Templates and Compensation

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Applying new compensation matrices to data loaded into templates can be a bit confusing. This document will help! When a template is created on compensated parameters, and new data is loaded that was compensated on the machine (includes an acquisition matrix), these data will load right into the template and gates will be applied. However,… Read more »

FlowJo and CyTOF files

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The CyTOF is a Time of Flight based mass spectrometer that produces FCS files as an output.  The data can thus be analyzed in FlowJo. What is a CyTOF? The CyTOF is a mass cytometer produced by DVS Sciences.  The name is an abbreviation for ‘cytometry Time Of Flight’, and the machine is used to… Read more »

10.0.7 Exhaustive Release Notes

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For a digest of these release notes, please see this page.  This page contains an exhaustive list of issues that have been reported and fixed, new features implemented, and known issues. Fixed:   FlowJo 10.0.7r2: Significant Improvements: Compensation is now “remembered” in templates Compensation population size restriction has been reduced to a warning if under… Read more »

Data De-identification Utility

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A standalone tool for de-identifying FCS files. The Data De-identification Utility scrubs FCS data’s keyword values. It supports batching a large selection of FCS files and features an easy interface for selecting which keyword values to scrub. Click here to download the tool and How-to document. NOTE: The de-identification utility is not a commercially sold… Read more »

Cell Cycle: Univariate

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Univariate modeling can be used to create a fit to cell cycle data based on statistics in one dimension, traditionally DNA content. FlowJo provides a simple interface to performing fairly sophisticated DNA/Cell Cycle analysis.  To launch the univariate cell cycle model click on the population of interest in the workspace, then select the Cell Cycle task from… Read more »

SP6800 Spectral Analyzer

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The SP6800 Spectral Analyzer uses software, developed by Sony, which performs spectral unmixing and exports FCS files for analysis in FlowJo. Spectral analyzers collect all emitted florescence simultaneously, then use spectral unmixing to separate the individual colors.  Spectral unmixing is the process in which a set of controls that represent each fluorescent color individually, similar to… Read more »

EC800 Software

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Preferences in FlowJo are set by default to rescale the data based on our understanding of the differences between SONY’s acquisition display and the written format of the file.  FlowJo’s default preferences should display the data the same way as seen on the instrument. You can change these default preference sets in the cytometer specific preferences…. Read more »

Experiment Band

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The Plate Editor Experiment Band facilitates experiment-level annotation as well as the movement of keyword-value pairs from workspace groups to the plate and vice versa.   Annotate Experiment Brings up the MIFlowCyt annotation tool allowing you to add experimental details.   Read Attributes from Group Assigns the keywords from the data files in the currently selected group… Read more »

Settings Band

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The Settings Band allows visualization of the number of attributes added to a well, numerical keys, and categories of wells through the use of borders in FlowJo’s Plate Editor. The Plate Editor: Settings Band   Show number of attributes Puts an indicator of the number of keyword-value pairs for each well in the bottom right-hand corner… Read more »

Configure Band

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The Configure Band allows a user to set plate dimensions, annotate wells with a dilution series, and add/remove staging wells in FlowJo’s Plate Editor.   Set Plate Dimensions Allows the user to define the plate layout (number of wells) and change between 96, 384, and 1536 well plates. Dilution Series Set up a titration keyword… Read more »