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Port shared VisCy package changes from DynaCell v1.1 - #533

Merged

alxndrkalinin merged 39 commits into

mainfrom

viscy-packages-from-dynacell-v1.1

Nov 3, 2026

Merged

Port shared VisCy package changes from DynaCell v1.1#533
alxndrkalinin merged 39 commits into
mainfrom
viscy-packages-from-dynacell-v1.1

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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- 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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- 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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- refactor(viscy-utils): share the fit-callbacks lookup between CLI injectors
  
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- refactor(viscy-utils): drop MonitorHealthCheck's unused check_finite flag
  
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- 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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- 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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Commits on Oct 27, 2026
- fix(viscy-utils): resolve viscy_utils.callbacks names lazily
  
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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(viscy-utils): take last.ckpt from every monitored checkpoint
  
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Commits on Oct 30, 2026
- fix(viscy-utils): write AnnData zarr without switching pandas string inference off
  
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- fix(dynaclr): drop the session-wide pandas string-inference switch
  
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  1b2e227

Commits

Commits on Oct 26, 2026

Commits on Oct 27, 2026

Commits on Oct 30, 2026