cindra

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 cindra-compatible TIFFs, and organizing data directories. Use when the user needs to prepare data for processing, create acquisition parameter files, or convert existing data into cindra-compatible format.

Diagnoses and resolves cindra and cindra-gui MCP server connectivity issues. Covers environment verification, command availability, Python version checks, dependency validation, and conda/pip/uv environment configuration. Use when the cindra or cindra-gui MCP tools are unavailable, when either MCP server fails to start, when the user reports cindra connection issues, or when starting a session that requires the cindra MCP tools.

End-to-end orchestration guide for the cindra neural imaging pipeline and the entry point for cindra work. Covers canonical phase ordering with handoff conditions for the single-recording and multi-recording pipelines, the single-vs-multi-recording decision, dataset planning, and the MCP-first execution model. Use when planning a full processing workflow, deciding which pipeline to run, or orienting at the start of a cindra session.

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 tools for generating configurations and discovering candidates. Use when configuring multi-recording processing or when the user asks about multi-recording configuration parameters.

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 as a tracked dataset, monitor multi-recording batch jobs, re-run a multi-recording processing phase, or when invoking /multi-recording-processing.

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 processing results or when the user asks about multi-recording output data.

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 recordings. Use when configuring single-recording processing or when the user asks about single-recording configuration parameters.

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 single-recording batch pipeline, monitor single-recording batch jobs, re-run a single-recording processing phase, or when invoking /single-recording-processing.

Complete reference for single-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 single-recording processing results or when the user asks about single-recording output data.

Launches and manages cindra GUI viewers for visual inspection of processing results, queries live viewer display state, and guides users through viewer interactions. Covers ROI, tracking, and registration viewers via the cindra-gui MCP server. Use when the user asks to visualize results, inspect ROIs, review registration quality, examine tracking, launch a viewer, or when a processing workflow completes and visual inspection is needed.