SPIMquant Documentation

Welcome to the documentation for SPIMquant, a Snakemake-based BIDS app for quantitative analysis of SPIM (lightsheet) brain data.

Overview

SPIMquant performs automated nonlinear template registration and quantification of pathology from SPIM microscopy datasets. It bridges the gap between raw microscopy data and quantitative brain analysis through a robust, scalable workflow.

Key Features

• Deformable Registration: High-quality template registration using greedy and ANTs
• Atlas-Based Quantification: Automated quantification of pathology using brain atlases
• High-Resolution Crops: Create Imaris dataset crops from atlas region bounding boxes
• Group-Level Statistics: Statistical analysis with contrast comparisons across experimental groups
• Parallelization: Efficient processing using Snakemake and Dask for both coarse and fine-grained tasks
• Cloud Support: Direct reading from cloud-based object storage (S3, GCS)
• Scalable Processing: Simple deployment on cloud infrastructure with Coiled integration

Supported Templates

SPIMquant supports multiple brain templates for registration:

• ABAv3: Allen Brain Atlas version 3
• gubra: Gubra mouse brain atlas
• MBMv3: Marmoset Brain Maps version 3
• turone: Turone mouse brain atlas
• MouseIn: Mouse MRI template

Quick Links

• How It Works: Narrative overview of the full pipeline
• Installation: Get started with SPIMquant
• Quick Start: Run your first workflow
• CLI Reference: Command-line interface documentation
• Output Files: Description of all output types
• Examples: See SPIMquant in action
• Contributing: Help improve SPIMquant

Workflow Overview

graph LR
    A[SPIM Data] --> B[Registration]
    B --> C[Segmentation]
    C --> D[Quantification]
    D --> E[Statistics]
    E --> F[Results]

The typical SPIMquant workflow:

1. Input: BIDS-formatted SPIM microscopy data (OME-Zarr format)
2. Registration: Deformable registration to a reference template
3. Segmentation: Automated segmentation of pathology signals
4. Quantification: Atlas-based regional quantification
5. Statistics: Group-level statistical analysis and visualization

Getting Help

• Issues: Report bugs or request features on GitHub Issues
• Discussions: Ask questions on GitHub Discussions
• FAQ: Check the FAQ page for common questions

Citation

If you use SPIMquant in your research, please cite:

Citation information coming soon

License

SPIMquant is licensed under the MIT License. See the LICENSE file for details.