Medical Python Packages

torchxrayvision

TorchXRayVision: A library of chest X-ray datasets and models. Classifiers, segmentation, and autoencoders.

medmnist

[pip install medmnist] 18x Standardized Datasets for 2D and 3D Biomedical Image Classification

medpy

Medical image processing in Python

biomcp-python

BioMCP: Biomedical Model Context Protocol

ngff-zarr

A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.

edsnlp

Modular, fast NLP framework, compatible with Pytorch and spaCy, offering tailored support for French clinical notes.

asset-aware-mcp

Asset-Aware MCP Server — AI Agent precisely accesses tables, figures, sections from PDFs + .docx round-trip editing (DFM) with 46 tools / 13 resources, segmentation export, layout overlay, OCR preprocessing, knowledge graph (LightRAG)

med-imagetools

Med-Imagetools: Transparent and Reproducible Medical Image Processing Pipelines in Python

pydicom-seg

Python package for DICOM-SEG medical segmentation file reading and writing

deid

best effort anonymization for medical images using python

biomcp-cli

BioMCP: Biomedical Model Context Protocol

paperai

AI for medical and scientific papers

medical-mcps

MCP servers for biological and medical APIs

fuse-med-ml

A python framework accelerating ML based discovery in the medical field by encouraging code reuse. Batteries included :)

labelfusion

Label fusion strategies for multi-class labels.

mikan-rs

A medical image kit for segmentation metrics evaluation

fhir-kindling

Python library to simplify working with FHIR servers and resources.

zensols-mednlp

A natural language medical domain parsing library.

rdm

Our regulatory documentation manager. Streamlines 62304, 14971, and 510(k) documentation for software projects.

delia

DICOM Extraction for Large-scale Image Analysis (DELIA).

llm-medical-guard

Guardrails for LLM-generated medical and health content

medical-ocr

Multi-engine OCR pipeline for medical and legal documents

crashs

CRASHS: Cortical Reconstruction for Automatic Segmentation of Hippocampal Subfields (ASHS)

faker-healthcare-provider

Generate realistic healthcare test data in 6 languages (en, es, pt, zh, fr, de): 150+ diseases with correlated ICD-10 codes, medications, symptoms, and more