Preprocess Imaging

Preprocess-Imaging Skill

Purpose

This skill designs and audits the data-preparation stage of a medical-imaging model — the stage

*before* a training repo is built — and proves it is leakage-safe by construction. Data leakage

enters one step earlier than the split table can see: a normaliser fit on the whole dataset, a

data-fitted transform run before the split exists, or a patient whose slices land in more than one

partition. Each silently inflates every downstream metric (Kapoor & Narayanan, *Patterns* 2023;

Varoquaux & Cheplygina, *npj Digit Med* 2022; CLAIM 2024 data items).

It is the missing first link in the lane: preprocess-imaging (prepare + audit) →

/model-scaffold (build) → /model-validation (validate the split) → /model-evaluation +

/analyze-stats (metrics) → /write-paper + /check-reporting (publish). It integrates

MONAI / TorchIO transforms (referenced in the emitted plan); it does not reimplement them, and it

never executes preprocessing on real patient data.

When to use

• You have a data manifest (one row per image/slice with a patient/subject ID) and want a

leakage-safe preprocessing plan + a machine-checkable manifest before scaffolding a model.

• You want to audit an existing preprocessing pipeline for data-stage leakage.

When NOT to use

• Auditing the train/val/test split table itself → /model-validation (split-leakage gate).
• Building the training repo / model code → /model-scaffold (it consumes this manifest).
• Choosing the architecture → /architecture-zoo.
• Held-out metrics / calibration → /model-evaluation then /analyze-stats.
• Reimplementing MONAI / TorchIO transforms → out of scope (this skill wires and audits them).

Workflow

Phase 1 — Inventory the data and the intended steps

Collect: modality (CT / MR / X-ray / US / path), the data manifest (one row per image/slice with a

patient_id), the intended resample spacing, the intensity transform (fixed HU window vs a fitted

z-score / min-max / histogram match), and the augmentation plan. See

references/preprocessing_guide.md for modality-aware guidance

(what normalisation is standard per modality, which augmentations preserve vs break physiology).

Phase 2 — Decide fit scope and order (the leakage-safe rules)

• Fit dataset-level normalisation on the training split only — never on all/full/test.
• Run any data-fitted transform AFTER the split — before the split there is no train/test

distinction, so the fit spans partitions.

• Prefer per-image (per-sample) normalisation where clinically appropriate: it uses only that

image's own statistics and is leakage-free even before the split.

• Keep augmentation train-only — augmenting val/test folds undisclosed test-time augmentation

into the reported metric.

• Split at the patient level, then map slices to their patient's split (never split slices).

Phase 3 — Emit the preprocessing manifest

Write a declarative JSON manifest that model-scaffold consumes and the gate checks:

{
  "split_seed": 42,
  "transforms": [
    {"name": "hu_window", "type": "clip", "fit_scope": "none", "stage": "before_split"},
    {"name": "train_zscore", "type": "standardize", "fit_scope": "train", "stage": "after_split"},
    {"name": "flip_rotate", "type": "augmentation", "stage": "after_split", "applies_to": ["train"]}
  ],
  "split_assignment": [
    {"patient_id": "P001", "unit_id": "P001_s1", "split": "train"}
  ]
}

fit_scope: train (OK) · all/full/dataset/test (leak) · sample/per_image/none/fixed

(not data-fitted, leakage-free). stage: before_split / after_split.

Declare the fit scope of resampling too. A target spacing you chose in advance is fixed and

never leaks (fit_scope: fixed). A target *derived* from the cohort does: nnU-Net sets its target

spacing from a percentile of the dataset fingerprint, so a resample fitted over every case carries

held-out geometry into the training grid exactly as an intensity statistic would. Which one you

have is decided by the fingerprint's scope, not by the word "resample".

Phase 4 — Gate the manifest (deterministic)

python3 scripts/check_preprocessing_leakage.py --manifest preprocessing_manifest.json --strict

That gate asks whether a transform was fit on the right scope. Before an *inference* run on a

cohort the model was not trained on, ask the other question — is that cohort in the intensity

domain the trained normaliser assumes?

python3 scripts/check_normalizer_domain.py \
    --profile eda/<cohort>_profile.json \
    --contract work/nnUNet_results/.../plans.json \
    --splits external_mri --out qc/normalizer_domain.json --strict

Verdicts: PREPROCESS_BEFORE_SPLIT, NORMALIZATION_LEAKAGE, PATIENT_CROSS_SPLIT (Major);

AUGMENTATION_ON_EVAL, UNSPECIFIED_FIT_SCOPE, MISSING_SEED (Minor). The verdict is reproduced

by set arithmetic + rule on the manifest, never asserted from prose. A green gate is a precondition

for handing the manifest to /model-scaffold.

Integration

• Feeds /model-scaffold — the audited manifest is the scaffold's preprocessing input; its

split_assignment is the same patient-level split /model-validation later re-verifies.

• /self-review model_development probe audits data-stage leakage in a finished manuscript;

this skill *produces* the leakage-safe pipeline it looks for.

• /check-reporting — the manifest documents the CLAIM 2024 / TRIPOD+AI data-preprocessing items.

Anti-Hallucination

• Never fabricate image statistics, patient IDs, or split assignments. Every value in the

manifest comes from the real data manifest and the researcher's declared pipeline — never invented.

This skill designs and audits the plan; it does not run preprocessing on real patient data or

synthesise the images it describes.

• Never report a preprocessing-audit "pass" without running check_preprocessing_leakage.py. The

leakage verdict is reproduced deterministically (rule + set arithmetic on the manifest), never

asserted from prose.

• Never label a dataset-fitted transform as per-sample to clear the gate. The manifest's

type / fit_scope / stage must describe what the code actually does; a mislabelled transform

hides a real leak the gate would otherwise catch.

• Integrate, don't reimplement. Reference MONAI / TorchIO transforms; do not write a new

normalisation/resampling implementation or claim results for one.

Reproducible challenge

scripts/check_normalizer_domain_challenge/ ships a synthetic profile/contract triple: a cohort in

the contract's own domain that must come back clean (the false-positive guard), an arbitrary-unit

cohort that must raise a Major, and an unreadable contract that must refuse rather than pass.

scripts/check_preprocessing_leakage_challenge/ ships a synthetic leak/clean manifest pair with a

network-free verify.sh wired into the skill's validation commands.