Owl-AuraID 1.0: An Intelligent System for Autonomous Scientific Instrumentation and Scientific Data Analysis

We present Experiment Automation Agents (EAA), a vision-language-model-driven agentic system designed to automate complex experimental microscopy workflows. EAA integrates multimodal reasoning, tool-augmented action, and optional long-term memory to support both autonomous procedures and interactive user-guided measurements. Built on a flexible task-manager architecture, the system enables workflows ranging from fully agent-driven automation to logic-defined routines that embed localized LLM queries. EAA further provides a modern tool ecosystem with two-way compatibility for Model Context Protocol (MCP), allowing instrument-control tools to be consumed or served across applications. We demonstrate EAA at an imaging beamline at the Advanced Photon Source, including automated zone plate focusing, natural language-described feature search, and interactive data acquisition. These results illustrate how vision-capable agents can enhance beamline efficiency, reduce operational burden, and lower the expertise barrier for users.

The automation of scientific research workflows has emerged as a transformative frontier in artificial intelligence, yet existing autonomous research agents remain largely domain-agnostic, lacking the specialized reasoning, method selection, and data acquisition capabilities required for rigorous spatial data science. This paper introduces NORA (Night Owl Research Agent), a harness-engineered, multi-agent autonomous research system purpose-built for GIScience and spatial data science. NORA orchestrates the complete research lifecycle through a skills-first architecture comprising 21 domain-specialized workflow skills, 9 specialist sub-agents, and custom Model Context Protocol (MCP) servers. Central to the system's design are two novel domain-specialized skills: a spatial analysis skill unit that encodes decision frameworks for exploratory spatial data analysis, spatial regression, and diagnostics; and a spatial data download skill that supports reproducible acquisition from authoritative geospatial data sources. We formalize the concept of harness engineering for scientific research agents, demonstrating how lifecycle hooks, safety gates, generator-evaluator separation, human-in-the-loop, and state persistence ensure reliable and reproducible autonomous research. We evaluate NORA through case studies by 6 domain specialists and 3 LLM reviewers across seven dimensions (novelty, quality, rigor, etc). Results demonstrate that domain-specialized harness engineering substantially improves the efficiency and quality of research output compared to general-purpose agent configurations.

A language-model agent asked to analyse an experiment will usually return working code. Whether the analysis is defensible is a different question. A defensible analysis depends on procedural choices: which test the field accepts, which identifier namespace is authoritative, and which caveats must accompany a result. We present Scientific Agent Skills, an open library of 163 such procedures in 16 areas of practice, including genomics, cheminformatics, medical imaging, study design and scientific communication. Each skill is a directory built around a versioned, human-readable instruction file. An agent loads the file only when a task calls for it; the directory often also contains reference material and runnable scripts. We report no task-level evaluation and no host selection rate. We measure two properties of the documentation corpus: the always-resident descriptions of all 163 skills cost 7.1% of a 200,000-token window, and the median documented workflow fits within 23.9% of it, although 29 of 46 would overflow if every reference file were loaded. Openly licensed and available at https://github.com/K-Dense-AI/scientific-agent-skills.