domain-medical-imaging
Skill8 starsChanged 4 months agoMITView on GitHub
Use for medical-image AI: tumor/cancer detection & classification, brain tumor MRI, mammography (benign vs malignant), chest X-ray, CT, histopathology, retinal/fundus, ultrasound, dermoscopy. Encodes hard-won rigor: patient-level splits (no leakage), medical preprocessing (CLAHE, ROI/organ cropping, artifact/pectoral removal), clinical operating points (high sensitivity), probability calibration, and skepticism toward inflated ROI-crop/leaky benchmark numbers. Triggers on 'detect cancer/tumor', 'MRI/CT/X-ray/mammogram/histopathology classification', 'benign vs malignant', 'medical images'.
In this repository22 other files it gives its agents.
- accuracy-improvement-loopSkill
- data-rigor-and-leakageSkill
- dataset-profilingSkill
- deployment-explainabilitySkill
- domain-3dSkill
- domain-anomaly-detectionSkill
- domain-audio-speechSkill
- domain-computer-visionSkill
- domain-generativeSkill
- domain-graphSkill
- domain-multimodalSkill
- domain-nlp-llmSkill
- domain-recommenderSkill
- domain-reinforcement-learningSkill
- domain-tabularSkill
- domain-time-seriesSkill
- domain-videoSkill
- literature-reviewSkill
- ml-research-methodologySkill
- notebook-deliverySkill
- rigorous-evaluationSkill
- training-optimizationSkill
The file
We split this skill into the rules it gives an agent
1 rule. About 0 are common, 0 are distinctive, and 1 is very specific to this project.
≈0
Common · estimate
Many files like this have a rule of this kind.
≈0
Distinctive · estimate
This author's own choices. Worth a look.
1
Very specific
Tied to their project's names, files or tools. Probably skip.
- Common
- Distinctive
- Very specific
- Very specific: line 21
PATIENT-LEVEL split: All images/views/slices of one patient in ONE split.
≈ “Common” is an estimate: at least 1 in 5 of the 350,495 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.
Files
Medical Imaging - Method Selection & Rigor
High stakes + small, leaky-prone datasets. Rigor matters more than architecture.
Decision table
| Sub-task | Recommended | Notes |
| 2D scan classification (mammo, X-ray, derm, fundus) | EfficientNet(-B3..B5) / ConvNeXt, ImageNet-pretrained | Modern-but-not-huge backbones win on low/medium-quality medical data; giant models often don't transfer better. |
| Whole-image with tiny lesions | Weakly-supervised localization (GMIC-style) or patch-pretrain then whole-image (Shen-style) | Best whole-image ceiling; also yields saliency maps for clinicians. |
| Multi-view study (e.g., CC+MLO mammo) | Two-view / multi-input fusion | Biggest research-backed lever over single view. |
| 3D volumes (CT/MRI) | 3D U-Net / nnU-Net (seg), 2.5D or 3D CNN (classify) | nnU-Net is a very strong segmentation default. |
| Histopathology WSI | MIL / CLAM on tiles | Gigapixel images, so tile them and use multiple-instance learning. |
| Lesion/organ segmentation | U-Net / nnU-Net / SegFormer | Dice/IoU. |
Non-negotiable rigor (this is where most medical ML fails)
- PATIENT-LEVEL split. All images/views/slices of one patient in ONE split. Use the dataset's official split when it exists (often encoded in the ID). Add asserts (
data-rigor-and-leakage). Random per-image splitting is the classic fake-accuracy trap. - Whole-image vs ROI-crop honesty. Cropped-lesion ROI classification is an easier, different problem; ~98-99% papers are usually ROI-crop and/or leaky. Report which one you are doing and never conflate.
- Medical preprocessing: CLAHE for contrast; crop to the organ/breast (largest connected component) to drop background/labels/tape; remove confounders (e.g., pectoral muscle on mammogram MLO - verify the model isn't attending to it via Grad-CAM); intensity normalization (windowing for CT, z-score for MRI). Apply identically at inference (parity).
- Clinical operating point: report sensitivity AND specificity; prefer a high-sensitivity threshold (recall ≥ ~0.90) chosen on validation - missing cancer >> a false alarm. Don't ship a 0.5 or Youden threshold blindly.
- Calibration: temperature-scale probabilities so "78% malignant" is trustworthy for decision support.
- Framing: decision-support / second-reader, NOT autonomous diagnosis; prototype needs clinical + regulatory validation (
deployment-explainability).
Realistic ceilings (whole-image, rigorous)
State honest targets from literature-review rather than chasing leaderboard peaks (e.g., CBIS-DDSM whole-image benign-vs-malignant ≈ 0.83 AUC single-view, ~0.86 two-view; higher numbers are typically ROI/leaky). Use accuracy-improvement-loop to push toward the ceiling.
Does it work?
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Your trail
Files you open will collect here, so you can find them again.
Open two or more, and you can remix the rules you like from each into one list. Kept in this browser only.
Now do this for your own.
Bring your CLAUDE.md, AGENTS.md or skills. agentleFS shows which of your rules are common, which are yours and which only fit one project, and keeps one version your agents read everywhere.

