Medical Python Packages

medpy

Medical image processing in Python

ngff-zarr

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

biomcp-python

BioMCP: Biomedical Model Context Protocol

medmnist

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

edsnlp

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

torchxrayvision

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

deid

best effort anonymization for medical images using python

biomcp-cli

BioMCP: Biomedical Model Context Protocol

pydicom-seg

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

glam-radiomics

Gray Level Affinity Metrics (GLAM)

med-imagetools

Transparent and reproducible medical image processing pipelines in Python.

afya-mcp

MCP server for Kenya health system — NHIF/SHA coverage, facility finder, CHW services, maternal health. 6 tools.

faker-healthcare-provider

🏥 Faker provider for generating healthcare fake data - diseases, ICD-10, drugs, procedures

crashs

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

ngff-zarr-mcp

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

medical-mcps

A collection of MCP tools for AI agents to interact with major biomedical databases

mikan-rs

A medical image kit for segmentation metrics evaluation

doctoreto-mcp

Unofficial read-only MCP server for Doctoreto (دکترتو), Iran: find doctors, visit fees, free appointment slots, reviews, clinics, labs and offers. For Claude, Cursor and Copilot via uvx.

fhir-kindling

HL7 FHIR client library. Sync and async crud operations against R4 FHIR servers. Resource validation & serialization

delia

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

fuse-med-ml

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

labelfusion

Implementation of various label fusion approaches for medical imaging.

bmlib

Shared Python library for biomedical literature tools — LLM abstraction, quality assessment, transparency analysis, full-text retrieval, publication ingestion, and database utilities.

rdm

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