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Rodrigolab's Flow Cytometry Analyzer Documentation

Welcome to the documentation for Rodrigolab's Flow Cytometry Analyzer, a free, open-source tool for interactive filtering of Flow Cytometry Standard (FCS) files.

What is This Tool?

Rodrigolab's Flow Cytometry Analyzer is a desktop application that allows you to: - Load and visualize FCS (Flow Cytometry Standard) files - Interactively select regions of interest using lasso selection on scatter plots - Apply multiple filters with automatic intersection - Export filtered data in multiple formats (CSV, Excel, Parquet)

It serves as a free alternative to FlowJo for basic gating operations.

Features

  • Interactive Scatter Plots: Visualize your flow cytometry data with customizable axes
  • Lasso Selection: Draw freehand selections to filter data points
  • Multiple Filters: Create and combine multiple filters with automatic intersection
  • Log/Linear Scales: Toggle between logarithmic and linear scales for each axis
  • Zoom and Pan: Navigate large datasets with intuitive controls
  • Theme Support: Light, dim, and dark themes with system preference detection
  • Multiple Export Formats: CSV, Excel (with metadata), and Parquet
  • Cross-Platform: Works on macOS, Windows, and Linux

System Requirements

  • macOS: 10.13 or later (Apple Silicon or Intel)
  • Windows: Windows 10 or later
  • Linux: Ubuntu 22.04+, Debian 11+ (x86_64)

Getting Started

  1. Download and install the application for your platform
  2. macOS users: If you see an "app is damaged" error, see the Installation Guide for instructions on bypassing macOS Gatekeeper
  3. Windows users: If SmartScreen shows a warning, see the Installation Guide for instructions on bypassing the warning
  4. Learn the basics of using the tool
  5. Start analyzing your FCS files!

License

This project is licensed under the MIT License.

Support

For issues, feature requests, or questions, please visit the GitHub repository.