Analysis Software

Flow Cytometry Analysis Software

Flow cytometry analysis requires efficient and specialized software. While most analysis software will accommodate basic cytometry experiments, many cater to specific techniques such as image cytometry, high throughput, and sorting. This compiled list of popular software can help you identify the best fit for your experiment. 

Commercially Available Software

We recommend the following analyzers for your experiment design.

FlowJo® – FlowJo

FlowJo® is the leading analysis platform for single-cell flow cytometry analysis. With an intuitive interface, specialized analysis platforms, and open-ended plugin architecture, FlowJo® provides a rich analysis environment that is easy to use, versatile, and extensible. The FlowJo® workspace is a powerful statistical environment that is used for immunophenotyping, cell cycle, proliferation, kinetics studies, quantitative population comparison, or plate screening assays to name a few. Compatible on Mac and Windows. 

CellEngine™ – CellCarta

Cloud-based analysis optimized for speed and convenience in any study, from small pilots to multi-year clinical studies with thousands of files. Analyze deep hierarchies with Boolean and combination gates, and use machine learning-based automatic gating to breeze through large studies. Metadata-driven analysis rapidly generates figures comparing treatment groups, timepoints, or any other variables. Easy-to-use clustering and dimensionality reduction algorithms run in minutes. Use the API to integrate with bioinformatics pipelines and LIMS. Available with 21 CFR 11 compliance features.

FCS Express 7 - DeNovo Software

FCS Express is the premier flow and image cytometry data analysis software for RUO, IVD and image cytometry analysis. A modern, Microsoft Office™ style interface combined with powerful analysis capabilities makes FCS Express the tool of choice for both research and clinical labs. Compatible on Mac and Windows. 


NovoExpress® - ACEA Biosciences

The NovoExpress® software enables researchers with varying levels of experience to do efficient sample acquisition and analysis. This software automates multiple fluidic functions eliminating cumbersome and time consuming procedures. User hands-on time is minimized with the walk-away software engine that drives the cytometer and the autosampler acquisition and analysis.

WinList™ - Verity Software House

WinList 9.0 is a cytometry software designed to be powerful and easy-to-use. WinList continues to raise the bar for data analysis with a great new interface, t-SNE clustering, ‘magic contour’ and ‘sticky’ regions, 3D graphics, and validated accuracy.

iQue Forecyt®

Forecyt® Software available with the iQue® Advanced Flow Cytometry Platform, provides plate level annotation, analytics, and visualization tools not found in traditional flow-based analysis software packages. From linking well data together to combining multiple assay outcomes together to identify “hits”, the time saving features help you get data insights that drive discovery.

Building on the productivity of iQue®, the 21 CFR Part 11 Compliance-Enabling Module, helps maintain electronic records, with seamless, integrated global event tracking, electronic signatures and more.

BD FACSDiva™ - BD Biosciences

BD FACSDiva™ software is a collection of rich tools for flow cytometer and application setup, data acquisition, and data analysis that help streamline flow cytometry workflows for today’s busy laboratory. Its new features help users integrate flow systems into new application areas, including index sorting for stem cell and single-cell applications, as well as automation protocols for high-throughput and robotic laboratories. Compatible on Windows. 

CytoBank - CytoBank

Cytobank is built from the ground up on the concept of single-cell flow cytometry analysis, with all data visualizations connected to the individual cell events. This enables unparalleled communication between clinical researchers, scientists, and informaticians that takes full advantage of what cytometry has to offer. Compatible on Windows. 

Flowlogic™ - Miltenyi Biotec

The Flowlogic™ Software makes a fast and accurate analysis of big data possible. The integrated statistical analysis and the advanced layout options for publication make secondary software packages unnecessary. Simply adjust your gating strategy and the software performs the analysis within seconds. The Flowlogic Software provides state of the art features such as batch analysis, flexible gating, offline auto compensation, overlays, and many more. It is designed to work seamlessly in all JAVA-supported operating systems such as Windows®, Mac OS®X, and Linux®.

Kaluza™ - Beckman Coulter

With features designed to simplify life in the lab, Kaluza aims to provide a greater understanding of the data generated by modern cytometers. Kaluza technology offers real-time analysis of high content files to free up valuable time for discovery. Kaluza was designed with uncompromising quality and reliability for multi-file, high content data analysis. Compatible on Windows 7 and WIN 7 64-bit, WIN 8, WIN 8.1 and WIN 10. 

CellCapTure - Stratedigm

From running conventional flow cytometry analysis to complex high-throughput experiments, Stratedigm’s CellCapTure™ software gives you unmatched experiment flexibility and ease of use. With powerful built-in features like templates and auto-compensation tools, analysis has never been this easy; analyze your experiments with post-color compensation, batch analysis, calculation sheets, custom parameters, overlays, and much more. Compatible on Windows 7 and Windows 10. 

Free Flow Cytometry Analysis Software

We recommend the following analyzers for your experiment design. is a web-based free flow cytometry analysis application. It is available from any platform with a web browser including phones and tablets. Released in 2020, it supports FCS2.0, FCS3.0 and FCS3.1 files.

Red Matter App

Red Matter App is a free flow cytometry analysis software. The beta version went live on August 28, 2017. This is a major new release which brings Red Matter in line with the Data File Standards for Flow Cytometry, Version FCS 3.1 and Gating-ML 2.0 standards.

Free Software List - Purdue Univ. Cytometry Labs

This list is designed to provide comprehensive educational materials in all areas of flow cytometry analysis, including free flow cytometry software, and demonstrations of commercial packages.

CyFlogic - CyFlo

 Cyflogic is a flow cytometry analysis tool for Microsoft Windows environment. It has all regular analysis capabilities, such as dot plot, histogram, and statistics. In addition, Cyflogic offers new innovative tools for your data analysis.

Flowing Software

Flowing Software is a project which combines high throughput data analysis with flowing usability. The easy-to-use visual interface ensures an effective data analysis with your personal computer.