# Organoid Tracker: A SAM2-Powered Platform for Zero-shot Cyst Analysis in Human Kidney Organoid Videos

arXiv: https://arxiv.org/abs/2509.11063 · HTML: https://mlsanity.com/paper/2509.11063/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 4 of its 11 references that are in the map.
- First posted on arXiv 14 Sep 2025.

## Builds on (most cited first, 4 of 4)

- [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)
- [Segment Anything in Medical Images and Videos: Benchmark and Deployment](https://mlsanity.com/paper/2408.03322/) (2024)
- [Unleashing the Potential of SAM2 for Biomedical Images and Videos: A Survey](https://mlsanity.com/paper/2408.12889/) (2024)

## Abstract (arXiv)

Recent advances in organoid models have revolutionized the study of human kidney disease mechanisms and drug discovery by enabling scalable, cost-effective research without the need for animal sacrifice. Here, we present a kidney organoid platform optimized for efficient screening in polycystic kidney disease (PKD). While these systems generate rich spatial-temporal microscopy video datasets, current manual approaches to analysis remain limited to coarse classifications (e.g., hit vs. non-hit), often missing valuable pixel-level and longitudinal information. To help overcome this bottleneck, we developed Organoid Tracker, a graphical user interface (GUI) platform designed with a modular plugin architecture, which empowers researchers to extract detailed, quantitative metrics without programming expertise. Built on the cutting-edge vision foundation model Segment Anything Model 2 (SAM2), Organoid Tracker enables zero-shot segmentation and automated analysis of spatial-temporal microscopy videos. It quantifies key metrics such as cyst formation rate, growth velocity, and morphological changes, while generating comprehensive reports. By providing an extensible, open-source framework, Organoid Tracker offers a powerful solution for improving and accelerating research in kidney development, PKD modeling, and therapeutic discovery. The platform is publicly available as open-source software at https://github.com/hrlblab/OrganoidTracker.