API Documentation

API reference for SPIMquant Python modules.

Main Modules

spimquant.run

Main entry point for the SPIMquant CLI.

spimquant.workflow

Snakemake workflow definitions.

Scripts

Registration Scripts

Segmentation Scripts

Quantification Scripts

Using the API

# Example: Using SPIMquant programmatically
# TODO: Add Python API examples

Next Steps

• Configuration Options
• Workflow Rules