User Guide#
Welcome to the user guide for photon-mosaic-pipeline.
This guide walks you through installation, configuration and basic usage of Snakemake.
🏗️ Installation
How to install photon-mosaic-pipeline and its dependencies.
📁 Configuration
How to configure photon-mosaic-pipeline for your specific needs.
📁 Snakemake tutorial
Basic Snakemake tutorial to get you started.
🔄 Preprocessing
Learn about the preprocessing steps available in photon-mosaic-pipeline.
🗂️ Data input
How to organise raw data in NeuroBlueprint format and filter which TIFFs the pipeline processes.