automation

Ataraxis

Bridging AI Coding Assistants and Scientific Hardware

Ataraxis is an open-source framework that enables AI coding assistants to interact with laboratory hardware. It provides optimized hardware interface libraries, Model Context Protocol (MCP) servers for structured device discovery, and domain-specific skills that encode expert workflows. AI agents use these components to generate efficient data acquisition pipelines, configure systems, and troubleshoot hardware issues.

Core Insight: AI assistance operates at configuration time while runtime data acquisition remains deterministic and AI-independent. This separation ensures that network latency, API rate limits, or model errors never disrupt a running experiment.

Authored by Ivan Kondratyev. Copyright: 2026, NeuroAI Lab, Cornell University.

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Features

Hardware Discovery & Validation

• MCP-based device enumeration: AI agents can query connected cameras, microcontrollers, and motor controllers through structured tool interfaces.
• Pre-session diagnostics: Validate hardware connectivity and configuration through natural language queries.
• Real-time status checking: Query device responsiveness, serial port status, and camera capabilities without manual debugging loops.

Optimized Hardware Interfaces

• High-speed camera acquisition: Support for OpenCV and GeniCam cameras with real-time FFMPEG encoding (CPU/GPU).
• Microcontroller communication: Bidirectional serial communication with Arduino and Teensy boards at microsecond speeds.
• Precision timing: Microsecond-accurate timers using C++ chrono library bindings.
• Inter-process data sharing: Thread-safe shared memory arrays and scalable data logging.

AI-Assisted Development

• Code generation: AI agents generate hardware interface code following established patterns.
• Configuration management: Interactive experiment configuration using task templates.
• Domain-specific skills: Reusable workflows for camera interfaces, microcontroller modules, and system health checks.
• Cross-repository coordination: Skills encode knowledge spanning multiple interdependent libraries.

Deterministic Runtime

• Static acquisition pipelines: Experiments run independently of AI systems.
• Validated configurations: Pre-runtime parameter validation ensures reliable data collection.
• Reproducible execution: Configuration files capture complete experimental setups.

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Architecture

┌─────────────────────────────────────────────────────────────────────────────┐
│                           Ataraxis Architecture                             │
├─────────────────────────────────┬───────────────────────────────────────────┤
│       Configuration Time        │           Runtime (No AI)                 │
├─────────────────────────────────┼───────────────────────────────────────────┤
│                                 │                                           │
│    ┌─────────────────────┐      │      ┌─────────────────────────┐          │
│    │  AI Agent (Claude)  │      │      │ Static Acquisition      │          │
│    └──────────┬──────────┘      │      │ Pipelines               │          │
│               │                 │      └────────────┬────────────┘          │
│               ▼                 │                   │                       │
│    ┌─────────────────────┐      │                   ▼                       │
│    │  Skills & MCP       │      │      ┌─────────────────────────┐          │
│    │  Discovery Tools    │ ─────┼────▶│ Ataraxis Libraries      │          │
│    └──────────┬──────────┘      │      └────────────┬────────────┘          │
│               │                 │                   │                       │
│               ▼                 │                   ▼                       │
│    ┌─────────────────────┐      │      ┌─────────────────────────┐          │
│    │  Config Files &     │      │      │ Physical Hardware       │          │
│    │  Pipeline Code      │      │      └────────────┬────────────┘          │
│    └─────────────────────┘      │                   │                       │
│                                 │                   ▼                       │
│                                 │      ┌─────────────────────────┐          │
│                                 │      │ Session Data & Logs     │          │
│                                 │      └─────────────────────────┘          │
└─────────────────────────────────┴───────────────────────────────────────────┘

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Libraries

Core Infrastructure