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 »



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 »



The PeacoQC plugin for FlowJo ! The Peak Extraction and Cleaning Oriented Quality Control (PeacoQC) plugin performs quality control on cytometry data, evaluating the sample signal for regions of irregularity. This algorithm can help remove clogs and changes in flow rate, helping clean up the data. The algorithm identifies density peaks within each parameter and… 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 »



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 »

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 »


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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 »

AutoSpill Compensation


AutoSpill is a new algorithm for calculating spillover and producing a compensation matrix developed and incorporated into FlowJo v10.7 in collaboration with researchers from the Vlaams Instituut voor Biotechnologie in Belgium and the the Babraham Institute in Cambridge, UK. This form of gate-less compensation removes some of the requirements of traditional compensation making compensation faster and simpler…. Read more »

10.6.2 Exhaustive Release Notes


Updates Functional within Mac OS 10.15 (Catalina) – Requests permissions to access files and folders Update to use Java version 9 Increased absolute value of negative option for scaling in BiExponential Include No More Than option in Export/Concatenate menu is being updated for full functionality Open Original Graph option from the Layout Editor now opens… Read more »