majiayu000 Acquisition System Setup
Guides users through configuring data acquisition systems on local machines. Supports both complete system setup and flexible ad-hoc configuration changes for any supported acquisition system.
Prerequisites
The MCP server must be running. Start it with: sl-configure mcp
Supported Acquisition Systems
| System | Description | Reference |
|---|---|---|
mesoscope |
Two-photon mesoscope imaging system | MESOSCOPE_REFERENCE.md |
Each system has its own reference file documenting all configurable parameters, their purposes, valid ranges, and default values based on actual usage in sl-experiment.
Usage Modes
This skill supports two modes of operation:
Flexible Mode (Default)
For users who want to check or modify specific configuration parameters without following a structured workflow. Use this mode when the user:
- Asks about a specific configuration section (e.g., "What are my camera settings?")
- Wants to update specific parameters (e.g., "Change the lick threshold to 500")
- Needs to reconfigure one aspect of an existing system
- Asks general questions about system configuration
In flexible mode, respond directly to the user's request using the appropriate query or update tools. Refer to the system-specific reference file for parameter details.
Complete Setup Mode
For users setting up a new machine or performing a full system reconfiguration. Use this mode when the user:
- Explicitly asks to "set up" or "configure" the acquisition system from scratch
- Is working with a machine that has no existing configuration
- Asks for a "complete setup" or "full configuration"
In complete setup mode, follow the structured workflow in the Complete Setup Workflow section.
Quick Reference
Check Current Configuration
| What to Check | Tool |
|---|---|
| Working directory | get_working_directory_tool() |
| System overview | get_system_configuration_tool() |
| Available sections | list_system_configuration_sections_tool() |
| Directory paths | get_filesystem_configuration_tool() |
| Google Sheet IDs | get_sheets_configuration_tool() |
| Camera settings | get_cameras_configuration_tool() |
| Microcontroller settings | get_microcontrollers_configuration_tool() |
| External assets | get_external_assets_configuration_tool() |
| Google credentials | get_google_credentials_tool() |
Update Configuration
| What to Update | Tool |
|---|---|
| Working directory | set_working_directory_tool() |
| Create/replace system | create_system_configuration_tool() |
| Directory paths | update_filesystem_configuration_tool() |
| Google Sheet IDs | update_sheets_configuration_tool() |
| Camera settings | update_cameras_configuration_tool() |
| Microcontroller ports | update_microcontroller_ports_tool() |
| Wheel/encoder settings | update_wheel_configuration_tool() |
| Brake calibration | update_brake_configuration_tool() |
| Lick sensor calibration | update_lick_sensor_configuration_tool() |
| Torque sensor calibration | update_torque_sensor_configuration_tool() |
| Valve calibration | update_valve_calibration_tool() |
| Timing parameters | update_timing_configuration_tool() |
| Zaber/MQTT settings | update_external_assets_configuration_tool() |
| Google credentials | set_google_credentials_tool() |
Flexible Mode Guidelines
When operating in flexible mode, follow these guidelines:
Responding to Queries
When the user asks about configuration, query the relevant section and present the information clearly. Refer to the system-specific reference file to explain what each parameter controls.
Responding to Update Requests
When the user wants to change a parameter:
- Confirm you understand what they want to change
- Check the reference file for valid ranges and constraints
- Call the appropriate update tool with the new value(s)
- Confirm the change was successful
Handling Ambiguous Requests
If the user's request is ambiguous, ask for clarification. Reference the system-specific documentation to help guide them to the correct parameter.
Proactive Assistance
When the user modifies one parameter, you may suggest related parameters they might also want to check or update based on the reference documentation, but do not make changes without explicit confirmation.
Complete Setup Workflow
Use this workflow when the user requests a complete system setup.
Workflow Checklist
Acquisition System Setup Progress:
- [ ] Step 1: Check/set working directory
- [ ] Step 2: Check/create acquisition system configuration
- [ ] Step 3: Configure system parameters
- [ ] Step 4: Configure Google credentials
- [ ] Step 5: Verify complete setup
Step 1: Working Directory
Check if configured:
get_working_directory_tool()
If not configured, ask the user for their preferred location and set it:
set_working_directory_tool(directory="/path/to/sun_lab_data")
Step 2: Acquisition System
Check if configured:
get_system_configuration_tool()
If not configured, ask which system type to create:
create_system_configuration_tool(system="mesoscope")
If already configured, ask the user if they want to:
- Keep the current system and proceed to parameter configuration
- Replace with a new configuration
- Skip to Google credentials
Step 3: System Parameters
Show available configuration sections:
list_system_configuration_sections_tool()
For each section the user wants to configure:
- Query current values with the appropriate
get_*tool - Reference the system-specific documentation file to explain parameters
- Ask which parameters they want to change
- Apply changes with the appropriate
update_*tool
Step 4: Google Credentials
Check current status:
get_google_credentials_tool()
If not configured or user wants to replace, ask for the credentials path:
set_google_credentials_tool(credentials_path="/path/to/credentials.json")
Step 5: Verification
Verify all configurations are working:
get_working_directory_tool()
get_system_configuration_tool()
get_google_credentials_tool() # If configured
Configuration Sections Overview
Each acquisition system has these configurable sections:
| Section | Purpose |
|---|---|
| Filesystem | Directory paths for data storage and network mounts |
| Google Sheets | Sheet identifiers for lab records |
| Cameras | Video camera indices and encoding parameters |
| Microcontrollers | USB ports and hardware calibration parameters |
| External Assets | Motor controllers and communication settings |
See the system-specific reference file for detailed parameter documentation including:
- What each parameter controls in practice
- Which sl-experiment component uses it
- Valid ranges and constraints
- Default values and why they matter
Troubleshooting
| Error | Cause | Solution |
|---|---|---|
Unable to resolve the path |
Working directory not configured | Call set_working_directory_tool() |
found 0 files |
No system configuration exists | Call create_system_configuration_tool() |
found N files (N > 1) |
Multiple configuration files exist | Delete extra files, keep only one |
Unable to resolve...credentials file |
Google credentials not set | Call set_google_credentials_tool() |