PySPIM¶

Selective Plane Illumination Microscopy Analysis

Documentation that simply works

Process SPIM data with GPU acceleration – powerful, interactive, and research-ready.

See PySPIM in Action

PySPIM makes advanced SPIM data analysis easy and interactive. Watch this short video to see how you can go from raw data to beautiful results in just a few clicks!

Quick Install¶

Install from git repository

git clone https://github.com/matt-black/pyspim.git
cd pyspim
uv sync --extra dev
uv pip install -e packages/pyspim
uv pip install -e packages/napari-pyspim

Note

PySPIM is currently in development and not yet available on PyPI. Installation requires cloning the repository.

Quick Start¶

Launch PySPIM in napari

# Launch napari
napari

# Navigate to: Plugins → pyspim → pyspim
# This opens the DiSPIM Pipeline interface

Key Features¶

GPU Acceleration - Fast processing with CuPy-powered operations
Interactive Visualization - Seamless napari integration for instant results
Workflow Automation - Batch processing with Snakemake integration
HPC Ready - Built-in SLURM support for cluster computing
Open Source - GPL-3.0 licensed and actively maintained

Documentation¶

Getting Started¶

Installation - Set up PySPIM
Quick Start - Your first workflow
Basic Usage - Step-by-step tutorial

User Guide¶

Examples Overview - Available examples
Fruiting Body Workflow - Complete pipeline
Advanced Features - Advanced techniques

Packages¶

Napari Plugin - Interactive GUI
Core Package - Library reference
API Documentation - Complete API

Development¶

Contributing - How to contribute
License - GPL-3.0 License