Medical Imaging Segmentation Toolkit

About

The Medical Imaging Segmentation Toolkit (MIST) is a simple, scalable, and end-to-end 3D medical imaging segmentation
framework. MIST allows researchers to seamlessly train, evaluate, and deploy state-of-the-art deep learning models for 3D
medical imaging segmentation.

Please cite the following papers if you use this code for your work:

A. Celaya et al., "PocketNet: A Smaller Neural Network For Medical Image Analysis," in IEEE Transactions on Medical Imaging, doi: 10.1109/TMI.2022.3224873.

A. Celaya et al. "MIST: A Simple and Scalable End-To-End 3D Medical Imaging Segmentation Framework," arXiv preprint arXiv:2407.21343

Documentation

Please see our Read the Docs page here.

What's New

• September 2025 - MIST takes 3rd place (repeat) in BraTS 2025 adult glioma challenge @ MICCAI 2025
• November 2024 - MedNeXt models (small, base, medium, and large) added to MIST.
  These models can be called with --model mednext-<small, base, medium, large>.
• October 2024 - MIST takes 3rd place in BraTS 2024 adult glioma challenge @ MICCAI 2024!