用SAM2模型实现肾类器官视频零样本囊肿分析,自动量化生长数据。
Organoid Tracker: A SAM2-Powered Platform for Zero-shot Cyst Analysis in Human Kidney Organoid Videos
- 基于SAM2的零样本分割,无需训练即可识别类器官囊肿。
- 自动计算囊肿形成率、生长速度和形态变化,精度达像素级。
- 无需编程的可视化平台,适合生物学家快速开展药物筛选研究。
类器官模型的进展推动了人类肾脏疾病机制研究与药物发现,实现了无动物实验的可扩展、低成本研究。本文提出针对多囊肾病(PKD)高效筛选优化的肾类器官平台。尽管该系统生成丰富的时空显微视频数据集,现有手动分析方法仍局限于粗略分类(如有效/无效),常忽略像素级与纵向信息。为此,我们开发了Organoid Tracker,一个基于模块化插件架构的图形界面平台,使研究人员无需编程即可提取详细定量指标。平台基于前沿视觉基础模型Segment Anything Model 2(SAM2),实现对时空显微视频的零样本分割与自动化分析,量化囊肿形成率、生长速度及形态变化,并生成完整报告。通过提供可扩展的开源框架,Organoid Tracker为肾脏发育、PKD建模及治疗发现研究提供了强大工具。该平台已公开,源码地址:https://github.com/hrlblab/OrganoidTracker。
原文摘要 · Abstract (English)
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.
Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品;中文卡片由大模型生成,请以原文为准。