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

arXiv: https://arxiv.org/abs/2507.19626 · HTML: https://mlsanity.com/paper/2507.19626/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 27 references that are in the map.
- First posted on arXiv 25 Jul 2025.

## Builds on (most cited first, 18 of 18)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [nnU-Net Revisited: A Call for Rigorous Validation in 3D Medical Image Segmentation](https://mlsanity.com/paper/2404.09556/) (2024)
- [Boundary loss for highly unbalanced segmentation](https://mlsanity.com/paper/1812.07032/) (2018)
- [nnU-Net for Brain Tumor Segmentation](https://mlsanity.com/paper/2011.00848/) (2020)
- [MedPerf: Open Benchmarking Platform for Medical Artificial Intelligence using Federated Evaluation](https://mlsanity.com/paper/2110.01406/) (2021)
- [The 2024 Brain Tumor Segmentation (BraTS) Challenge: Glioma Segmentation on Post-treatment MRI](https://mlsanity.com/paper/2405.18368/) (2024)
- [A Generalized Surface Loss for Reducing the Hausdorff Distance in Medical Imaging Segmentation](https://mlsanity.com/paper/2302.03868/) (2023)
- [PocketNet: A Smaller Neural Network for Medical Image Analysis](https://mlsanity.com/paper/2104.10745/) (2021)
- [MIST: A Simple and Scalable End-To-End 3D Medical Imaging Segmentation Framework](https://mlsanity.com/paper/2407.21343/) (2024)

## Abstract (arXiv)

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.