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Configuration

SPIMquant is configured through a combination of command-line arguments and a YAML configuration file.

Configuration File Location

The main configuration file is located at:

spimquant/config/snakebids.yml

Basic Configuration

The configuration file defines:

  • Input data specifications
  • Analysis parameters
  • Template settings
  • Segmentation methods
  • Output options

Configuration Structure

# TODO: Add example configuration structure

# BIDS input specification
pybids_inputs:
  spim:
    filters:
      suffix: 'SPIM'
      extension: '.ome.zarr'
    wildcards:
      - subject
      - sample
      - stain

# Analysis parameters
registration:
  template: 'ABAv3'
  method: 'greedy'

segmentation:
  method: 'otsu'
  stains:
    - 'Abeta'
    - 'Iba1'

Template Configuration

SPIMquant supports multiple templates:

  • ABAv3: Allen Brain Atlas v3
  • gubra: Gubra atlas
  • MBMv3: Marmoset Brain Maps v3
  • turone: Turone atlas
  • MouseIn: Mouse MRI template

Segmentation Configuration

Configure segmentation methods and parameters:

# Example configuration
segmentation:
  method: 'threshold'  # or 'otsu+k3i2'
  intensity_correction: 'gaussian'  # or 'n4'

Advanced Configuration

Dask Configuration

Configure parallel processing with Dask:

dask:
  scheduler: 'threads'
  num_workers: 8

Cloud Storage Configuration

Configure S3 or GCS access:

storage:
  s3:
    endpoint: 's3.amazonaws.com'
  gcs:
    project: 'my-project'

Example Configurations

Basic Processing

# Minimal configuration for basic processing

Advanced Workflow

# Configuration for advanced processing with custom parameters

Configuration Validation

SPIMquant validates configuration on startup. Common validation errors:

  • Missing required fields
  • Invalid template names
  • Incorrect file paths

Next Steps