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Rescale and LOT correction - #424

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Soorya19Pradeep wants to merge 113 commits into

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rescale-lot-correction

Open

Rescale and LOT correction#424
Soorya19Pradeep wants to merge 113 commits into
mainfrom
rescale-lot-correction

Commits on Jun 29, 2026
- Port scale-aware inference and LOT batch correction to modular-viscy-staging
  
  authored and
  edyoshikun
  committed
  0b529dd
- Add visualization script for TripletDataModule scale-aware rescaling
  
  authored and
  edyoshikun
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  5e6407a
- fix(viscy-data): handle nested timepoint_statistics in _collate_norm_meta
  
  edyoshikun
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  claude
  committed
  378a4ac
- feat(viscy-data): add Z-reduction and focus-centered z_range to TripletDataModule
  
  edyoshikun
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  claude
  committed
  19a3301
- docs(dynaclr): triplet inference DAG + sample 2D-from-3D predict config
  
  edyoshikun
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  claude
  committed
  365fc42
- docs(dynaclr): add triplet z-projection dataloader inspection script
  
  edyoshikun
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  dc39073
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  a14a0ac
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  52c72a1
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  6d320ae
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  2a1b327
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  dbe22f2
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  4a2de14
Commits on Jun 30, 2026
- fix(viscy-data): address triplet z-reduction/rescaling review findings
  
  edyoshikun
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  claude
  committed
  5b81c2c
Commits on Jul 6, 2026
- CLI to split ann data by a column to group by
  edyoshikun
  committed
  c7f8a16
Commits on Jul 10, 2026
- perf(viscy-utils): GPU-accelerate MMD via PyTorch
  
  Soorya19Pradeep
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  claude
  committed
  b39205f
- feat(viscy-utils): add MMD witness function
  
  Soorya19Pradeep
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  claude
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  f85cc7e
Commits on Jul 14, 2026
- feat(dynaclr): add MMD-witness weak-label source for linear classifiers
  
  edyoshikun
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  claude
  committed
  fa09832
- test(dynaclr): cover MMD-witness weak labeling for linear classifiers
  
  edyoshikun
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  c9d67ec
- config(dynaclr): add witness-labeled LC recipe for infectomics
  
  edyoshikun
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  c643e95
- docs(dynaclr): witness-score LC DAG with flow diagrams and mock plots
  
  edyoshikun
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  claude
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  bfc1936
- fix(dynaclr): evaluate witness LC against ground-truth annotations
  
  edyoshikun
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  361a8a5
- config(dynaclr): add eval_against to witness LC recipe
  
  edyoshikun
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  1d8bffa
- docs(dynaclr): reflect annotation-based eval in witness DAG + visuals
  
  edyoshikun
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  1af4f03
Commits on Jul 15, 2026
- feat(dynaclr): add witness gating diagnostic page to LC summary PDF
  
  edyoshikun
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  claude
  committed
  faf741d
- feat(dynaclr): filter-based witness references + annotation-scored eval
  
  edyoshikun
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  claude
  committed
  0a17c20
- fix(dynaclr): witness ROC/F1 plots use annotation-scored eval, not witness label
  
  edyoshikun
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  claude
  committed
  b6015a9
- feat(dynaclr): per-marker eval target for witness classifiers
  
  edyoshikun
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  claude
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  401a38a
Commits on Jul 17, 2026
- feat(dynaclr): witness-GMM annotations replace the witness label source
  
  edyoshikun
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  claude
  committed
  b769bc0
- chore(dynaclr): untrack mock DAG visuals
  
  edyoshikun
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  claude
  committed
  d01e749
- refactor(mmd): debloat MMD utilities
  
  edyoshikun
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  claude
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  68f3543
- fix(triplet): reject non-positive pixel size in rescaling
  
  edyoshikun
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  claude
  committed
  a3d7a5f
- fix(data): clear error when batch mixes FOV timepoint stats
  
  edyoshikun
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  claude
  committed
  9b0a114
- fix(triplet): pre-resolve timepoint_statistics norm_meta to sample t
  
  edyoshikun
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  claude
  committed
  4c6aa9f
- refactor(triplet): lazy-import viscy_transforms in rescale/z_reduction
  
  edyoshikun
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  claude
  committed
  4a28b20
Commits on Jul 22, 2026
- feat(dynaclr): per-marker embedding-consistency QC (MMD + correlation matrices)
  
  edyoshikun
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  claude
  committed
  7fa02de
- docs(dynaclr): gate-free witness reference default + rationale
  
  edyoshikun
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  claude
  committed
  10bea7b
- chore(ruff): ignore D and E501 under scripts/
  
  edyoshikun
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  claude
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  6306aa3
- feat(dynaclr): occlusion-attribution report script for classifier eval
  
  edyoshikun
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  claude
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  06f6655
- feat(dynaclr): add clustering PoP eval configs (infection/remodel/velocity)
  
  edyoshikun
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  claude
  committed
  8549598
- feat(dynaclr): add embedding clustering proof-of-principle scripts
  
  edyoshikun
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  claude
  committed
  5b18944
- feat(dynaclr): MMD significance gate before witness-GMM labeling
  
  edyoshikun
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  claude
  committed
  7cf6674
- feat(dynaclr): add canonical per-marker prediction paths
  edyoshikun
  committed
  f86b9e5
- feat(dynaclr): evaluate reusable dataset-scoped embeddings
  edyoshikun
  committed
  b28e38a
- feat(dynaclr): add train-predict-eval model matrix launcher
  edyoshikun
  committed
  85374c6
- config(dynaclr): add organelle-box remodeling matrix
  edyoshikun
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  cd03f60
- feat(data): support parquet focus planes and cell-level splits
  edyoshikun
  committed
  1650293
- config(dynaclr): add Zuben gut preparation and training recipes
  edyoshikun
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  576c124
- docs(dynaclr): document run-once eval-many pipeline
  edyoshikun
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  8192d75
- feat(dynaclr): Benjamini-Yekutieli FDR control for the MMD significance gate
  
  edyoshikun
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  claude
  committed
  111af49
- feat(viscy-utils): model-agnostic visualization module (occlusion + PCA-RGB)
  
  edyoshikun
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  claude
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  87763f9
- feat(dynaclr): expose occluder fill in occlusion report CONFIG
  
  edyoshikun
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  claude
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  1ac6b49
Commits on Jul 23, 2026
- Revert "config(dynaclr): add Zuben gut preparation and training recipes"
  edyoshikun
  committed
  32bf4f0
- Revert "feat(data): support parquet focus planes and cell-level splits"
  edyoshikun
  committed
  a405e30
- qc for the embeddings via pearson and mmd
  edyoshikun
  committed
  6ac217e
- plotting for mmd
  edyoshikun
  committed
  1897b8f
- markdown cleanup
  edyoshikun
  committed
  214b398
- cleanp the markdowns dags
  edyoshikun
  committed
  0396452
- feat(dynaclr): witness-GMM label provenance + diagnostic hardening
  
  edyoshikun
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  claude
  committed
  55b559d
Commits on Jul 24, 2026
- remove eval matrix from gitignore
  edyoshikun
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  7fe82c1
- feat(dynaclr): time-matched MMD-vs-HPI diagnostic for witness-GMM
  
  edyoshikun
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  claude
  committed
  7498c50
- feat(dynaclr): control-anchored gate for weak-channel witness labels
  
  edyoshikun
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  claude
  committed
  f6018f9
- fix(dynaclr): make LOT MMD comparisons consistent
  edyoshikun
  committed
  a63d374
- fix(dynaclr): repeat marker options in batch prediction
  edyoshikun
  committed
  13bb401
- fix(dynaclr): forward matrix prediction settings
  edyoshikun
  committed
  c854754
Commits on Jul 27, 2026
- fix(viscy-data): resize rescaled patches exactly
  edyoshikun
  committed
  7f3ceca
- fix(dynaclr): make LOT output replacement safe
  edyoshikun
  committed
  b9952de
- refactor(viscy-utils): unify LC train/val split behind one helper
  
  edyoshikun
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  claude
  committed
  89c17a0
- feat(dynaclr): witness-GMM phase-classifier configs + driver
  
  edyoshikun
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  claude
  committed
  eb970dc
- feat(dynaclr): witness-GMM diagnostic plots (AUROC, prob grids, %-remodeled)
  
  edyoshikun
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  claude
  committed
  5ff2c28
Commits on Jul 28, 2026
- fix(data): normalize MIP depth across z sampling
  edyoshikun
  committed
  7b03e1b
- feat(dynaclr): nest embedding zarrs under {ckpt}/embeddings/
  
  edyoshikun
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  claude
  committed
  d89f9ed
- feat(dynaclr): predict-triplet foundation models, focus-centered Z, obs enrichment
  
  edyoshikun
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  claude
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  37e3312
- feat(dynaclr): matrix foundation rows + skip-existing progressive collections
  
  edyoshikun
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  claude
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  1fd4def
- feat(dynaclr): organelle_remodeling collection + DynaCLR/MorphEm matrix
  
  edyoshikun
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  claude
  committed
  1c6455d
- docs(dynaclr): un-defer 04_21 in organelle_remodeling collection description
  
  edyoshikun
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  claude
  committed
  f676a9a
- feat(qc): audit_focus_slice — flag suspect focus detections (Z-aware)
  
  edyoshikun
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  claude
  committed
  655a18f
Commits on Jul 31, 2026
- fix(dynaclr): iter_embeddings glob missing embeddings/ segment
  
  edyoshikun
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  claude
  committed
  3f2a500
- feat(dynaclr): embedding-consistency-qc v1/v2 split, Fréchet, HPI pooling, temporal-std
  
  edyoshikun
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  claude
  committed
  3ec6934
- feat(dynaclr): microscope field + mock→uninfected on organelle collections; build-collection skill
  
  edyoshikun
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  claude
  committed
  7aa2c3d
- fix(dynaclr): fixed Pearson-r heatmap scale (vmin=0.8) across markers
  
  edyoshikun
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  claude
  committed
  e3fd8f7
Commits on Aug 3, 2026
- feat(viscy-utils): per-plate HPI-binned control-reference normalization
  
  edyoshikun
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  claude
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  d3af40e
Commits on Aug 4, 2026
- docs(viscy-utils): when to use control-reference normalization
  
  edyoshikun
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  claude
  committed
  13d0547
- feat(dynaclr): optional control-reference normalization in linear classifiers
  
  edyoshikun
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  8ea80b7
- Revert "docs(viscy-utils): when to use control-reference normalization"
  edyoshikun
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  79a2634
Commits on Aug 7, 2026
- feat(dynaclr): expand organelle remodeling matrix
  edyoshikun
  committed
  f719022
Commits on Aug 12, 2026
- feat(dynaclr): normalize biological MMD representations
  edyoshikun
  committed
  2abcc52
- feat(dynaclr): persist normalized PCA representations
  edyoshikun
  committed
  2150116
Commits on Aug 13, 2026
- docs(dynaclr): clarify pooled PCA balancing
  edyoshikun
  committed
  c7c889d
- feat(dynaclr): promote pooled witness TCN stack
  edyoshikun
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  d719a66
- feat(dynaclr): normalize embeddings in model matrix
  edyoshikun
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  3c17cb9
Commits on Aug 18, 2026
- feat(dynaclr): expand organelle matrix evaluation
  edyoshikun
  committed
  57b9616
Commits on Aug 19, 2026
- feat(dynaclr): add systematic infection controls
  edyoshikun
  committed
  b8beff7
Commits on Aug 28, 2026
- research(protocol): test CELL-DINO RoPE history shortcuts
  edyoshikun
  committed
  242466d
- research(eval): add RoPE history shortcut interventions
  edyoshikun
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  7f77932
- fix(eval): tolerate FP32 RoPE replay drift
  edyoshikun
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  5a62aaa
Commits on Oct 7, 2026
- feat(dynaclr): add CP-DINO cell phenotyping pipeline
  
  edyoshikun
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  claude
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  03ca826
Commits on Oct 14, 2026
- research(dynaclr): add pooled ZIKV pAL17 witness/GMM teacher
  
  edyoshikun
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  claude
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  8a5d6fa
- research(dynaclr): add direct-pAL lineage onset alignment
  
  edyoshikun
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  5653477
- research(dynaclr): add pAL alignment QC and per-dataset audit
  
  edyoshikun
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  f966ca8
- research(dynaclr): add pAL-aligned pseudotime figure scripts
  
  edyoshikun
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  0647928
- feat(dynaclr): add temporal forecast and DynaFormer evaluation pipeline
  
  edyoshikun
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  bbb5c31
Commits on Oct 15, 2026
- fix(dynaclr): accept untracked and concave nuclei in track-label check
  
  edyoshikun
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  claude
  committed
  8978893
- feat(dynaclr): add side-by-side cell-mask comparison for phenotyping attempts
  
  edyoshikun
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  claude
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  1d53957
Commits on Oct 20, 2026
- research(dynaclr): add TOMM20 set-classifier analysis of cell cycle vs infection
  
  edyoshikun
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  claude
  committed
  77113ba
- research(dynaclr): require TCN and sensor agreement in TOMM20 set classifier
  
  edyoshikun
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  claude
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  09ef516
Commits on Nov 2, 2026
- feat(viscy-data): flag blank patches during triplet prediction
  
  edyoshikun
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  claude
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  9c05825
- feat(dynaclr): add Katamari predict and eligibility filtering to predict-triplet
  
  edyoshikun
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  claude
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  8d62ae9
- feat(dynaclr): persist pooled normalized representations for matrix evaluation
  
  edyoshikun
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  40185c2
- feat(dynaclr): add phenotyping-batch planner and AI-readiness audit
  
  edyoshikun
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  15ecd6d
- feat(dynaclr): wire eligibility, phenotyping, and temporal forecast into the model matrix
  
  edyoshikun
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  41753e5
- feat(dynaclr): add DINOv3, Katamari, and PCNA rows to the organelle-remodeling matrix
  
  edyoshikun
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  e0c423d
- chore: stop tracking .ed_planning protocol
  
  edyoshikun
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  9dd7013
- fix(dynaclr): forward eligibility and Katamari options through predict.sbatch
  
  edyoshikun
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  claude
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  ed6f6ff

Commits

Commits on Jun 29, 2026

Commits on Jun 30, 2026

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Commits on Jul 31, 2026

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Commits on Aug 4, 2026

Commits on Aug 7, 2026

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Commits on Aug 18, 2026

Commits on Aug 19, 2026

Commits on Aug 28, 2026

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Commits on Oct 15, 2026

Commits on Oct 20, 2026

Commits on Nov 2, 2026