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Rescale and LOT correction - #424
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…staging Scale-aware patch extraction (packages/viscy-data): - Add _read_pixel_size() helper to read X pixel size from OME-Zarr metadata - Add reference_pixel_size parameter to TripletDataModule: when set, computes initial_yx_patch_size from the pixel-size ratio so the same physical area is covered at inference time - Replace BatchedRescaleYXd (removed per review) with existing BatchedZoomd using scale_factor=(1.0, final_y/initial_y, final_x/initial_x) and mode="bilinear" with antialias; import is lazy to avoid a hard dep LOT batch correction (applications/dynaclr): - Add dynaclr.evaluation.lot_correction submodule with core logic (fit, apply, save, load), Pydantic configs, and Click CLI entry points - Register fit-lot-correction and apply-lot-correction in cli.py via LazyCommand - Add pot and joblib to optional-dependencies.eval in pyproject.toml Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
Plots n cell patches side-by-side: - Left: raw patch at initial_yx_patch_size (larger physical area) - Right: same patch bilinearly downscaled to final_yx_patch_size (model input) Both columns share the same percentile contrast window so differences are spatial. Physical scale (µm × µm) is shown in each panel title. Usage: python visualize_triplet_rescaling.py --data-path /path/to/data.zarr --tracks-path /path/to/tracks --source-channel Phase3D --z-range 0 5 --final-yx-patch-size 224 224 --reference-pixel-size 0.325 --output rescaling_comparison.png Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
…meta
_collate_norm_meta iterated every normalization level and called
torch.stack on each stat, but timepoint_statistics is nested
{timepoint: {stat: tensor}} rather than flat {stat: tensor}. Any zarr
carrying timepoint_statistics (alongside fov/dataset stats) crashed
batch collation in TripletDataModule with "expected Tensor as element 0
... but got dict". Stack within each timepoint sub-dict instead.
Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
…etDataModule
Lets a 3D OME-Zarr feed a 2D model without materializing a separate MIP
dataset, and centers the extracted Z window on each FOV's focus plane.
- z_reduction ("mip"/"center"): collapse the extracted z_range to one
slice via BatchedChannelWiseZReductiond. Label-free channels (resolved
by parse_channel_name) take the center slice; others are max-projected.
on_after_batch_transfer expects Z=1 when reduction is on.
- z_extraction_window/z_focus_offset/focus_channel: resolve a per-FOV
focus-centered window from each position's
focus_slice[ch].fov_statistics.z_focus_mean (fallback z_total//2), all
windows the same width. z_range stays as an explicit override; exactly
one of z_range / z_extraction_window must be given. Per-FOV windows are
resolved at setup() and looked up per patch in the dataset.
Tests cover both reduction strategies (discriminating center vs MIP),
the normalize-then-reduce order, per-FOV focus resolution, and the
z_range/z_extraction_window XOR guard.
Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
Documents the TripletDataModule predict path (zarr + tracking, not parquet) and adds a runnable sample config demonstrating z_reduction + reference_pixel_size to feed a 3D dataset to a 2D model. Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
Notebook-style script (no CLI) that loads a 3D OME-Zarr + tracking, extracts a per-FOV focus-centered Z window, collapses it via z_reduction, applies a random affine so anchor/positive diverge, and visualizes a couple of batches to a PNG. Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
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Pull request overview
This PR expands the Triplet-based data loading path to better support cross-dataset inference (pixel-size aware patch extraction + on-the-fly Z reduction + focus-centered per-FOV Z windows), and adds a LOT (Linear Optimal Transport) batch-correction pipeline with CLI entrypoints for embedding-space correction.
Changes:
- Extend
TripletDataModule/TripletDatasetto support per-FOVz_rangeresolution viaz_extraction_window+focus_slicemetadata, plus optionalz_reductionand pixel-size aware rescaling. - Add LOT correction core functions + Pydantic config models +
dynaclrCLI commands for fitting/applying correction pipelines. - Add tests for the new Triplet Z-window/Z-reduction behavior and update docs/config examples for inference.
Reviewed changes
Copilot reviewed 14 out of 14 changed files in this pull request and generated 7 comments.
Show a summary per file
| File | Description |
|---|---|
| packages/viscy-data/src/viscy_data/triplet.py | Adds pixel-size rescaling, per-FOV focus-centered Z windows, and optional Z-reduction in the Triplet datamodule/dataset. |
| packages/viscy-data/tests/test_triplet.py | Adds tests for z_extraction_window XOR validation, per-FOV focus-centered windows, and Z-reduction behavior/order. |
| packages/viscy-data/src/viscy_data/_utils.py | Extends norm-meta collation to correctly stack nested timepoint_statistics. |
| applications/dynaclr/src/dynaclr/evaluation/lot_correction/lot_correction.py | Implements LOT correction fit/apply + pipeline save/load helpers. |
| applications/dynaclr/src/dynaclr/evaluation/lot_correction/config.py | Adds Pydantic models for fit/apply configs and filter specs. |
| applications/dynaclr/src/dynaclr/evaluation/lot_correction/fit_lot_correction.py | CLI wrapper for fitting and saving a LOT pipeline from YAML config. |
| applications/dynaclr/src/dynaclr/evaluation/lot_correction/apply_lot_correction.py | CLI wrapper for applying a saved LOT pipeline to an embedding zarr. |
| applications/dynaclr/src/dynaclr/evaluation/lot_correction/init.py | Exposes LOT correction functions at the package level. |
| applications/dynaclr/src/dynaclr/cli.py | Registers new fit-lot-correction and apply-lot-correction CLI subcommands. |
| applications/dynaclr/pyproject.toml | Adds joblib + pot to eval extras for LOT correction dependencies. |
| applications/dynaclr/scripts/dataloader_inspection/visualize_triplet_rescaling.py | Adds a visualization utility for the new pixel-size rescaling behavior. |
| applications/dynaclr/scripts/dataloader_inspection/triplet_dataloader_zprojection.py | Adds an inspection notebook/script for focus-centered Z windows + Z-reduction. |
| applications/dynaclr/docs/DAGs/inference_triplet.md | Documents Triplet inference path and new options (needs a small wording update for z-window semantics). |
| applications/dynaclr/configs/prediction/predict_triplet_2d_from_3d.yml | Provides a sample prediction config demonstrating reference_pixel_size + z_reduction. |
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Co-authored-by: Copilot Autofix powered by AI <[email protected]>
Co-authored-by: Copilot Autofix powered by AI <[email protected]>
Co-authored-by: Copilot Autofix powered by AI <[email protected]>
Co-authored-by: Copilot Autofix powered by AI <[email protected]>
Co-authored-by: Copilot Autofix powered by AI <[email protected]>
Co-authored-by: Copilot Autofix powered by AI <[email protected]>
- Declare viscy-transforms in viscy-data's triplet extra and hoist the BatchedZoomd/BatchedChannelWiseZReductiond imports to module top; the inline imports were masking a missing runtime dependency that would ImportError for anyone using z_reduction or reference_pixel_size. - Raise in _resolve_per_fov_z_ranges when a FOV's Z is smaller than z_extraction_window, instead of silently emitting a narrower window that breaks cross-FOV batch stacking. - Remove a dead duplicate break in test_focus_centered_z_range. - Correct the inference DAG doc: embeddings live in .X (the embedding_key array), mirrored to obsm["X_backbone"]/["X_projections"]. uv.lock intentionally omitted: the workspace glob currently entangles the untracked applications/eet package, so a clean regen of the single viscy-transforms edge is not possible until eet is committed or removed. Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
Replace the NumPy/scipy.cdist backend with PyTorch so the pooled RBF kernel matrix is built once on the available device (CUDA if usable, else CPU) and reused across all permutations. Device selection probes a trivial kernel launch and falls back to CPU, so a present-but-unusable GPU (e.g. compute capability older than the torch build) does not crash. Public API is unchanged: median_heuristic/compute_mmd_unbiased return the same bandwidth-convention values, and mmd_permutation_test still returns (mmd2, p_value, null_distribution) so dynaclr's effect-size and activity z-score computations keep working. Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
Add witness_function to the MMD module: the per-point empirical witness w(z) = mean_i k(z, x_i) - mean_j k(z, y_j), the RKHS direction along which distributions P (X) and Q (Y) differ. Positive scores lean toward X, negative toward Y. Reuses the GPU RBF-kernel helpers and bandwidth (median-heuristic) convention already in the module, and chunks over query points to bound the intermediate kernel matrices. Tests cover distribution separation, X<->Y antisymmetry, and chunk-size invariance. Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
Adds `label_source: witness` to the linear-classifier eval as a second option to annotation-CSV labels. Per marker, cells are pooled across experiments, control/perturbed references are built from per-experiment wells, the MMD witness is fit and scored per cell, and scores are gated (sign + dead-zone) into control/perturbed pseudo-labels. Everything downstream (train_linear_classifier, publish, append-predictions, plots) is unchanged — only the label source differs. - evaluate_config.py: WitnessLabelSource, WitnessSettings, label_source switch on LinearClassifiersStepConfig (annotations stays the default). - witness_labels.py: well->reference mask (path-component match so C/1 != C/10), witness fit/score, dead-zone gating. - orchestrated.py: branch label assembly into _annotation_run_specs / _witness_run_specs / _build_labeled_adata; training loop unchanged. Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
Five integration tests exercising the real code path: - well-prefix match rejects C/1 vs C/10 confusion - witness scores separate control/perturbed clusters - dead-zone drops ambiguous near-origin cells - empty AnnData when a reference group has no cells - end-to-end run_linear_classifiers witness mode → metrics + summary PDF Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
Mirrors linear_classifiers_infectomics.yml but with label_source: witness. Per-experiment control/perturbed wells replace annotation CSVs; wells are templates to edit per plate layout. One classifier per marker (G3BP1, SEC61B, Phase3D, viral_sensor), dead_zone 0.1, track-level split. Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
- witness_score_classifiers.md: full DAG (why, step-by-step, gating rule, config, notes) plus embedded visuals. - visuals/: three Graphviz flow diagrams (data flow, gating, pipeline) as .dot + png + pdf, and four mock example-output plots (witness-score histogram, per-marker metrics bar, ROC, F1-over-time) with a reproducible generator (mock_witness_plots.py). Mock plots are watermarked synthetic. - Cross-links from evaluation.md and linear_classifiers/README.md so the new DAG is discoverable from the annotation path. Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
The witness label is a deterministic function of the embedding, so
evaluating a witness-trained classifier against that same label is
circular — it reports a trivial ~1.0 (verified on real infectomics
embeddings: 1.000 vs witness label, 0.712 vs true infection_state).
WitnessSettings gains eval_against (default "infection_state") and
eval_class_map ({control: uninfected, perturbed: infected}). In witness
mode, val metrics are recomputed on the val split against the ground-truth
obs column via the class map; the summary records eval_source. When the
column is absent, metrics fall back to the witness label flagged as
eval_source="witness_label". Adds two tests (annotation eval + fallback).
Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
Score the witness-trained classifier against infection_state (not the self-referential witness label) with the control→uninfected / perturbed→infected class map, matching the leakage fix. Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
- witness_score_classifiers.md: add "Evaluation: avoid the circularity trap" section with the real per-marker metrics table (scored vs infection_state), eval_against/eval_class_map in the config block, and step 7 in the flow; refresh the Notes caveat (metrics are honest now, check eval_source; note class imbalance). - witness_dataflow.dot/png/pdf: add the EVALUATE-vs-annotations node. - mock_witness_plots.py + bar/ROC png/pdf: use real run values (viral_sensor 0.87, SEC61B 0.76, Phase3D 0.58, G3BP1 0.49) instead of invented all-high numbers; watermark clarifies bar/ROC are real, hist/F1 synthetic. Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
…bs enrichment
Expand the per-reporter triplet predict path (dynaclr predict-triplet):
- foundation model_type: instantiate the model: block of a LightningCLI
training_config (frozen encoder loads its own weights) instead of loading a
ContrastiveModule checkpoint; --checkpoint / --training-config gate by type.
- focus-centered Z: --z-window WIDTH centered per-FOV on the focus plane
(--focus-channel / --z-focus-offset), mutually exclusive with fixed --z-range;
--reference-pixel-size-z-um converts the reference-grid slice count to the
native count covering the same physical depth.
- obs enrichment: append collection metadata (experiment/marker/perturbation/
organelle/microscope/hours_post_perturbation/interval_minutes) to each
embedding's obs so triplet and parquet embeddings are consumed identically;
--no-enrich-obs opts out. New enrich-obs-from-collection subcommand backfills
obs onto already-written embeddings.
- exclude_fovs from the collection experiment is forwarded to predict.
Update the {ckpt}/embeddings/{marker}.zarr path expectation in
test_output_path_is_dataset_centric (embeddings/ nesting from d89f9ed).
Co-Authored-By: Claude Opus 4.8 <[email protected]>
…lections
run-matrix / predict-batch gain:
- foundation rows (model_type: foundation): resolve from explicit identity +
training_config (no train_sbatch parsing), never emit a train stage, and
forward --model-type/--training-config through predict-batch and predict.sbatch
instead of a checkpoint.
- focus-centered Z + physical Z reference (z_window/focus_channel/z_focus_offset/
reference_pixel_size_z_um) forwarded as the trailing predict positionals;
z_range and z_window validated mutually exclusive.
- skip-existing (default) via resolve_datasets_to_run: prune datasets whose
per-marker embeddings already exist for a row's (family, run, ckpt_name);
drop fully-done rows, write a pruned temp collection for partial ones. A dir
without group metadata (crash mid-write) counts as incomplete and re-runs.
--overwrite bypasses the check; default --stages is predict,eval.
Point _mark_done at the {ckpt}/embeddings/ path so completion detection matches
the nested layout (d89f9ed).
Co-Authored-By: Claude Opus 4.8 <[email protected]>
Add the merged organelle_remodeling collection (9 experiments: SEC61B/TOMM20/ G3BP1 reporters under ZIKV/DENV, one experiment per dataset, all prepared on VAST with normalization + focus_slice). Includes 2026_03_24_A549_SEC61_ZIKV (re-concatenated + QC'd clean, mantis_v2 at 0.1133/0.16995 um); 04_21 G3BP1 DENV stays deferred. Repoint the matrix configs at the new progressive-collection workflow: - organelle_remodeling.yml matrix: one row per MODEL (DynaCLR-2D-MIP-BoC single marker + MorphEm-frozen foundation baseline) over the shared collection; focus-centered Z (z_window 16, focus_channel Phase3D, reference_pixel_size_z_um 0.174); output root on intracellular_dashboard. - example.yml: document model_type foundation rows, focus-centered vs fixed Z, and skip-existing defaults. - 07_01 collection: add the Phase3D channel. Co-Authored-By: Claude Opus 4.8 <[email protected]>
…ription 2026_04_21_A549_G3BP1_DENV was re-concatenated to a flat store on VAST (odd 5-assemble layout resolved) and verified predict-ready. Note the residual z_focus=0 frames (12/54 FOVs, mean 2.4 timepoints each). Co-Authored-By: Claude Opus 4.8 <[email protected]>
Add audit_focus_slice() + a `qc audit-focus` CLI command that reads already-
written focus_slice.{channel}.per_timepoint metadata and reports where in-focus
detection landed at a stack edge (z == 0 or z == Z-1), the signature of a failed
search on a 3D stack. Z-depth-aware: a 2D acquisition (Z == 1) trivially focuses
at slice 0 for every timepoint, so it is reported as 2D with zero flags rather
than misclassifying every frame as failed.
Returns per-FOV suspect counts, dataset totals, and the valid (non-edge) focus
distribution — the summary previously computed ad hoc while vetting datasets for
focus-centered predict.
Co-Authored-By: Claude Opus 4.8 <[email protected]>
embedding_store writes .../{ckpt}/embeddings/{marker}.zarr since the embeddings/
nesting landed (d89f9ed), but iter_embeddings still globbed .../{ckpt}/*.zarr —
so it returned [] and ALL cross-dataset pooling (embedding-consistency-qc, MMD,
linear classifiers) silently found zero embeddings. Add the missing EMBEDDINGS_DIR
segment; fix the test_paths fixtures that encoded the pre-nesting layout.
Co-Authored-By: Claude Opus 4.8 <[email protected]>
…ling, temporal-std Extend the per-marker embedding-consistency QC: - split_by: partition datasets by a per-dataset obs column (e.g. microscope) into within-group + cross-group blocks; degenerate blocks (single-dataset within, or empty cross side) are skipped with a log line. - metrics knob: choose any of pearson/mmd/frechet (default all three). MMD pass is skipped when not requested. - Fréchet (mean+covariance) matrix: 2-Wasserstein between Gaussian summaries of each dataset's control cells — richer than Pearson-of-means, cheaper than full MMD. - Time-aware Pearson (pearson_hpi_bin_hours): mean per hours_post_perturbation bin then mean-of-means, so uneven time sampling can't masquerade as a batch effect; plus a per-dataset temporal-std drift diagnostic (std of the control centroid across HPI bins). - Annotated, auto-scaled correlation heatmaps. Organelle-box recipe (metrics: [pearson], split_by: microscope, 2 h HPI bins). Co-Authored-By: Claude Opus 4.8 <[email protected]>
…tions; build-collection skill Add per-experiment microscope (mantis_v1 for the 0.1494 um/px dataset, mantis_v2 for the 0.1133 ones) to organelle_remodeling so obs enrichment writes it and the consistency QC can split v1/v2. Normalize the 2024_11_07 control label mock→uninfected in both organelle_remodeling and the source organelle-box collection so a single uninfected filter catches every dataset's controls. Update the airtable-build-collection skill to always populate microscope (field table, schema, derivation rule). Co-Authored-By: Claude Opus 4.8 <[email protected]>
plot_corr_matrix auto-scaled vmin to each matrix's own off-diagonal minimum, so
heatmaps for different markers used different colour scales and couldn't be
compared by eye. Use a shared fixed vmin (default 0.8). Fix the title
("mean-embedding" -> "control-cell summary correlation").
Co-Authored-By: Claude Opus 4.8 <[email protected]>
Add control_normalization.py: robust z-score of embeddings against the control (uninfected) population of the same plate and HPI bin. Stores only per-(plate, bin) median/IQR statistics and applies (x - median) / IQR on the fly rather than materializing a normalized array. - control_reference_stats: per-experiment median + IQR of control cells, pooled across control wells, in fixed-width HPI bins anchored at 0h. - control_reference_stats_multi: same at several bin widths (default 1h + 2h). - ControlReference.apply: robust z-score against the matched bin, nearest occupied bin as fallback; zero-IQR dimensions floored to 1.0. - Raises if a plate has cells but no controls (no silent drop). 8 unit tests cover recovery of the control center, control/perturbed separation, nearest-bin fallback, zero-IQR flooring, multi-bin widths, and the control-less-plate guard. Co-Authored-By: Claude Opus 4.8 <[email protected]>
Standalone README next to control_normalization.py documenting the empirical finding so a teammate knows when NOT to use it: it flattens control temporal drift (−32 to −53% control-centroid std across 3 plates) but LOWERS held-out infection/remodeling classifier AUROC on every ZIKV DynaCLR classifier tested (−0.008 to −0.032), because flattening control-relative time removes infection-trajectory signal. Per-dimension only (not multivariate batch correction). Full write-up under .ed_planning/dynaclr/batch_correction/. Co-Authored-By: Claude Opus 4.8 <[email protected]>
…ssifiers Add a control_normalize flag (+ control_normalize_bin_hours, default 2.0) to LinearClassifiersStepConfig and wire it into run-linear-classifiers: when set, embeddings are robustly z-scored per plate/HPI-bin against control cells before training/scoring, via viscy_utils.evaluation.control_normalization. Off by default and backward-compatible. It is off because the held-out A/B showed it lowers infection/remodeling AUROC (see control_normalization_README); the flag exists to reproduce that result and for cases where matched-time cross-condition comparability is the actual goal. Co-Authored-By: Claude Opus 4.8 <[email protected]>
This reverts commit 13d0547.
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Segment cells from the projected virtual-stain membrane with Cellpose CP-DINO, assign tracked nuclei to cells, derive cytoplasm masks, and measure per-cell fluorescence for track eligibility. Includes the 0.58 um recipes (April pilot and organelle_remodeling rollout), the per-FOV Slurm array scripts, the review tools behind the pilot diagnostics, and the recipe doc. The reader accepts OME-Zarr identity transforms used by legacy tracking stores. Co-Authored-By: Claude Opus 5.5 <[email protected]>
Fit the pooled pAL17 teacher used for pAL-anchored alignment: per-dataset control median/MAD normalization, pooled PCA80, an RBF witness against controls, and an all-cell joint control+ZIKV GMM with tied covariance and 0.8/0.2 posterior gates. Leave-one-dataset-out pAL->pAL and pAL->Phase classifiers measure agreement with the teacher. The threshold sweep writes predictions_by_threshold.parquet, the per-cell posterior table that the onset alignment reads. Co-Authored-By: Claude Opus 5.5 <[email protected]>
Align ZIKV organelle remodeling to each lineage's pAL response. Track segments are grouped into parent-linked families within dataset and FOV, descendants are collapsed by median pAL posterior, and tau=0 is the first of three frames with posterior >=0.8 after three frames <=0.2. SEC61B, G3BP1, and TOMM20 embeddings are centered on the smoothed exact-HPI control median, scaled by the control MAD, and reduced to PCA80. Null-standardized MMD then compares HPI and tau on the same onset-bearing cohort in 30-minute bins. quantify_pal_alignment_gain.py computes the spline-fit alignment metrics, and bootstrap_pal_alignment_gain.py resamples whole families within dataset, well, and condition. Co-Authored-By: Claude Opus 5.5 <[email protected]>
Plot pAL posterior curves on the HPI and tau axes, onset support, and five-bin organelle-divergence calls. The DENV module holds the shared plotting functions, and the ZIKV script reuses them. The per-dataset audit freezes normalization, PCA, bandwidth, and onsets, reconstructs the pooled curves, and then compares each marker's datasets individually. Co-Authored-By: Claude Opus 5.5 <[email protected]>
Render the HPI-versus-tau MMD figure, the per-marker lineage montages sampled every 3 hours from tau=-9 to +9 h, and the shared organelle UMAP. The assembler combines the ZIKV and DENV panels into the pseudotime paper figure under paper_figure_pseudotime/. Co-Authored-By: Claude Opus 5.5 <[email protected]>
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The following have been implemented in this branch:
TripletDataModulethat rescales the patches to a reference pixel and a uses the Z-MIP projection transform