Medical Python Packages

torchxrayvision

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

ngff-zarr

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

medpy

Medical image processing in Python

edsnlp

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

medmnist

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

biomcp-python

BioMCP: Biomedical Model Context Protocol

pydicom-seg

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

deid

best effort anonymization for medical images using python

glam-radiomics

Gray Level Affinity Metrics (GLAM)

med-imagetools

Transparent and reproducible medical image processing pipelines in Python.

biomcp-cli

BioMCP: Biomedical Model Context Protocol

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)

mikan-rs

A medical image kit for segmentation metrics evaluation

fuse-med-ml

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

zensols-mednlp

Medical natural language parsing and utility library

medical-mcps

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

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).

faker-healthcare-provider

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

crashs

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

ngff-zarr-mcp

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

labelfusion

Implementation of various label fusion approaches for medical imaging.

rdm

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

paperai

AI for medical and scientific papers