tSNE

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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…. Read more »

Installing Plugins

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Plugins are executable java files that extend functionality of the FlowJo application. Five plugins are included with the FlowJo v10 installation package. These can be installed and used as shown below. Installing Plugins in FlowJo v10.1r7+: Download the latest release of FlowJo v10 for Mac or Windows Follow the steps outlined by the installer and save the plugins folder to your… Read more »

Plugins

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Plugins are apps that extend functionality of the FlowJo application, which may be developed by 3rd-party developers or by the team at FlowJo. Please see Installing Plugins page for details on how to obtain and setup FlowJo plugins. To learn more about the available plugins, click on the links below: DownSample: Create a new gate which selects a limited number… Read more »

10.1 Exhaustive Release Notes

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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

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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 indebeted to our loyal users whose feedback was critical in delivering this release.   New Features & Major Revisions: Jo file reading: Multiple improvements to .jo file reading including a fix… Read more »

Naming Timeslices

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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

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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

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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

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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 »

10.0.8 Release notes

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You’ll notice some major improvements in this 10.0.8 release, from the very start of the application through the interface to new platforms.  In terms of user feedback, features, quality, and performance, this represents a major release and we are grateful for the many conversations with loyal users and work with beginning users whose feedback help… Read more »