Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 2606.02080

Agentic-J: An AI Agent for Biological Microscopy Image Analysis

Lukas Johanns·Marilin Moor·Davide Panzeri·Yu Zhou·Xinyi Chen·Nora F. K. Pauly·Zixuan Pan·Matthias Gunzer·Andreas Müller·Yiyu Shi·Hedi Peterson·Jianxu Chen
View original source ↗Read source document ↗Export metadata ↓

Abstract

Biological image analysis increasingly demands integration across heterogeneous tools, programming environments, and domain knowledge that few researchers can command simultaneously. We present Agentic-J, a containerised, multi-agent AI assistant, primarily for ImageJ/Fiji that enables biologists to specify analysis tasks in natural language, from nuclei segmentation and cell tracking to multi-condition quantification. The agent generates executable scripts organised into a documented project structure, so every analysis decision is traceable and the workflow can be reproduced or shared. The specialised sub-agents handle plugin management, code generation, debugging, quality assurance, and statistical reporting. In this paper we introduce the system's design, demonstrate real biological microscopy image analysis workflows, and detailed the technical implementation.

Explore related subjects

cs.MAcs.AIcs.CV

Keep this discovery

BibTeXRIS

Lukas Johanns, Marilin Moor, Davide Panzeri, Yu Zhou, Xinyi Chen, Nora F. K. Pauly, Zixuan Pan, Matthias Gunzer, Andreas Müller, Yiyu Shi, Hedi Peterson, Jianxu Chen. 2026-06-01. Agentic-J: An AI Agent for Biological Microscopy Image Analysis. https://arxiv.org/abs/2606.02080

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Evaluating Scaffolding-Oriented Multi-Agent Large Language Model System for Clinical Interview Training

Clinical education must prepare medical students to conduct safe and coherent patient interviews under conditions of uncertainty. Traditional standardized patient (SP) training is resource-intensive and difficult to scale. We developed a scaffolding-oriented multi-agent Large Language Model (LLM) AI Standardized Patient (AI-SP) training platform1. The system includes a patient agent for simulated dialog, a tutor agent providing Socratic prompts without disclosing diagnostic information, and a turn-level evaluator agent that monitors clinical progress without revealing summative scores. In a randomized controlled study (N = 100 medical students), participants were assigned to either a multi-agent (MA) scaffolding condition or a control condition. All students completed two learning sessions under their assigned condition followed by an examination conducted in a patient only environment. Performance was assessed using a standardized Objective Structured Clinical Examination (OSCE) based rubric. While no significant difference was observed in final diagnostic accuracy between groups, the multi-agent AI standardized patient system improved final examination scores compared to the control group utilizing structured progressive information disclosure; the most substantial and consistent improvements were observed in communication, the expression of empathy, and specific history-taking behaviors. These findings suggest that specialized LLM agents enhance the process quality of simulated clinical interviews without artificially inflating examination outcomes. To support future research, we release a multi-expert annotated dataset comprising transcripts, checklist annotations, turn-level evaluations, and OSCE-aligned scoring outcomes. This resource aims to facilitate the development of pedagogically grounded AI-SP systems and advance research on AI-supported clinical reasoning training.

cs.MA↗
arXiv2026

But How Would AI Agents Run a Town's Economy?

We placed 100 memory-equipped large language model (LLM) agents in charge of a closed, money-conserving spatial economy on real Pokhara Lakeside geography (earning wages, running businesses, setting prices) and ran this multi-agent simulation for up to 26 simulated weeks, well past the 1-2 weeks typical of agent-society studies. Across 91 validated runs (2.44M agent decisions, 21.5B tokens), the money stops moving, in a specific and measurable way. A 12x tourist demand shock raises business revenue 4.62x ($p<0.001$), which we decompose exactly into a 1.50x extensive margin (more businesses trading) and a 3.07x intensive margin (more revenue each). Monetary transmission stops there. Wages move 1.03x ($p=0.42$); 0.3% of 3,981 menu items are ever repriced ($p=0.47$). A randomized cash transfer (NPR 5,000 to 20 of 100 agents) shows the same pattern from the opposite direction: 96.7% is still held 311 pulses later, marginal propensity to consume 3-4% by two independent measures, indistinguishable from zero. The wealth distribution is consequently near-frozen at the horizon this literature uses ($\rho=0.964$ over 2 simulated weeks), but not frozen. $\rho$ falls to 0.832 at 12 weeks and 0.752 at 26, a horizon-dependence no short study can see. Matched ablations show which knob actually matters. Swapping the backing LLM moves every outcome we measure ($p=0.0039$); deleting agents' memory moves none of them detectably. A purely social tool fails 94-97% of the time across two model families, compared with ~96% success on economic tools, with no measurable shift away from it. Every headline number is verified twice, by a live validator and by an offline recomputation that reconciles each agent's wealth against its own signed transaction history, and we release the full run corpus for reanalysis.

cs.MA↗
arXiv2026

ORCH: Organizational Principles Enable Collective Intelligence in Embodied AI

Collective intelligence depends not only on the capabilities of individual members, but also on how those members are organized. Yet artificial multi-agent systems are typically assembled using fixed organizational structures, even when the physical tasks they perform impose fundamentally different coordination requirements. Here we show that principles from human organization theory can be operationalized to organize large, heterogeneous collectives of embodied artificial agents. We introduce ORCH (Organizing Roles and Coordination Hierarchies), which constructs task-specific hierarchical organizations by combining pooled interdependence for work that can proceed concurrently with sequential interdependence for work governed by prerequisite relationships. Across 25 wildfire-response missions spanning reconnaissance, rescue, transportation, resource management, containment and suppression, we evaluated teams of up to 50 heterogeneous agents using eight large language models. Organizations constructed using these principles consistently outperformed four representative embodied multi-agent approaches across mission outcome, execution efficiency, exploration and computational resource use. Human-designed ORCH organizations improved final score by 63.97% and execution efficiency by 74.29% on average relative to the four prior frameworks. Organizations generated automatically by language models improved these measures by 43.63% and 52.53%, respectively. These advantages persisted across missions and underlying language models. Notably, collective performance was not monotonically determined by model scale. Analysis of long-horizon missions showed that hierarchical organization enabled teams to preserve concurrent activity within specialized groups while coordinating ordered transitions between mission phases.

cs.MA↗