 27, 2026

Commits on Oct 29, 2026

Commits on Nov 2, 2026

Commits on Nov 3, 2026

Commits on Nov 4, 2026