Choosing the "best" flow cytometry software can be challenging, as it largely depends on your unique needs, workflow and research objectives.
Factors such as data complexity, collaboration and integration requirements significantly influence the selection process.
However, based on our experience and evaluation of the various flow cytometry software options on the market, we’ve curated a list of top contenders.
What is the best flow cytometry software?
To keep this article focused, we’ve limited our list to a few top contenders to ensure quality over quantity, focusing on those that excel in various aspects of flow cytometry analysis.
The best flow cytometry software:
- FlowJo: Traditional analysis with a large user base
- OMIQ: Cloud-based, modern and user-friendly for both classical and high dimensional analysis
- FCS Express: Desktop software with a PowerPoint-like interface, popular for regulatory compliance
- Cytobank: Cloud-based platform for high-dimensional data analysis
- Further & Free Options: These alternatives may cater to different needs and budgets
Read on to discover the key reasons to consider each of the shortlisted options for your flow cytometry analysis software.
Keep in mind that what works for one lab, may not work for another. The best software is one that meets your current needs and can also adapt to future requirements.
FlowJo
Key points for you to know:
- Desktop program with support for traditional, spectral, and mass analysis (within confines of machine’s capacity)
- Plugins available for many advanced biological models and statistical tools
- Separate collaboration cloud designed for experiments using BD instruments and BD software
- Web-based portal to authenticate user licensing for desktop software
(only licensing option available for newer FlowJo versions) - No Prism integration (manual process)
Key reasons to choose FlowJo for flow cytometry analysis:
- Add-Ons and Extensibility: FlowJo offers extensibility through various plug-ins and supplemental programs, supporting tasks like experimental setup, advanced analyses, data sharing, and single-cell sequencing. It's suitable for users comfortable managing multiple licenses and switching between different software solutions.
- R-Dependent Analyses: Users with strong R expertise may feel confident installing and setting up the R packages needed to run FlowJo’s many R-dependent features and plugins, such as those for automating gating, which require proper installation and understanding of both R and Rtools (for PC) or XCode/XQuartz (for Mac).
- Local Processing: FlowJo performs analyses locally making it practical for users with high local processing power and storage. It is reported that underpowered devices result in lagging and freezing.
- Legacy Reputation and Assumed Dependencies: A well-known product even before its acquisition by medtech giant BD, FlowJo benefits from both its legacy and BD’s breadth. Some experts quickly adapt to the steep learning curve, while others assume they are locked into existing BD machines or software.
- Basic Visualization and Graphing Tools (no Prism Integration): Teams who rarely rely on specialized programs, such as GraphPad Prism, may find what they’re looking for with FlowJo’s visualization and graphing tools; but those who want to leverage Prism will face a cumbersome process that requires exporting files from FlowJo in standard formats (e.g., CSV) and then manually reshaping them, such as via an intermediary spreadsheet editor or scripting.
OMIQ
Key points for you to know:
- Powerful cloud platform for both classical and advanced high-dimensional analysis of traditional, spectral and mass cytometry data
- Online collaboration and sharing, including auditable and reproducible analytical pipelines
- Automated gating and 30+ natively integrated algorithms
- End-to-end connectivity of your instruments, ELNs, databases and analysis through Dotmatics Luma
- Choice of results export formats (PRISM, CSV, PDF, FCS, PPT, PNG, SVG) and direct export from OMIQ to GraphPad Prism
Key reasons to choose OMIQ for flow cytometry analysis:
- Complete Cloud Analysis Platform: OMIQ provides a central hub for classical and advanced high-dimensional flow cytometry analyses, visualizations, workflow creation, data sharing, and collaboration.
- Rapid Analysis and Prism Integration: With a direct OMIQ to Prism integration, as well as a wide range of tools for viewing and exporting, OMIQ enables rapid analysis and gets users from ideas to XY, grouped and column graphs (and more) in minutes.
- Streamlined User Experience: OMIQ eliminates the need for data reshaping, software updates, plugin downloads, and dependency maintenance, truly optimizing the user experience and workflow.
- Automated Workflow and Dataflow: OMIQ supports nearly full automation of workflows and metadata management, reducing manual data handling and its associated risks.
- Long-Term Data Value: In combination with Luma, OMIQ allows for the integration and modeling of data with other datasets, like sequencing data, enhancing idea generation and providing long-term value.
In addition to what we have covered above, OMIQ's inclusion in the Dotmatics Luma Flow Cytometry Workflow facilitates instrument, database, and ELN integration. This transforms the process of acquiring raw data, performing analysis, and pushing insights back into the broader R&D context.
OMIQ is our flow cytometry analysis software of choice. It's fast, modern, cloud based and integrates with Prism.
FCS Express
Key points for you to know:
- All-in-one desktop program with PowerPoint-like interface
- Validation Ready Package for GxP compliance
- Comprehensive cytometry support (flow, spectral, mass, image)
- Classical and advanced high-dimensional analysis
- Direct export from FCS Express to GraphPad Prism
- Integration with Dotmatics Luma and custom LIS/LIMS/ELN
Key reasons to choose FCS Express for flow cytometry analysis:
- All-in-One Solution with Flexible Licensing Options: With its familiar look-and-feel, broad set of classical and advanced analysis capabilities, comprehensive cytometry coverage, reusable analysis templates, and advanced graphing tools, FCS Express can provide many organizations everything their diverse teams need for cytometry analysis within one easy-to-use, plugin-free package. A wide variety of license types are available to meet different needs (e.g., shareable USB or internet dongles, user-based site licenses, server-based network licenses).
- Clinical and Regulated Editions: FCS Express offers different versions, including a Validation-Ready Package for regulated environments and a Clinical Edition for diagnostic labs, supporting compliance with CFR 21 Part 11. This package ensures compliance with CFR 21 Part 11 by providing integrated features such as security, audit trails, and e-signatures, addressing regulatory and Computer System Validation (CSV) requirements cohesively.
- Live-Updating: Thanks to real time charting, FCS Express users avoid the headache of updating plots, statistics, and graphs to reflect changes to gates, quadrants, and markers. Changes are automatically reflected in real-time, on both ends.
- Specialized Research Support: FCS Express can support the unique research demands of teams undertaking specialized analysis, such as cell proliferation, DNA cell-cycle, kinetics (e.g. calcium flux) and high-throughput plate-based analysis. The direct export to Dotmatics Luma and to custom LIS/LIMS/ELN, allow to easily and quickly integrate FCS Express-derived data with data generated by other sources.
- Prism Integration and Publication-Ready Results: FCS Express lets users directly and easily generate high-quality graphics and reports (e.g., PowerPoint, PDF), and it can quickly export to GraphPad Prism without any tedious reformatting tasks.
FCS Express is a strong contender to be your flow cytometry software of choice. It's desktop based, compliance friendly, has a interface that is similar to PowerPoint and integrates with Prism.
Cytobank
Key points for you to know:
- Cloud-based architecture for flow cytometry data analysis
- Enables collaborative workflows between multiple researchers
- Designed to handle large, complex flow cytometry datasets
- Provides advanced analysis capabilities, including dimensionality reduction and clustering
- Supports a variety of flow cytometry data formats
Key reasons to choose Cytobank for flow cytometry analysis:
- Cloud-based Platform: Cytobank is a cloud-based software solution.
- Collaborative Features: The platform facilitates collaboration between multiple researchers working on the same data simultaneously.
- Large Dataset Management: Cytobank is designed to handle and analyze large, high-dimensional flow cytometry datasets.
- Flexible Data Integration: Cytobank supports a wide range of flow cytometry data formats and integrates with some data repositories.
- Secure Environment: The platform operates in a secure, HIPAA-compliant manner, which may be a consideration for research involving sensitive information.
Notable Mentions
While we’ve highlighted some of the top flow cytometry software contenders, there are several other options worth considering. These alternatives may cater to different needs and budgets.
- Kaluza - High-dimensional analysis and integrates with Beckman Coulter instruments
- CytExpert - Optimized for Beckman Coulter instrument integration
- Flowlogic - User-friendly interface suitable for all skill levels
- WinList - A classic software option for more straightforward tasks
- Free Flow Cytometry Software
There are several free flow cytometry analysis software options available, which can be suitable for specific use cases or when budgets are tight. However, it’s important to approach these options with caution. Free software may lack the features, thorough testing, and technical support that is included in the paid products that are widely trusted in the research community.
Before opting for free software, we recommend taking a free trial of commercial flow cytometry software.
These trials often provide enough time to thoroughly test all features and familiarize yourself with the product. If you find you need more time to complete your project, you'll have a solid benchmark for comparison. Additionally, many labs utilize commercial software, so gaining experience with these tools can be beneficial.
Instrument Integration
Integrating instruments in flow cytometry research can significantly improve efficiency, data quality, and the overall scientific workflow. By connecting flow cytometers with other devices and systems, researchers can streamline data acquisition, analysis and data sharing. This is an important step to consider for future proofing your lab.
How to integrate instruments in your flow cytometry workflow?
Dotmatics Luma is a powerful platform that can significantly enhance flow cytometry workflows by integrating instruments, external systems and data analysis tools.
- When combined with other programs like OMIQ, Luma streamlines the entire flow cytometry analysis process from instrument to insight
- Integrates ELNs, flow cytometers, external systems/data, and Dotmatics flow cytometry analysis software
- Intelligent parsing and tagging of data
- Cloud-based data storage, sharing, and analysis
- Contextualized, multimodal data analysis
Key reasons users choose Dotmatics Luma for managing their flow cytometry workflow
- End-to-End Workflow Support: From experiment design to autogating to advanced analysis, flow cytometry workflows have never been more cohesive; all the data, instruments, systems, and analysis tools that teams need are united in one solution, a major plus for flow cytometry data management.
- Seamless Dataflow: Thanks to intelligent FCS file tagging, metadata capture, and automatic uploads, scientists don’t need to waste time annotating, massaging and moving data, and internal development teams don’t need to create homegrown workarounds or impossible-to-upkeep databases.
- Easier Data Access and Collaboration: Centralized cloud data storage, with secure access management, means well-organized and tagged data is always available for searching, sharing, and advanced analysis through Dotmatics flow cytometry analysis software.
- Deep Insights: Analyzed flow results can be inspected against other data sources (e.g., clinical, trial, patient) connected to Luma, helping researchers spot trends, make correlations, and garner insights that drive forward their work.
- Optimized User Experience: An integrated solution simplifies everything from preparing and uploading flow results, to searching for datasets, to performing analysis without constantly switching software. Life is just easier when your R&D solution is working with you, not against you.
How do I choose?
Now it’s time to dive deep and explore your team’s biggest needs and frustrations.
To choose the best flow cytometry software for you, there are three crucial steps in evaluating software solutions for research labs.
The process involves:
Defining baseline requirements by identifying essential features and pain points
Assessing usability through hands-on trials and considering factors like accessibility and user-friendliness
Evaluating the broader impact on workflows, scalability, and long-term research and development goals
By following these steps, labs can make informed decisions on software that will best support their growing output and evolving demands in the field of cytometry and related research areas.
1. Define your baseline requirements
Compile a list of your team’s biggest needs and pain points. What features are absolute must-haves to support your workflows?
Consider the following factors and their impact on you:
- Breadth of classical and advanced high-dimensional analysis tools (e.g., batch functionality and automation for classical analysis, cleaning and batch normalization, dimensionality reductions, clustering, differential expression, trajectory mapping, statistics, autogating, ML algorithms, etc.)
- Ease of access to, and maintenance of, most needed functionality (e.g., native feature or plugin with dependencies)
- Support for special circumstances (e.g., clinical or regulatory requirements, different cytometry types, specific experiment types)
- Compute power (e.g., desktop or cloud) relative to the size of your datasets and analysis demands
2. Assess usability
Get a firsthand look with a trial or demo. How well will the solution optimize day-to-day work and ease common frustrations?
Consider the following factors and their impact on you:
- Accessibility via desktop or cloud
- Efficiency and intuitiveness for completing common tasks (e.g, layout, gating, plot editing, compensation or unmixing, graphing, visualization, etc.)
- Time-saving and error-reduction features (e.g., developing workflows, reusable templates, automated gating, data tagging)
- Learning curve for new and novice users
- Depth of training and customer support available
- Facilitation of data sharing and collaboration across labs, locations, and users
- Ease for exporting data to other necessary software, like GraphPad Prism
3. Look at the bigger picture
Look beyond individual needs. Can the solution support end-to-end collaborative workflows and address broader R&D and IT concerns?
Consider the following factors and their impact on you:
- Ability to meet different users’ unique needs throughout end-to-end workflows, from initial experiment setup to instrument-data acquisition to advanced analyses
- Support for downstream analysis (e.g., modeling with multimodal data sets; exporting to other specialty software)
- Extensibility (e.g., adding new features, adopting additional solutions from the vendor, integrating with your tech stack)
- Scalability (e.g., adding users, handling growing output and analysis demands)
- Licensing options and maintenance costs (e.g., flexibility of pricing and licensing options, burden of administrative and IT demands)
- Security (e.g., user authentication, access controls, data protection measures)
Our Shortlist
As we've explored in this Flow Cytometry Software Guide, the landscape is rapidly evolving.
Modern research demands sophisticated tools that can handle complex, classical and high-dimensional data while facilitating collaboration and integration with other research modalities.
If you are looking for an alternative to Flowjo, we recommend:
OMIQ: Stand out cloud based innovation in flow cytometry
OMIQ is the choice for individuals and teams looking to embrace the positives of modern flow cytometry analysis.
- Seamless integration of classical and advanced high-dimensional analysis
- Robust online collaboration features
- Over 30 natively integrated algorithms for automated analysis
- Direct integration with GraphPad Prism for streamlined data visualization
- End-to-end connectivity through Dotmatics Luma, bridging instruments, ELNs, and databases
For research teams seeking to maximize efficiency, collaboration, and analytical power, OMIQ provides a comprehensive solution that adapts to the growing complexities of cytometry data.
FCS Express: Versatility meets familiarity for quick results
For those preferring a compliance focused desktop-based solution with a familiar interface, FCS Express offers a compelling alternative.
- All-in-one desktop program with a PowerPoint-like interface
- Specialized editions for clinical and regulated environments (GxP compliance)
- Comprehensive support for various cytometry types (flow, spectral, mass, image)
- Real-time charting and live-updating features
- Direct export to GraphPad Prism and easy integration with Dotmatics Luma
FCS Express combines the ease of use with powerful analytical capabilities, making it an excellent choice for teams that value compliance and a shorter learning curve.
Making your choice
Whether you opt for the cloud-based innovation of OMIQ or the desktop versatility of FCS Express, both solutions offer significant advantages over legacy software. They address the key challenges faced by modern flow cytometry teams. FlowJo is of course another popular flow cytometry software option. While it doesn't offer the same level of innovation as OMIQ or FCS Express, it has been the traditional choice for many researchers.
We encourage you to take advantage of the lengthy free trials of both OMIQ and FCS Express. Both are instant access and don't require to talk to anyone. Play around with example data sets or upload your own to quickly compare to your current workflow and see what you like or dislike about each.
By choosing a solution that aligns with your team's specific needs and future goals, you'll be well-equipped to stay at the forefront of cytometry research and discovery.
