The World of FlowJo™ Software
Interview with Dr. Serena Di Cecilia, BD Application Scientist
September 23, 2021
Data analysis is an extremely important part of a flow cytometry experiment. FlowJo™, the leading platform for superior analysis is a powerful tool that is helping scientists further their immunology and immunophenotyping results. FlowJo™ users enjoy the support and assistance of a large group of expert BD application scientists. Want to know what BD’s FlowJo™ experts have to offer? This month we are pleased to feature an interview with Dr. Serena di Cecilia, a BD application scientist who helps BD’s customers get the best out of their flow data.
1. Can you give us an elevator pitch on the capabilities of FlowJo™?
FlowJo™ is a do-it-all program for flow cytometry data analysis, the language the scientists speak in when communicating their analysis. As a desktop application, it allows the processing of flow cytometry standard files coming from different instruments, enabling the analysis of immunophenotyping, cell cycle, proliferation, kinetics and high-dimensional data. The user-friendly interface and the ability to create statistics allow users to obtain a complete report including figures and data ready for publication.
2. Plug-ins have added new capabilities to FlowJo™. How has the offering changed in the past few years and what have the major drivers been?
When I joined FlowJo™, about 3 years ago, we had few plug-ins available (including tSNE); the algorithms were computationally “heavy” and the users were not aware of all the possibilities FlowJo™ was offering to them. In the past years, we have developed and released more than 30 plug-ins (and we keep releasing and updating plug-ins monthly). The tSNE algorithm has been embedded within the software given its increasing use by the scientific community. Improved cytometers and fluorochromes require new methods of analysis to truly understand the information-rich data that can now be acquired. We continuously develop new plug-ins to meet the needs of our users, and frequently in collaboration with them, to push forward on dimensionality reduction, clustering, and data visualisation tools which allow for the discovery of previously uncharacterised cell populations.
3. 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, BD offers strong scientific support for panel design and there are 3 different plug-ins available in FlowJo™ for data quality processing (FlowAI, FlowClean and CytoNorm). 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™ 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, or triMAP for dimensionality reduction; Phenograph, FlowSOM, and Xshift clusters ready to be explored with ClusterExplorer or sorted via computational sorting enabled by HyperFinderTM.
4. What are the various FlowJo™ training programs that BD offers?
The FlowJo™ website is a “treasure chest” of knowledge. As Application Scientists, we hold monthly live webinars for the basic and advanced features of FlowJo™. Users can interact with us and ask questions live or watch the recorded webinars available on the website. A full “FlowJo™ Documentation”, or as I call it: “Our Bible” is available for any doubt or question they may have, and the 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!
5. Are there any major data processing challenges in specific areas like high-dimensional or small particle 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 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 FlowJo™ is already aware and someone from our amazing engineering team is already working on it.
The new versions of FlowJo™ 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.