Synapse3D

A FLIKA plugin for 3D cluster analysis of superresolution microscopy data, with a focus on synaptic protein organization.

Overview

Synapse3D provides tools for analyzing the spatial organization and clustering of synaptic proteins using superresolution microscopy data. The plugin enables:

• 3D visualization and analysis of protein localizations
• DBSCAN-based cluster detection in 3D
• Analysis of spatial relationships between protein clusters
• Quantification of cluster properties (volume, density, etc.)
• Statistical analysis of cluster distributions
• Batch processing capabilities

Features

• 3D Data Visualization: Interactive 3D visualization of protein localizations and clusters
• Cluster Detection: DBSCAN-based clustering algorithm optimized for 3D protein distribution analysis
• Dual Channel Analysis: Compare and analyze relationships between two protein channels
• ROI Analysis: Define and analyze regions of interest in 2D and 3D
• Statistical Tools: Built-in tools for analyzing cluster distributions and spatial relationships
• Batch Processing: Process multiple datasets with consistent parameters
• Data Export: Export analysis results in CSV format for further processing

Installation

Requirements

• FLIKA (http://flika-org.github.io/)
• Python 3.x
• PyQt5
• numpy
• scipy
• scikit-learn
• pandas
• pyqtgraph

Dependencies

The following Python packages are required:

numpy
scipy
pandas
scikit-learn
PyQt5
pyqtgraph

Installing the Plugin

1. Install FLIKA following the instructions at http://flika-org.github.io/
2. Clone this repository:

git clone https://github.com/username/Synapse3D.git

3. Add the plugin directory to your FLIKA plugins folder

Usage

Basic Workflow

1. Launch FLIKA and enable the Synapse3D plugin
2. Load your localization data (supported format: .txt files with x,y,z coordinates)
3. Select analysis parameters:
   • Clustering distance (eps)
   • Minimum points per cluster (min_samples)
   • Maximum distance between clusters
4. Run cluster analysis
5. Visualize and analyze results in 2D and 3D views

Analysis Options

• Cluster Analysis: Detect and analyze protein clusters using DBSCAN
• ROI Analysis: Define regions of interest and analyze cluster properties
• Distance Analysis: Measure distances between clusters in different channels
• Statistical Analysis: Compare cluster distributions to random distributions
• Batch Processing: Process multiple files with consistent parameters

Data Export

Results can be exported in various formats:

• Cluster statistics (CSV)
• ROI measurements (CSV)
• Coordinate data (CSV)
• Analysis parameters and settings

Interface Overview

The plugin provides several key interface elements:

• Main 2D view for data visualization
• 3D viewer for spatial analysis
• ROI manager for region selection
• Analysis parameters panel
• Results table for measurements

Keyboard Shortcuts

• Ctrl+O: Open file
• Ctrl+R: Reset layout
• Ctrl+G: Show titles
• Ctrl+H: Hide titles

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

[License information to be added]

Authors

• George Dickinson
• Brett Settle

Acknowledgments

Originally developed from code by Brett Settle (https://github.com/BrettJSettle/SynapseAnalysis) for the Ian Smith Lab (https://faculty.sites.uci.edu/ianfsmithlab/) at the University of California, Irvine.