| name | cindra-pipeline |
| description | 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. |
| user-invocable | true |
Cindra pipeline
End-to-end orchestration reference and entry point for cindra neural imaging processing, covering both the
single-recording and multi-recording pipelines, their phase ordering, handoff conditions, and decision guidance.
Scope
Covers:
- The single-vs-multi-recording decision and when each pipeline applies
- Canonical phase ordering with handoff conditions for both pipelines
- Multi-recording dataset planning (grouping, dataset names, prerequisite chain)
- The MCP-first execution model and where the CLI fits
- Quick-start references that dispatch to the phase-specific skills
Does not cover:
- Detailed tool usage, parameters, or troubleshooting for any phase (see the phase-specific skills below)
- Configuration parameter reference (see
/single-recording-configuration, /multi-recording-configuration)
- Output data formats (see
/single-recording-results, /multi-recording-results)
- MCP server connectivity (see
/cindra-mcp-environment-setup)
Handoff rules: This skill dispatches to phase-specific skills at each stage. Always invoke the relevant skill
for detailed tool usage, parameter reference, and troubleshooting. This skill owns the cross-phase map and the
single-vs-multi decision only — not the work performed within any single phase.
Single-vs-multi-recording decision
Cindra provides two pipelines. Determine which the user needs before planning any work.
Does the goal require tracking the SAME ROIs across multiple recordings (e.g. cross-day longitudinal analysis)?
NO → Single-recording pipeline (within-recording ROI detection and signal extraction). Run once per recording.
YES → Multi-recording pipeline (cross-recording ROI tracking). Requires >= 2 recordings, each of which must
ALREADY be fully single-recording processed first.
The multi-recording pipeline is not a replacement for the single-recording pipeline — it is a second stage that
consumes single-recording outputs. Every recording in a multi-recording dataset must complete all three
single-recording phases before multi-recording processing can run.
Single-recording pipeline
Environment Acquisition Configuration Processing Results Visual
Setup → Data Prep → → → → Inspection
| | | | | |
/cindra-mcp- /acquisition- /single- /single- /single- /visualization
environment- data- recording- recording- recording-
setup preparation configuration processing results
Phase 1: Environment setup
- Skill:
/cindra-mcp-environment-setup
- Actions: Verify the cindra MCP server is connected and the
cindra command is available
- Handoff condition: cindra MCP tools are accessible
- Skip condition: MCP already verified in this session
Phase 2: Acquisition data preparation
- Skill:
/acquisition-data-preparation
- Actions: Create and validate
cindra_parameters.json, confirm TIFF layout, run
validate_recording_readiness_tool
- Handoff condition:
validate_recording_readiness_tool reports the recording ready
- Skip condition: Recording already binarized or beyond (confirm via
get_recording_status_tool)
Phase 3: Configuration
- Skill:
/single-recording-configuration
- Actions: Generate a template configuration with
generate_config_file_tool, set main.tau and
main.two_channels, validate with validate_config_file_tool
- Handoff condition: A validated template configuration file exists (one template can serve many recordings)
Phase 4: Processing
- Skill:
/single-recording-processing
- Actions: Prepare and execute the three-phase pipeline (binarize, process, combine) via the MCP execution tools
- Handoff condition: All recordings report
completed; verify_single_recording_output_tool returns
complete: true
Phase 5: Results
- Skill:
/single-recording-results
- Actions: Verify output completeness and query metadata, registration quality, ROI statistics, and traces
- Handoff condition: Outputs verified; metrics reviewed
Phase 6: Visual inspection
- Skill:
/visualization
- Actions: Launch the ROI and registration viewers to inspect detection and motion-correction quality
Multi-recording pipeline
Prerequisite: every recording in the dataset has completed all three single-recording phases (Phases 1-5 above).
Single-Recording Configuration Processing Results Visual
Complete (all) → → → → Inspection
| | | | |
(see single- /multi- /multi- /multi- /visualization
recording recording- recording- recording-
pipeline) configuration processing results
Phase 1: Configuration
- Skill:
/multi-recording-configuration
- Actions: Generate a multi-recording template configuration, set ROI selection and registration/tracking
parameters, validate it
- Handoff condition: A validated multi-recording template configuration file exists
Phase 2: Processing
- Skill:
/multi-recording-processing
- Actions: Confirm all recordings are single-recording complete, group recordings into datasets, resolve
dataset names with
resolve_dataset_name_tool, then prepare and execute the two-phase pipeline (discover,
extract)
- Handoff condition: All datasets report
completed; verify_multi_recording_output_tool returns
complete: true
Phase 3: Results
- Skill:
/multi-recording-results
- Actions: Verify output completeness and query dataset overview, cross-recording registration quality,
tracking summary, and cross-recording traces
- Handoff condition: Outputs verified; tracking reviewed
Phase 4: Visual inspection
- Skill:
/visualization
- Actions: Launch the tracking and ROI viewers to confirm backward-deformed templates overlap the same
structures across recordings (the only reliable cross-day registration-quality check)
Multi-recording dataset planning
A dataset is a named group of recordings tracked together. Plan datasets before preparing a multi-recording batch.
- Prerequisite chain: If any recording is not single-recording complete, route to the earliest missing step:
/acquisition-data-preparation → /single-recording-configuration → /single-recording-processing.
- Grouping: Group recordings by common parent directory, explicit user grouping, or semantic analysis of
recording paths. Each group becomes one dataset.
- Dataset names: Call
resolve_dataset_name_tool once per group to construct a unique qualified name from a
shared base name and a per-batch specifier. See /multi-recording-processing for the full workflow.
There is no separate multi-recording data-preparation skill: multi-recording input preparation is simply
"single-recording processing complete," so raw-data preparation is handled entirely by the single-recording
pipeline. This asymmetry is intentional.
Execution interface
Cindra is MCP-first for agentic work. Every phase skill mandates the cindra MCP tools for its operations and routes
to /cindra-mcp-environment-setup when they are unavailable.
| Operation | Use |
|---|
| Discovery, configuration, processing | cindra MCP tools (cindra-mcp server) via the phase skills |
| Results querying and output verification | cindra MCP tools (cindra-mcp server) via the results skills |
| Viewer lifecycle and live display state | cindra-gui MCP tools (cindra-gui server) via /visualization |
The cindra and cindra-gui CLIs (cindra run, cindra-gui roi, etc.) exist for manual, non-agentic execution.
Do not drive the pipeline through the CLI or direct Python imports during agentic work — use the MCP tools so
resource management, prerequisite validation, and phase sequencing are handled consistently.
Quick-start scenarios
Single recording, first run
/cindra-mcp-environment-setup — verify MCP connectivity (if first session)/acquisition-data-preparation — create and validate cindra_parameters.json/single-recording-configuration — generate and validate a template configuration/single-recording-processing — run binarize, process, combine/single-recording-results — verify and review outputs/visualization — inspect ROIs and registration
Batch of recordings sharing parameters
/single-recording-configuration — create one reusable template configuration/single-recording-processing — pass the same template path for all recordings in one batch/single-recording-results — verify each recording's outputs/visualization — spot-check representative recordings
Cross-day ROI tracking
- Confirm every recording is single-recording complete (run the single-recording pipeline first if not)
/multi-recording-configuration — create the multi-recording template configuration/multi-recording-processing — group into datasets, resolve dataset names, run discover and extract/multi-recording-results — verify tracking outputs/visualization — confirm tracking quality across recordings
Related skills
| Skill | Relationship |
|---|
/cindra-mcp-environment-setup | Phase 1 (both pipelines): MCP server connectivity |
/acquisition-data-preparation | Single-recording phase 2: raw data preparation |
/single-recording-configuration | Single-recording phase 3: configuration reference |
/single-recording-processing | Single-recording phase 4: processing orchestration |
/single-recording-results | Single-recording phase 5: output verification and querying |
/multi-recording-configuration | Multi-recording phase 1: configuration reference |
/multi-recording-processing | Multi-recording phase 2: processing orchestration |
/multi-recording-results | Multi-recording phase 3: output verification and querying |
/visualization | Final phase (both pipelines): visual inspection of results |
Proactive behavior
You SHOULD proactively invoke this skill when:
- A cindra session begins and the user's goal spans multiple pipeline phases
- The user is unsure whether they need single-recording or multi-recording processing
- The user describes an end-to-end goal ("process and inspect my data") without naming a specific phase
Verification checklist
Cindra Pipeline Orchestration:
- [ ] Pipeline selected (single-recording vs multi-recording) for the user's goal
- [ ] Environment verified (cindra MCP server connected)
- [ ] For multi-recording: all recordings confirmed single-recording complete
- [ ] Phases executed in canonical order with each handoff condition met
- [ ] Detailed work delegated to the phase-specific skill at every stage
- [ ] Outputs verified via the results skill before visual inspection
- [ ] Visual inspection performed for the relevant viewers
