Cytogence FCS
A high-performance flow cytometry analysis platform built from the ground up in Rust, with an AI copilot that understands your data and accelerates your workflow.
Built in Rust
Native speed. 100K+ events rendered without lag.
AI Copilot
Automated gating and strategy suggestions powered by LLMs.
Privacy First
All analysis runs locally. Your data never leaves your machine.
Cross-Platform
Windows, macOS, and Linux with identical features.
Everything you need for flow cytometry analysis
From file loading to publication-ready figures, Cytogence FCS covers the entire analysis workflow.
Intelligence built into every step
Cytogence FCS integrates AI at the core of the analysis workflow — not as a bolt-on feature, but as a native part of how you interact with your data.
Multi-Provider AI Copilot
Choose from Claude, GPT-4, AWS Bedrock, or run local models via Ollama. Three assistant modes: Copilot for analysis, Tutor for learning, and Designer for workflows.
ML Auto-Gating
Three clustering algorithms — K-means, DBSCAN, and Gaussian Mixture Models with BIC-based model selection — for unsupervised population identification.
17 AI-Exposed Tools
The AI assistant can create gates, compute statistics, suggest strategies, analyze distributions, name populations, and run statistical tests — all with your approval.
Professional-grade analysis tools
Built on validated statistical methods and a comprehensive gating engine that supports hierarchical gate trees, boolean operations, and real-time population statistics.
Complete Gate Types
Rectangle, polygon, ellipse, range, quadrant, and boolean (AND/OR/NOT) gates with full hierarchy support, undo/redo, and real-time statistics.
5 Transform Types
Linear, logarithmic, biexponential (logicle), arcsinh, and hyperlog transforms with automatic tick generation for proper axis scaling.
Comprehensive Statistics
Mean, median, geometric mean MFI, robust CV, plus paired/unpaired t-tests, ANOVA, Kruskal-Wallis, and Mann-Whitney U tests.
Auto-Compensation
Calculate spillover matrices from single-stain controls with diagnostic metrics including stain index and FMO thresholds. Import/export matrices for sharing.
Proliferation Analysis
GMM-based dye dilution modeling with automatic generation peak fitting. Calculates division index, proliferation index, percent divided, and expansion index.
Dose-Response Fitting
4-parameter logistic (4PL) curve fitting with Levenberg-Marquardt optimization. EC50/IC50 calculation with R² goodness-of-fit and convergence diagnostics.
GPU-Accelerated Plots
Scatter, histogram, density, contour, zebra, and overlay plots rendered via PixiJS with WebGPU/WebGL. Interactive zoom, pan, and configurable point rendering.
Publication-Ready Export
Export plots as SVG or PDF vector graphics for journals, or PNG for presentations. Export statistics and event data as CSV for downstream analysis.
Workspace Persistence
Save complete analysis sessions — files, gates, compensation, plot views — and restore them later. Auto-save with configurable intervals for data safety.
Full FCS Standard Support
Cytogence FCS reads FCS 2.0, 3.0, and 3.1 files with support for integer, float, double, and ASCII data types. Drag and drop files to get started — metadata, parameters, and spillover matrices are extracted automatically.
Ready to try Cytogence FCS?
Request a demo and see how AI-powered flow cytometry analysis can accelerate your research workflow.