# Interactive Medical-SAM2 GUI: A Napari-based semi-automatic annotation tool for medical images

arXiv: https://arxiv.org/abs/2602.22649 · HTML: https://mlsanity.com/paper/2602.22649/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 6 of its 28 references that are in the map.
- First posted on arXiv 26 Feb 2026.

## Builds on (most cited first, 6 of 6)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [SAM 2: Segment Anything in Images and Videos](https://mlsanity.com/paper/2408.00714/) (2024)
- [Medical SAM 2: Segment medical images as video via Segment Anything Model 2](https://mlsanity.com/paper/2408.00874/) (2024)
- [MONAI Label: A framework for AI-assisted Interactive Labeling of 3D Medical Images](https://mlsanity.com/paper/2203.12362/) (2022)
- [DeepEdit: Deep Editable Learning for Interactive Segmentation of 3D Medical Images](https://mlsanity.com/paper/2305.10655/) (2023)

## Abstract (arXiv)

Interactive Medical-SAM2 GUI is an open-source desktop application for semi-automatic annotation of 2D and 3D medical images. Built on the Napari multi-dimensional viewer, box/point prompting is integrated with SAM2-style propagation by treating a 3D volume as a slice sequence, enabling mask propagation from sparse prompts using Medical-SAM2 on top of SAM2. Voxel-level annotation remains essential for developing and validating medical imaging algorithms, yet manual labeling is slow and expensive for 3D scans, and existing integrations frequently emphasize per-slice interaction without providing a unified, cohort-oriented workflow for navigation, propagation, interactive correction, and quantitative export in a single local pipeline. To address this practical limitation, a local-first Napari workflow is provided for efficient 3D annotation across multiple studies using standard DICOM series and/or NIfTI volumes. Users can annotate cases sequentially under a single root folder with explicit proceed/skip actions, initialize objects via box-first prompting (including first/last-slice initialization for single-object propagation), refine predictions with point prompts, and finalize labels through prompt-first correction prior to saving. During export, per-object volumetry and 3D volume rendering are supported, and image geometry is preserved via SimpleITK. The GUI is implemented in Python using Napari and PyTorch, with optional N4 bias-field correction, and is intended exclusively for research annotation workflows. The code is released on the project page: https://github.com/SKKU-IBE/Medical-SAM2GUI/.