Update `app-cytoland` with latest changes in `app-dynaclr` by alxndrkalinin · Pull Request #381 · Biohub/VisCy

alxndrkalinin · 2026-03-17T00:08:05Z

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…istry - 19 test cases covering config creation, defaults, channel maps, validation errors, YAML loading, tau-range conversion, and lookups - All tests fail with ModuleNotFoundError (module not yet implemented) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- ExperimentConfig dataclass with all fields and defaults - ExperimentRegistry with fail-fast validation at __post_init__: empty check, duplicate names, source_channel membership, channel count consistency, interval_minutes positivity, condition_wells non-empty, data_path existence, zarr channel match - channel_maps: per-experiment source position -> zarr index mapping - from_yaml classmethod for YAML config loading - tau_range_frames for hours-to-frames conversion with warning - get_experiment lookup by name with KeyError - All 19 tests pass Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

… member - Fix ruff I001 (import sorting) and F401 (unused import) in test file - Exclude applications/dynacrl (typo) from uv workspace to unblock builds Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- SUMMARY.md with TDD execution results, self-check passed - STATE.md updated with position, decisions, session continuity Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Add iohub>=0.3a2 and pyyaml as explicit dependencies in dynaclr pyproject.toml - Re-export ExperimentConfig and ExperimentRegistry from dynaclr __init__.py - Both classes now importable via `from dynaclr import ExperimentConfig, ExperimentRegistry` Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Demonstrate positional channel alignment across 2 experiments - SEC61 (30min interval, ER) and TOMM20 (15min interval, mito) - Show condition_wells with infected/uninfected/mock conditions - Include comments explaining channel alignment and tau_range conversion Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- SUMMARY.md with execution results and self-check - STATE.md updated: Phase 20 complete, 20/25 phases (80%) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Phase 20 Experiment Configuration verified (11/11 must-haves). ExperimentConfig + ExperimentRegistry with TDD, package wiring, example YAML. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- 17 test cases covering CELL-01 (unified tracks), CELL-02 (lineage), CELL-03 (border clamping) - All fail with ModuleNotFoundError (dynaclr.index not yet implemented) - Test fixtures create mini OME-Zarr stores with tracking CSVs Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

…lamping - Unified tracks DataFrame from all experiments with enriched columns - Lineage reconstruction linking daughters to root ancestor via parent_track_id - Border clamping: retains border cells with shifted patch origins instead of exclusion - All 23 tests pass Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Remove unused variable (F841) in test_global_track_id_unique_across_experiments - Use .to_numpy() instead of .values (PD011) in test_exclude_fovs_filter - Export MultiExperimentIndex from dynaclr __init__.py Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- 21-01-SUMMARY.md with full execution documentation - STATE.md updated for 21-01 completion, decisions, session continuity Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

…mary - 8 tests for valid_anchors: basic validity, subset check, end-of-track exclusion, lineage continuity, different tau ranges, empty tracks, gap handling, self-exclusion - 9 tests for properties/summary: experiment_groups, condition_groups, summary() - All 17 new tests fail with TypeError (tau_range_hours not yet accepted) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

…oups, summary - Add tau_range_hours parameter to MultiExperimentIndex.__init__ - _compute_valid_anchors: per-experiment tau conversion, lineage-based lookup - experiment_groups/condition_groups properties returning index arrays - summary() with experiment counts, observation counts, per-experiment breakdowns - All 40 tests pass (23 existing + 17 new) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- SUMMARY.md with self-check passed - STATE.md updated: Phase 21 complete, ready for Phase 22 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Experiment-aware batching: single-experiment restriction, all experiments appear - Condition balancing: 2-condition and 3-condition proportional tests - Leaky mixing: zero leak, 20% leak injection, no-effect when not experiment-aware - Small group fallback: no crash, warning emission - Determinism: same seed/epoch reproduces, set_epoch changes sequence - Sampler protocol: yields list[int], correct __len__ - DDP partitioning: disjoint interleaved batches across ranks Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

…ndition-balanced, leaky mixing - FlexibleBatchSampler(Sampler[list[int]]) with cascade batch construction - experiment_aware=True restricts each batch to a single experiment - condition_balanced=True balances condition representation per batch - leaky > 0.0 injects cross-experiment samples into restricted batches - Deterministic via np.random.default_rng(seed + epoch) - DDP support via interleaved batch partitioning across ranks - Small group fallback to replacement sampling with logged warning - Pre-computed group indices at __init__ for O(1) lookup - Fix lint issues in test file (import sorting, .values -> .to_numpy(), nunique -> len(unique)) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Add FlexibleBatchSampler to viscy_data.__init__.py public API - Place import in alphabetically correct position for ruff isort compliance - Add to __all__ exports under Utilities section Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Create 22-01-SUMMARY.md with TDD execution results - Update STATE.md: plan 01/02 complete, decisions, session continuity Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

… validation - 6 temporal enrichment tests (focal concentration, global_fraction edge cases, validation) - 5 DDP disjoint coverage tests (interleaving, coverage, epoch reproducibility) - 3 validation guard tests (missing experiment/condition/hpi columns) - 2 package import tests (import, __all__) - All 9 new feature tests fail as expected (RED) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

…verage - Add temporal_enrichment, temporal_window_hours, temporal_global_fraction params - Implement _enrich_temporal: focal/global sampling from experiment pool - Add column validation guards for experiment/condition/hpi columns - Conditional precomputation: only groupby columns when feature enabled - Fix stale smoke test __all__ count (45 -> 46) from Plan 01 - All 35 sampler tests pass, 107 total viscy-data tests pass Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- 22-02-SUMMARY.md with all metrics, decisions, deviations - STATE.md advanced to Phase 23, progress 22/25 (88%) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Phase 22 verified: FlexibleBatchSampler with all 5 SAMP requirements. 5/5 must-haves passed. 35 tests, 107 full suite pass. No regressions. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- 12 test cases covering subclass, beta=0 equivalence, hard negatives, gradients, temperature effect, edge cases, defaults, and CUDA - All fail with ModuleNotFoundError (dynaclr.loss not yet created) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Adds test_multi_experiment_fast_dev_run_with_parquet which verifies the full Lightning training loop works when loading from a pre-built cell index parquet via MultiExperimentDataModule. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

…aclr

…uracy and binary_f1_score

- Add `collection.py` for ML training collection definitions - Rename `hours_post_infection` → `hours_post_perturbation` in `_typing.py` - Update `cell_index.py` to use `collection_path` and renamed field - Add corresponding tests for new modules and updated cell index

… sampler

…calls deg2rad internally) - Fix docstrings to reflect ZYX input order, facet naming, and unit conventions - Remove stale timepoint_statistics lookup in _normalize.py

…data dep

…/norm maps - MultiExperimentIndex with parallel FOV loading and lineage-aware anchors - MultiExperimentDataModule with stratify_by, num_workers_index, FOV-level split - Dataset updates for new pipeline; remove ExperimentConfig from __init__ - Consolidate shared test helpers and constants into conftest.py

- Update build-cell-index, train-multi-experiment, troubleshooting recipes - Add sampling-strategies.md documenting FlexibleBatchSampler axes - Update README table - Add CLAUDE.md with data pipeline design principles

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alxndrkalinin · 2026-03-17T00:40:20Z

Code review

conv_block_3d.py and conv_block_2d.py model() method indexes self.norm (a string) instead of self.norm_list (an nn.ModuleList). self.norm is set to the string parameter (e.g. "batch"). if self.norm[i]: indexes into the string, returning individual characters which are always truthy, and crashes with IndexError when i >= len(string). The correct code is if self.norm_list[i]:, which is already used correctly in forward().

https://github.com/mehta-lab/VisCy/blob/0a3d2e688485c811b43d98fc20f4ba86a21799b1/packages/viscy-models/src/viscy_models/components/conv_block_3d.py#L321-L323

https://github.com/mehta-lab/VisCy/blob/0a3d2e688485c811b43d98fc20f4ba86a21799b1/packages/viscy-models/src/viscy_models/components/conv_block_2d.py#L365-L367

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edyoshikun and others added 30 commits February 21, 2026 20:40

docs(20): capture phase context

b6d85a0

docs(20): create phase plan for experiment configuration

3a54c8c

refactor(20-01): clean up imports and exclude stale dynacrl workspace…

4f2d772

… member - Fix ruff I001 (import sorting) and F401 (unused import) in test file - Exclude applications/dynacrl (typo) from uv workspace to unblock builds Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

docs(20-01): complete ExperimentConfig/ExperimentRegistry plan

afff429

- SUMMARY.md with TDD execution results, self-check passed - STATE.md updated with position, decisions, session continuity Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

docs(20-02): complete package wiring and example config plan

b7e7629

- SUMMARY.md with execution results and self-check - STATE.md updated: Phase 20 complete, 20/25 phases (80%) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

docs(phase-20): complete phase execution

2471288

Phase 20 Experiment Configuration verified (11/11 must-haves). ExperimentConfig + ExperimentRegistry with TDD, package wiring, example YAML. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

docs(21): create phase plan for Cell Index & Lineage

293cb44

docs(21-01): complete MultiExperimentIndex plan summary and state update

9c25895

- 21-01-SUMMARY.md with full execution documentation - STATE.md updated for 21-01 completion, decisions, session continuity Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

docs(21-02): complete valid anchors plan

ad55374

- SUMMARY.md with self-check passed - STATE.md updated: Phase 21 complete, ready for Phase 22 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

docs(22): research batch sampling phase domain

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docs(22): create phase plan for batch sampling

e85b3bb

docs(22-01): complete FlexibleBatchSampler core plan

45ec057

- Create 22-01-SUMMARY.md with TDD execution results - Update STATE.md: plan 01/02 complete, decisions, session continuity Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

docs(22-02): complete temporal enrichment + DDP plan

fc2b67a

- 22-02-SUMMARY.md with all metrics, decisions, deviations - STATE.md advanced to Phase 23, progress 22/25 (88%) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

docs(phase-22): complete batch sampling phase execution

76c35e8

Phase 22 verified: FlexibleBatchSampler with all 5 SAMP requirements. 5/5 must-haves passed. 35 tests, 107 full suite pass. No regressions. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

docs(23): create phase plan for Loss & Augmentation

a22b238

edyoshikun and others added 22 commits March 7, 2026 16:21

recipes

4f1e282

demo slurm code

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obs should use fov_name and track_id and id as UUID

e0950cb

add marker, task and channels to compute the crossval.

d87e34f

fix prediction remodeling analysis

f8e2b69

Merge branch 'app-dynaclr' of github.com:mehta-lab/VisCy into app-dyn…

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…aclr

Raw logits are now passed through sigmoid before computing binary_acc…

7eb594f

…uracy and binary_f1_score

fix the dataset statistics

7abdf96

add contributing and uv to claude.md

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pydantic >2.0

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uvx precommit

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refactor(viscy-data): replace condition_balanced with stratify_by in…

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… sampler

add norm_meta batching helpers and triplet None guard

eb60763

- Apply _radians_to_degrees to shear_range (Kornia expects degrees, …

31dc6c1

…calls deg2rad internally) - Fix docstrings to reflect ZYX input order, facet naming, and unit conventions - Remove stale timepoint_statistics lookup in _normalize.py

extend DatasetRecord from FOVRecord in viscy-data schemas; add viscy-…

0b3ea18

…data dep

pass batch_size to Lightning metric logging for correct step counts

37fd754

update recipes and add sampling-strategies guide; add CLAUDE.md

0a3d2e6

- Update build-cell-index, train-multi-experiment, troubleshooting recipes - Add sampling-strategies.md documenting FlexibleBatchSampler axes - Update README table - Add CLAUDE.md with data pipeline design principles

update pseudotime and linear classifier scripts for renamed fields

80f59eb

add configs

3d6007e

alxndrkalinin requested a review from Copilot March 17, 2026 00:08

Copilot AI reviewed Mar 17, 2026

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alxndrkalinin mentioned this pull request Mar 17, 2026

Add Predict Volume PR to applications/cytoland #374

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alxndrkalinin marked this pull request as ready for review March 17, 2026 18:02

physical nomrlaiztion and fix to mlp projetion layer for adapter.

fc08b62

alxndrkalinin merged commit fa03ecd into app-cytoland Mar 17, 2026

alxndrkalinin mentioned this pull request Mar 18, 2026

Applications: Cytoland refactor #379

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Update `app-cytoland` with latest changes in `app-dynaclr` - #381

Update `app-cytoland` with latest changes in `app-dynaclr`#381
alxndrkalinin merged 103 commits into
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