Problem
Research questions and friction points this paper is trying to address.
organoid analysis
manual segmentation
quantitative statistical analysis
experimental biologists
MorphoOrgaAgent: A Foundation-Model-Based Multi-Agent System for Autonomous Organoid Analysis
🤖 AI Summary
为解决手动分割类器官耗时费力及分析需定制编码的问题，MorphoOrgaAgent通过多代理系统实现了零样本分割、自动化数据分析和报告生成。
📝 Abstract
Organoids are three-dimensional tissue models whose morphology provides important insights into tumor development, disease progression, and drug testing. Extracting these morphological features relies heavily on manual segmentation, which is time-consuming and labor-intensive. Furthermore, performing quantitative statistical analysis typically requires custom coding skills and a mathematical background, presenting a major barrier for experimental biologists. To address these challenges, we introduce MorphoOrgaAgent, a multi-agent framework that achieves zero-shot organoid segmentation, automated data analysis, and report generation based on natural language input. The framework consists mainly of three core components: a TaskUnderstandingAgent that identifies requested measurements and visualization types; a hybrid segmentation module that combines Cellpose-derived geometric prompts with text prompts to guide SAM3 for zero-shot organoid instance segmentation; and a ReportAgent that computes quantitative metrics and compiles them alongside generated visualizations into a structured report. We further introduce MorphoOrgaVQA, a benchmark designed for quantitative evaluation of agent systems in organoid morphology analysis. Experimental results demonstrate that MorphoOrgaAgent handles both explicit and descriptive user requests, produces measurements closely matching ground truth, and generates complete analysis reports without requiring manual programming. The complete source code and MorphoOrgaVQA benchmark are publicly available at https://github.com/peng-lab/MorphoOrgaAgent.
Innovation
Methods, ideas, or system contributions that make the work stand out.
zero-shot organoid segmentation
automated data analysis
natural language input
hybrid segmentation module
MorphoOrgaVQA
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