Microscope Configurations

YAML configuration templates for QPSC microscope systems.

Part of the QPSC (QuPath Scope Control) system For complete installation instructions, see: https://github.com/uw-loci/QPSC

Overview

This repository contains configuration templates and examples for setting up QPSC with various microscope hardware configurations. These files define microscope-specific settings including hardware components, imaging modalities, autofocus parameters, and image processing settings.

Files

Configuration Templates

Located in the templates/ folder:

• templates/config_template.yml - Comprehensive microscope configuration template with examples for all modality types
• templates/autofocus_template.yml - Autofocus parameter template with detailed documentation
• templates/imageprocessing_template.yml - Image processing settings template (exposure, gain, white balance)

Example Configurations

Located in the root directory:

• config_PPM.yml - PPM (Polarized light) microscope example configuration
• config_CAMM.yml - CAMM (Multi-modal) microscope example configuration

Resources

• resources/resources_LOCI.yml - LOCI hardware component lookup tables (objectives, cameras, etc.)

Usage

For QPSC Users

Recommended: Use the QPSC installation instructions which includes automated setup of configuration templates.

Manual Setup

1. Clone this repository:

   git clone https://github.com/uw-loci/microscope_configurations.git
   cd microscope_configurations

2. Copy and customize a template:

   # Copy the main configuration template
   cp templates/config_template.yml config_my_microscope.yml
   
   # Edit with your hardware settings
   nano config_my_microscope.yml  # or use your preferred editor

3. Configure autofocus (optional):

   cp templates/autofocus_template.yml autofocus_my_microscope.yml
   # Edit autofocus parameters for your objectives

4. Configure image processing (optional):

   cp templates/imageprocessing_template.yml imageprocessing_my_microscope.yml
   # Edit exposure and gain settings for your camera

Configuration Structure

Main Configuration File (config_*.yml)

Defines the complete microscope setup:

microscope:
  name: "Your Microscope Name"
  type: "Multimodal"

modalities:
  ppm_20x:
    type: "ppm"
    angles: [0, 45, 90, 135]
    exposure_ms: 50

hardware:
  objectives:
    - id: "LOCI_4x_001"
      pixel_size_xy_um:
        LOCI_CAMERA_001: 1.105

Autofocus Configuration (autofocus_*.yml)

Defines autofocus parameters per objective:

autofocus_settings:
  LOCI_4x_001:
    interp_strength: 3
    score_metric: "NormalizedVariance"
    num_images: 30
    step_size_um: 50

Image Processing Configuration (imageprocessing_*.yml)

Defines camera settings per modality and camera:

imaging_settings:
  ppm_4x:
    LOCI_CAMERA_001:
      exposure_ms: 50
      gain_dB: 0

Important Notes

• Do NOT commit your custom configurations to this repository - The .gitignore file excludes all .yml files except templates
• Templates are for reference - Copy and customize them for your specific hardware
• LOCI resources - The resources/ folder contains shared hardware definitions used across multiple microscopes

Configuration Guide

For detailed configuration instructions, see the QPSC Configuration Guide.

Support

• Issues: https://github.com/uw-loci/microscope_configurations/issues
• QPSC Documentation: https://github.com/uw-loci/QPSC
• Micro-Manager: https://micro-manager.org/

License

MIT License