The FlowJo dongle has been a longstanding license type utilized by users to access FlowJo. A dongle is a USB loaded with a license.key file that grants access to the FlowJo desktop application. A user can plug their Dongle into a computer and open a fully authenticated FlowJo session. Dongles can be used by multiple… Read more »
Rosetta Calibration
Understanding the size of particles in flow cytometry is important in a number of applications. FlowJo™ Software with the Rosetta Calibration plugin, along with the Rosetta Calibration product from Exometry enables calibrated size measurements of small spherical particles (<10 μm). The plugin allows you to utilize FCS data captured from Rosetta Calibration beads to derive… Read more »
IndexSort
Introduction This plugin was designed in order to give researchers the ability to automatically gate wells from .fcs data generated using the BD FACSAriaTM, the BD FACSAriaIITM, the BD FACSAriaIIITM, the BD FACSAria FusionTM, the BD FACSMelodyTM, the BD Influx SystemTM, the BD FACSJazzTM, FACSVulcanTM, and the BD FACSymphonyTM S6 cell sorters. Please review FlowJo… Read more »
Cluster Explorer
IntroductionCluster Explorer is a FlowJo plugin. The tool creates an interactive cluster Profile graph, heatmap, and displays the cluster populations on a tSNE/UMAP plot. The plots are dynamic, can be copied to the clipboard or FlowJo Layout, and allow the user to select populations in one view and highlight the selected population in the other… Read more »
UMAP
How-to-UMAP Uniform Manifold Approximation and Projection (UMAP) is a machine learning algorithm used for dimensionality reduction to visualize high parameter datasets in a two dimensional space. (1) The UMAP plugin will run with both FlowJo and SeqGeq bioinformatics data analysis platforms. Note: The UMAP plugin for FlowJo requires requires a 64bit OS. This is due… Read more »
Performance Recommendations
Our recommendations for setting your performance preferences. Modifying the performance preferences can help improve your FlowJo experience if you have sufficient hardware. Below are the general recommendations for performance preferences settings on Mac or PC with varying amounts of RAM. We recommend having at least 4x the amount of RAM as the size of data… Read more »
Archive Files
The Archive file type (acs) is a convenient way of grouping the fcs files with their analysis. Saving the FlowJo Workspace as an archive files will create a large file that contains the workspace its associated data files and its plugin derived parameter files. A file can be saved as an archive file by selecting… Read more »
Batch Using Iterate by Keyword
For many types of batch reports, simply iterating by the Sample or Panel are the easiest option, but in some cases we need to be more specific about which samples to include in the batch reports. In this case we can use iterate by keyword. Iteration by keyword uses a pair of keywords to specify… Read more »
Phenograph
Introduction PhenoGraph is a clustering algorithm that robustly partitions high-parameter single-cell data into phenotypically distinct subpopulations. First, it constructs a nearest-neighbor graph to capture the phenotypic relatedness of high-dimensional data points and then it applies the Louvain graph partition algorithm to dissect the nearest-neighbor graph into phenotypically coherent subpopulations. The PhenoGraph algorithm has been implemented… Read more »
Sample Quality Check
The Sample Quality Badge can be used to simply access the quality of each of the samples using the metric discussed in Sample Properties. This check can be performed by simply double clicking on the circle to the left of the file name. The color of the dot will indicate the relative quality of the… Read more »