FlowJo

What FlowJo does

FlowJo, LLC is a life sciences software company specializing in desktop and cloud-based analysis tools for flow cytometry and single-cell RNA sequencing data. The company's product portfolio centers on FlowJo v11 (the current major version launched in May 2025) and the legacy FlowJo v10, supplemented by SeqGeq (a bioinformatics platform for scRNA-seq analysis that does not require R scripting) and BD Research Cloud (a collaboration and workflow platform). Underlying technology includes proprietary spectral unmixing via AutoSpill, native t-SNE/UMAP/PCA dimensionality reduction, MEM (Marker Enrichment Modeling) for automated cluster labeling, HyperFinder for computational gating strategy, and an open plugin architecture (FlowJo Exchange) hosting more than 40 third-party tools including FlowSOM, Phenograph, Seurat, and Monocle.

The software serves academic life sciences researchers (immunologists, cell biologists, translational researchers), flow cytometry core facilities, and pharmaceutical/biotech drug discovery organizations. FlowJo operates as a wholly-owned subsidiary of Becton, Dickinson and Company (BD), which was itself acquired by Waters Corporation in 2024 — FlowJo now sits within the Waters Biosciences division. The business model is predominantly annual subscription-based (individual licenses, group site licenses for 5+ users, and freemium/paid tiers for BD Research Cloud) with quote-based pricing that varies by region and institution type; legacy dongle licenses remain in use with trade-in incentives toward subscriptions. Distribution occurs through self-serve direct download, the BD Access Portal for licensing, an inside-sales Customer Order Center for enterprise deployments, and a dedicated China channel. The company is headquartered in Ashland, Oregon, with 11–50 employees globally.

Name

FlowJo

Legal name

FlowJo, LLC

Website

https://flowjo.com

Company type

Private

Founded year

1997

Operating status

Operating

Headcount range

11–50 employees

Short description

FlowJo provides desktop and cloud-based software for flow cytometry and single-cell RNA sequencing data analysis, serving academic researchers, pharmaceutical and biotech firms, and core facilities through annual subscription licensing as a wholly-owned subsidiary of BD/Waters Biosciences.

Ownership category

akta.pro rank

Product category

Flow Cytometry Analysis Software

NAICS

Software Publishers (5132), Software Publishers (51321)

SIC

Services-Prepackaged Software (7372)

akta.pro primary industry

Flow Cytometry & Cellular Analysis Diagnostics (HLAHAAAF)

akta.pro secondary industries

Bioinformatics & Multi-omics Analysis Software (HLAGAJAD), Laboratory Informatics for Diagnostics (LIS/Middleware/Analyzer Connectivity) (HLAHAAAO), Clinical & Translational Informatics (Clinical Data Integration/Real-World Data for R&D) (HLAGAJAF)

Keywords

• Flow cytometry software
• Single-cell analysis
• Bioinformatics platform
• ScRNA-seq analysis
• Phenotyping software

Headquarters

HQ city

Ashland

HQ country

United States

HQ region

North America

Offices1 record

Markets served

GTM type

B2B

Offering type

Software

Cost components

Personnel, Technology or R&D, Marketing or Sales, Infrastructure, Operations

Revenue model

1. Annual Software Subscriptions: Annual individual and group license subscriptions for FlowJo and SeqGeq software through BD Access Portal. Subscriptions include free updates to all future versions while the license is active.
2. Group Site Licenses: User-based annual license management for groups/institutions with 5+ users, providing administrators tools to invite users, manage registrations, and customize site settings.
3. Individual User Licenses: Single user licenses allowing access on up to 4 computers (one at a time) with internet connection. Includes 24-hour offline window for offline work capability.
4. Dongle Licenses (Legacy): Physical dongle-based licensing option for FlowJo v10 with electronic or physical upgrade capabilities. Dongle trade-in credit available for US and Europe customers switching to annual subscriptions.

Pricing tiers

Go-to-market motion3 records

Distribution channels4 records

Marketing channels7 records

Core offering

FlowJo develops and sells desktop and cloud-based software for flow cytometry and single-cell data analysis. Its product portfolio includes FlowJo v11/v10 for high-parameter flow cytometry analysis, SeqGeq for single-cell RNA sequencing (scRNA-seq) bioinformatics, and BD Research Cloud for collaborative experiment management, panel design, and workflow control for life sciences researchers.

Differentiator

Problem solved

Functional benefit

Brands

• FlowJo v11: Latest version of flow cytometry data analysis software with immersive interface and advanced features
• FlowJo v10
• SeqGeq
• BD Research Cloud
• FlowJo Exchange
• BD Access Portal

Products and services

• FlowJo v11 Latest version of FlowJo desktop software for flow cytometry data analysis, providing faster performance, an immersive user experience, advanced visualization, spectral unmixing, dimensionality reduction (t-SNE, UMAP, PCA, LDA), automated gating (HyperFinder), and publication-quality output for life sciences researchers.
• FlowJo v10 Previous major version of FlowJo desktop software for flow cytometry and mass cytometry data analysis, used by academic and pharmaceutical researchers for routine phenotyping, immunology research, and high-parameter data workflows.
• SeqGeq Desktop bioinformatics platform for analyzing single-cell RNA sequencing (scRNA-seq) data, providing clustering, subsetting, gene set navigation, dimensionality reduction, and visualization tools without requiring R scripting, targeted at researchers performing gene expression studies.
• BD Research Cloud Cloud-based ecosystem for research flow cytometry experiments enabling panel design, collaboration, project organization, reagent inventory, experiment control, and team-based workflow management for flow cytometry core facilities and research teams.

Quantifiable outcome

• Free updates to all future versions while subscription is active
• +2 more outcomes

Segments3 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Integration3 records

AI capability8 records

Feature8 records

Partnerships

Two partnerships are on record, tiered core.

• Waters CorporationcoreStrategic or Co-development Partner · 1 January 2024Waters Corporation acquired BD Biosciences, which includes FlowJo. FlowJo software remains the standard analysis platform for BD flow cytometry instruments. The acquisition combines BD's expertise in flow cytometry reagents and instruments with Waters' analytical laboratory capabilities.
• BD Biosciences (now Waters Biosciences)coreStrategic or Co-development Partner · 1 January 2024FlowJo was developed by BD Biosciences as the standard analysis software for BD flow cytometry instruments. BD Biosciences and Diagnostic Solutions have combined with Waters Corporation to accelerate benefits of pioneering science.

Scale indicators3 records

Recent moves7 records

Expansion highlights5 records

Direct peers

• Verity Software House (WinList / ModFit): Provides WinList for cell cycle/DNA analysis and ModFit for ploidy — overlapping with FlowJo in cell-cycle and ploidy workflows within flow cytometry analysis.
• Cytek (SpectroFlo): Cytek's SpectroFlo is the analysis software paired with Cytek spectral cytometers, making it a direct competitor in spectral flow cytometry workflows where FlowJo also competes.
• Partek Flow: Genomics-focused analysis suite that includes flow cytometry and single-cell workflows; competes with both FlowJo and SeqGeq in multi-omic and scRNA-seq analysis.
• De Novo Software (FCS Express): Long-standing competitor in flow cytometry data analysis, offering FCS Express as a desktop platform with similar gating, compensation, and high-parameter capabilities to FlowJo.
• Cytobank (Beckman Coulter Life Sciences): Cloud-based flow and mass cytometry analysis platform acquired by Beckman Coulter. Directly competes with FlowJo in high-parameter cytometry analysis, with a stronger cloud-native architecture for collaboration and storage.

Broad incumbents

• Genedata: Enterprise scientific informatics platform serving pharma R&D with screening, flow cytometry, and multi-omic analysis — broader and more enterprise-focused than FlowJo but addressing overlapping pharma customer use cases.
• Dotmatics: Scientific R&D informatics platform covering flow cytometry, high-content analysis, and lab data management; a broader incumbent competing for pharma/biotech informatics spend that could otherwise go to FlowJo + BD Research Cloud.
• BD FACSDiva Software: BD's instrument-acquisition software, complementary rather than fully competitive — FlowJo consumes FACSDiva exports. Relevant as a parent-ecosystem incumbent that overlaps with parts of FlowJo's workflow.

Others

• Bioconductor flowCore / Cytoverse: Open-source R packages for flow cytometry analysis (flowCore, Cytoverse, openCyto). Not a commercial peer but the primary free alternative cited by academic FlowJo users, capping pricing power.

Emerging players

• CellProfiler (Broad Institute): Open-source image-based cell analysis software with some overlap in single-cell biology workflows. Adjacent rather than direct, but competes for the same bioinformatics user attention in academic settings.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat5 records

Key risks5 records

Key highlights7 records

Customer concentration

• Xx.com/flowjonow
• Facebookfacebook.com/FlowJoSoftware
• LinkedInlinkedin.com/company/flowjo-llc

Revenue estimate

Valuation estimate

Number of profiles

Profiles1 record

Funding overview

Funding rounds

Investors

Funding detail is available on the Subscription and Enterprise plan.Contact sales →

M&A

Investments

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about FlowJo