Sun-Lab-NBB

Guides creation and configuration of MicroControllerInterface, ModuleInterface, and MQTTCommunication instances for microcontroller communication. Covers interface initialization and lifecycle, ModuleInterface subclassing with command and parameter sending,…

Guides creation and configuration of VideoSystem instances for camera acquisition. Covers constructor parameters, lifecycle methods, system ID allocation, and encoding selection. Use when writing code that creates VideoSystem instances or needs to understand…

Canonical reference for the human-facing axci command-line interface. Covers every command and option with its short form, long form, type, default, and effect, the MCP tool each command maps to, its failure modes, and how the CLI path diverges from the MCP…

Orchestrates batch log processing via the ataraxis-communication-interface MCP server: archive discovery, batch preparation, job execution, progress monitoring, cancellation, and error recovery. Use when processing microcontroller log archives, extracting…

Documents the human-facing axvs command-line interface. Covers every command and option with its short form, long form, type, default, and effect, the MCP tool each command maps to, its failure modes, and how the CLI path diverges from the MCP path. Use when…

Orchestrates batch log processing via the ataraxis-video-system MCP server: archive discovery, batch preparation, job execution, progress monitoring, cancellation, and error recovery. Use when processing camera log archives, extracting frame timestamps, or…

Guides use of ataraxis-video-system MCP tools for camera discovery, runtime verification, interactive video session testing, and GenICam camera configuration. Use when discovering connected cameras, verifying system encoding requirements, testing camera…

Documents the input data format required by the log processing pipeline: NPZ log archives produced by DataLogger and assemble_log_archives, source ID semantics, multi-logger recording structures, and archive internal layout. Use when the user asks about…

Guides agents through preparing raw imaging data for cindra processing. Covers creating and validating cindra_parameters.json acquisition parameter files, gathering acquisition metadata from users, converting data from common microscope formats into…

Orchestrates the cindra neural imaging pipeline end to end and serves as the entry point for cindra work. Covers canonical stage ordering with handoff conditions for the single-recording and multi-recording pipelines, the single-vs-multi-recording decision,…

Documents the human-facing cindra and cindra-gui command-line interfaces. Covers every command and option with its short form, long form, type, default, and effect, the MCP tool each command maps to, its failure modes, and how the CLI path diverges from the…

Complete reference for multi-recording pipeline configuration parameters, prerequisites, and MCP configuration tools. Documents all 7 configuration sections, parameter meanings, default values, prerequisites from single-recording processing, and available MCP…

Orchestrates multi-recording neural imaging batch processing via the cindra MCP server, dispatching to configuration and results skills as needed. Use when the user asks to run multi-recording (cross-day ROI tracking) processing, process multiple recordings…

Complete reference for multi-recording pipeline output data formats. Documents every file, directory, array shape, dtype, and NPZ key produced by the pipeline, plus verification checklists for output completeness. Use when evaluating multi-recording…

Complete reference for single-recording pipeline configuration parameters and MCP configuration tools. Documents all 9 configuration sections, parameter meanings, default values, and available MCP tools for generating configurations and discovering…

Orchestrates single-recording neural imaging batch processing via the cindra MCP server, dispatching to acquisition-preparation, configuration, and results skills as needed. Use when the user asks to process single-recording imaging data, run the…