FlowJo re-envisioned for the high-dimensional data era.
The new version of FlowJo maintains the friendly drag & drop, double-click user interface of past versions and adds a wide range of features all intended to match your experimental setup more closely and facilitate comparisons, enabling your next breakthrough whether that be in basic science or development of a cure.
Welcome
Hello new users of FlowJo, and welcome back old friends! We believe our mission is to facilitate the amazing work you do for the betterment of human health. Version 11 was built from the ground up with the philosophy of preserving as many of the basic mechanics and appearance of previous versions but being bold and attempting to innovate any aspect of the software that could facilitate the growing size, complexity, and power of single cell data. We have endeavored to build this version with you. To all of you who have tested our early access builds over years of development and generously provided well thought out feedback, you have our wholehearted thanks!
The first and most obvious update you will find is that we have made this version immersive, filling the screen with a single window that allows you to emphasize elements of the program as needed.
You will also notice the sample database has evolved from a list of groups and samples to be used in isolation, to a hierarchical analysis tree, comprised of three panes that work in concert. Hierarchical groups mirror experimental design, allowing for common populations to be passed down the hierarchy to various categories of data so that you may organize the data in FlowJo exactly how you think about it, making comparisons natural end points of working through the data.
Populations are now entirely group owned. This is a change in paradigm from previous versions in which each population was initially singular and had to be added to a group. The approach in this version allows us to display a single hierarchy of whatever group is in focus, highlighting whichever population and sample have unique gates, making navigation much simpler, while creating directly comparable populations at any level of the hierarchy.
The primary graph remains largely unchanged, but now supports Virtually Concatenated Populations (VCPs) that allow you to draw gates, run clustering algorithms, or do visual comparison on all data within a group on the fly, without needing to create additional files, or add extra annotation. There is also a flexible graph gallery present that will show you plots of either all the samples in a group for a chosen set of parameters, all the parameter combinations for a sample, or one of the special use options such as population ancestry. We believe immediately seeing so much more of your data, in a highly configurable manner, will facilitate comparison and lead to insight.
The new Metadata Manager elevates proper annotation appropriately. It contains places to view, edit, and create metadata and parameter sets. The number of parameters in typical single cell experiments has grown and diversified to include other modalities such as imaging, and managing parameters by grouping them into functional units is necessary. After creating parameter sets in the Metadata Manager, they will appear throughout the program and can be used to filter axis choices and display settings to be sufficiently concise.
The Report editor has replaced the Layout editor as we believe the graph gallery has replaced much of the exploratory functionality of the Layout editor, making the primary use of this tool assembling select parts of your analysis into a story amendable to reporting. You will find that both reports and tables now automatically batch. Tables will immediately populate with information from all samples added for any selected population. Reports will simply toggle between the initial exemplar and the fully batched version, allowing you to update on the fly, and facilitating automation.
Finally, we have built-in features that we believe are now part of the basic workflow. Quality Control (QC) is now a primary part of the program that can be run on an entire data set in just a few clicks. Tools for building statistical models, creating charts, clustering, and dimensionality reduction are now all native to FlowJo.
Feedback welcome
Software is meant to continuously evolve. We would love to hear from you and find out what your experiences were using this new version of FlowJo. If you have feedback to share, please write to us at e-mailaddressTBD@bd.com.
Thank you for doing the work you do!
Sincerely,
The FlowJo Team