New Features Note: This version of FlowJo is NOT compatible with FlowJo Enterprise. Stay tuned for the upcoming FlowJo Enterprise release that will work with this version. New FlowJo Plugin Architecture. FlowJo can now use plugins that can perform a variety of functions, including the creation of populations, creation of derived parameters, and actions when… Read more »
tSNE
T-Distributed Stochastic Neighbor Embedding (tSNE) is an algorithm for performing dimensionality reduction, allowing visualization of complex multi-dimensional data in fewer dimensions while still maintaining the structure of the data. tSNE is an unsupervised nonlinear dimensionality reduction algorithm useful for visualizing high dimensional flow or mass cytometry data sets in a dimension-reduced data space. The tSNE platform computes two new… Read more »
Installing Plugins
Plugins are executable java files that extend functionality of the FlowJo application. These can be installed and used as shown below. Installing Plugins in FlowJo v10: Create a folder named “plugins” on your computer. On a Windows computer this folder will already exist within the “FlowJo_v10.x” folder in the “Program Files”. On a Mac, it… Read more »
Plugins
Plugins are apps that extend functionality of the FlowJo application. Plugins are free add-ons, hosted on the FlowJo Exchange. A video demonstrating Plugin installation. FlowJo has an open API that allows us, or anyone else, to rapidly develop cutting edge tools without modifying the entire FlowJo application. Please visit the Exchange to peruse the current… Read more »
10.1 Exhaustive Release Notes
Below are the exhaustive release notes and known issues. For a digest of these release notes, please see this page. New Features: Performance: Background calculations are much less interruptive of user interaction. Boolean calculations and gate caching preference improves performance of of boolean gate calculations UI Improvements: Updated icons across the application, optimization of bands… Read more »
10.1 Release Notes
10.1 has many improvements to performance, platforms, and user experience. You should notice a major improvement in interactivity and performance with deep gating trees and Boolean gates, and we are indebted to our loyal users whose feedback was critical in delivering this release. New Features & Major Revisions: Jo file reading: Multiple improvements to .jo… Read more »
Naming Timeslices
Each kinetic analysis, or “node”, can contain multiple timeslices. Statistics will be reported for all of the events as well as for each time slice. The only control over timeslices are their placement, and their name. There are two ways to create time slices, either by clicking-dragging in the window, or by clicking one of… Read more »
How FlowJo Handles Time
New to Version 10 – a straight forward manner of handling the time parameter Time is collected in FCS data as an offset parameter – the amount of time steps that have passed since the last collected event is recorded. The $TIMESTEP keyword can then be used to decode the actual amount of time that passed… Read more »
Deriving a Kinetics Parameter
You can use the derived parameter platform to create ratios of parameters for use in the kinetics platform Some data files intended for kinetics analysis will contain parameters of the individual measures of bound and free calcium without containing the ratio parameter that is commonly used to measure cellular changes. In this case the derived… Read more »
10.0.8 Exhaustive Release Notes
Below are the exhaustive release notes and known issues. For a digest of these release notes, please see this page. New Features: Cell Cycle: New 1d Cell Cycle Platform with both Watson Pragmatic and Dean Jett Fox modeling. Export: Completely revised, Export/Concatenate now has all the features you loved in v9 Kinetics: New implementation of… Read more »