preprocess-imaging
FeaturedDesign or audit the data-preparation stage of a medical-imaging model — DICOM/NIfTI intake, resampling and intensity normalisation, and the augmentation plan — so the pipeline is leakage-safe before model-scaffold builds the training repo. Emits a declarative preprocessing manifest and a deterministic data-stage leakage gate that catches the leaks a split table cannot see: a dataset-level normaliser fit on non-train data, any data-fitted transform run before the split, and the same patient's slices crossing splits. Integrates MONAI / TorchIO transforms; it does not reimplement them, and it never runs preprocessing on real patient data.
Install
Quality Score: 95/100
Skill Content
Details
- Author
- Aperivue
- Repository
- Aperivue/medsci-skills
- Created
- 3 months ago
- Last Updated
- today
- Language
- Python
- License
- MIT
Bundled in these plugins
Similar Skills
Semantically similar based on skill content — not just same category
profile-imaging
Profile a medical-imaging dataset before any modelling decision is made — the acquisition grid, voxel spacing and orientation spread, the intensity domain, which label values are actually present, how much of the volume the target occupies, and how large the target is in millilitres — then gate that profile against the researcher's declared plan. Catches, at the point where it is still cheap, the dataset facts that otherwise surface after a training run: a "test set" that carries no ground truth, labels whose grid does not match their image, a stray label index, a target occupying a fraction of a percent while accuracy is planned as a metric, and acquisition heterogeneity nobody declared a resampling decision for. Emits a dataset-profile JSON and a deterministic gate that reads it (stdlib-only, so an audit travels with the JSON). It describes the data and audits the plan against it; it does not preprocess, split, or train.
model-scaffold
Generate a reproducible, runnable PyTorch training repo for a medical-imaging task — segmentation, classification, detection, image-to-image synthesis, self-supervised pretraining, or fine-tuning a pretrained backbone (transfer learning) — the missing middle link between choosing an architecture and validating a trained model. Emits a patient-level seed-locked split as an auditable artifact, a task-appropriate model, train and evaluate scripts that seed every RNG and infer under eval mode, a config, requirements, a reproducibility record, and a Methods stub with VERIFY placeholders (no fabricated numbers). Fine-tuning mode adds a frozen-then-unfrozen schedule, discriminative learning rates, and a pretrained-weight provenance record. The reproducibility guarantees hold by construction, so the build is leakage-safe before any training runs. Integrates with MONAI, nnU-Net, TorchIO, timm, and torchvision — it does not reimplement them.
model-validation
Design or audit the clinical-validation study for an engineer-built medical-imaging model (segmentation, classification, or detection) before the validation report or manuscript is written. Covers patient-level split disjointness and the data-leakage taxonomy, tuning-on-test, internal versus genuine external validation, comparator design, single-run versus multi-seed variance, task-correct metric selection, test-set sizing, and CLAIM 2024 / TRIPOD+AI / STARD-AI reporting fit. Ships a deterministic split-leakage gate that proves patient disjointness by set arithmetic on the emitted split-assignment table. Does not build or train models — it integrates with MONAI / nnU-Net, it does not replace them.