Pre- and Post-Treatment Glioma Segmentation with the Medical Imaging Segmentation Toolkit

TL;DR

The paper introduces the Medical Imaging Segmentation Toolkit (MIST), a flexible, modular tool for standardized and customizable glioma segmentation, enabling rapid experimentation and improved results in the BraTS 2025 challenge.

Contribution

It presents an extensible, open-source toolkit with advanced postprocessing capabilities tailored for glioma segmentation challenges.

Findings

MIST's postprocessing improves segmentation quality.

Flexible transforms enable tailored strategies.

Strategies ranked effectively in BraTS 2025 challenge.

Abstract

Medical image segmentation continues to advance rapidly, yet rigorous comparison between methods remains challenging due to a lack of standardized and customizable tooling. In this work, we present the current state of the Medical Imaging Segmentation Toolkit (MIST), with a particular focus on its flexible and modular postprocessing framework designed for the BraTS 2025 pre- and post-treatment glioma segmentation challenge. Since its debut in the 2024 BraTS adult glioma post-treatment segmentation challenge, MIST's postprocessing module has been significantly extended to support a wide range of transforms, including removal or replacement of small objects, extraction of the largest connected components, and morphological operations such as hole filling and closing. These transforms can be composed into user-defined strategies, enabling fine-grained control over the final segmentation output. We evaluate three such strategies - ranging from simple small-object removal to more complex, class-specific pipelines - and rank their performance using the BraTS ranking protocol. Our results highlight how MIST facilitates rapid experimentation and targeted refinement, ultimately producing high-quality segmentations for the BraTS 2025 challenge. MIST remains open source and extensible, supporting reproducible and scalable research in medical image segmentation.