The World of FlowJo™ Software

Data analysis is an extremely important part of a flow cytometry experiment. FlowJo^™ Software, is a powerful tool that is helping scientists further their immunology and immunophenotyping results. In 2024 FlowJo^™ Software was cited in leading immunology peer-reviewed journals more often than any other flow cytometry analysis software.

FlowJo^™ Software users enjoy the support and assistance of a large group of expert BD application scientists. Want to know what  FlowJo^™ Software experts have to offer?  We are pleased to feature an interview with Dr. Serena Di Cecilia, a Software Solutions Manager, who helps our customers get the best out of their flow data.

Can you give us an elevator pitch on the capabilities of FlowJo™ Software?

FlowJo^™ is the leading platform for flow cytometry data analysis.  Just as a desktop application, it allows the processing of flow cytometry standard files coming from different instruments, either conventional or spectral, enabling the analysis of immunophenotyping, cell cycle, proliferation, kinetics, imaging and high dimensional data. The user-friendly interface and the ability to create statistics and charts allow users to obtain a complete report including figures and data ready for publication.

Algorithms have added new capabilities to FlowJo^™ Software.  How has the offering changed in the past few years and what have the major drivers been?

When I joined FlowJo^™, about 8 years ago, we had few algorithms available (including tSNE) as “plugins” and many users were not aware of all the possibilities FlowJo™ had to offer. With time, we have developed more than 40 plugins and released a completely redesigned version of FlowJo^™:  FlowJo^™ v11. The tSNE algorithm, as well as the famous FlowSOM algorithm among others, has been embedded within the software given the increasing use by the scientific community. Imaging flow cytometry instruments and fluorochromes require new methods of analysis to truly understand the information-rich data that can now be acquired. We continuously update our software to meet the needs of our users and, frequently in collaboration with them, to push forward on dimensionality reduction, clustering and data visualization tools, which allow for the discovery of previously uncharacterized cell populations.

What are the most frequent challenges in flow cytometry data processing, and how can FlowJo™ help with them?

With the increased number of parameters that can be included in an experiment, one of the challenges is to obtain good quality data before moving on to the analytical step. Luckily, we  offer strong scientific support for panel design, together with BD(R) Research Cloud and the BD Horizon Panel Maker algorithm. To complement that, there are multiple tools available in FlowJo^™ Software for data quality preprocessing, including QC and Normalization. Sometimes, researchers feel overwhelmed with the amount of data they get from a single experiment and think that having bioinformatics knowledge is essential for them to be able to analyze their data. FlowJo^™ Software opens the door to high-dimensional data analysis using just a click of the mouse, thereby eliminating the need to know how to code. To complete a computation workflow without coding, users have tSNE, UMAP, PACMap or triMAP for dimensionality reduction; and Phenograph, FlowSOM and Xshift clusters ready to be explored with ClusterExplorer, labeled with MEM or sorted via computational sorting enabled by HyperFinder.

What are the various  FlowJo^™ training programs available?

The FlowJo website is a treasure chest of knowledge. Informatic scientific advisors hold monthly live webinars for the basic and advanced features of FlowJo^™ Software and BD (RC) Research Cloud. Users can interact with them and ask questions live or watch the recorded webinars available on the website. Full FlowJo documentation is available for any doubt or question they may have, and FlowJo University helps users get started or find tips and tricks with short videos when an experiment is running and there is not much time to watch a full webinar. Still, in-person training at each site remains my favorite!

Are there any major data processing challenges in specific areas like high-dimensional or Imaging flow cytometry? How is FlowJo™ going to solve these?

Challenges are always around the corner and science would be boring without them! For high-dimensional  and imaging data analysis, computational power remains an important pillar. The FlowJo team is actively working to always align with the latest technologies and scientific discoveries. If there is something new out there, you can be sure that they are aware and someone from our amazing engineering team is already working on it. The future updates of FlowJo^™ Software that we plan to release are proof that scientific discoveries are our priority and supporting researchers with the latest tools is our way of life.