medical-imaging-workflows

Trigger Boundary

Medical imaging workflows for CMR, DICOM/NIfTI, classical features, deep learning, and pathology imaging.

Use this aggregate Codex App skill when the task matches one of the source workflows below.

Source Workflows

• cardiac-mri: Use for cardiac MRI / CMR domain knowledge, cine SAX/LAX, ED/ES timing, LV/RV function, myocardial strain, tagged MRI, feature tracking, and cardiac phenotype validation independent of any single project. Reference: _src/cmr/source.md
• pydicom: Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications. Reference: _src/dicom/source.md
• medical-imaging-classical-features: Use when enforcing reproducible medical-imaging preprocessing, physical-space geometry, classical registration baselines, radiomics protocols, or DICOM SEG/SR provenance. Reference: _src/classic/source.md
• medical-imaging-deep-learning: Use for medical-imaging deep learning tasks involving segmentation, MONAI/nnU-Net baselines, registration or warping, temporal/video imaging, missing-modality fusion, proposal/cascade/refinement models, external method adaptation, and validation evidence gates. Reference: _src/dl/source.md
• pathml: Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler. Reference: _src/pathml/source.md

Workflow

1. Choose the source workflow whose trigger boundary best matches the user request.
2. Read that source workflow's source.md before acting.
3. Load only the needed files under that workflow's copied references, scripts, assets, or evals.
4. Follow the source workflow unless the current project gives stricter instructions.