FCS Express Resources for Cytek Users
Cytek and De Novo Software have collaborated to add the capability to seamlessly read the raw spectral data along with the unmixed FCS file in FCS Express. Users can then display, gate, color code, and compare the raw spectral data itself using specialized spectral plots in FCS Express designed specifically for spectral data analysis.
The resources below will help any level of Cytek or FCS Express user get started to combine technologies to help you get results!
Also see our Cytek free FCS Express license claim instructions.
Cytek Data Commonly Used Features
Gates are applied easily to Spectrum Plots with drag-and-drop as demonstrated in the example below.
Gates can be drawn on spectrum plots to identify subsets of interest for further quantification and analysis. In the example below, two rectangle gates are drawn on the spectrum plot to identify two subpopulations of interest, Pop1 and Pop2.
Similar to formatting other plots types, spectrum plots can be formatted and edited to display the data as you prefer. In the example below, the Display Mode is switched from Color on Density of all events to coloring based on gates in the layout.
Multiple samples or populations of interest can be displayed on a single Spectrum Plot. In the example below, three different colors of beads are overlaid with the unstained beads by dragging and dropping the samples from the Data List onto the plot.
To create an unmixing matrix in FCS Express simply use the Automatic Unmixing Setup wizard. The unmixing wizard functions similarly to the FCS Express compensation wizard making it easier than ever to move from standard flow cytometry data analysis to spectral data analysis. Select your single stain controls, parameters to unmix, and build histograms which will automatically set gates on positive an negative populations. Choose to calculate the matrix and get off and running with your analysis and reporting.
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When working with Cytek spectral data sets, users might prefer to visualize data from the individual detectors (V1, V2, V3, for example) rather than just the unmixed data channels (CD4, CD8, CD3, for example).
Also, users might prefer to not use the Unmixed data and only work with the Raw data in FCS Express.
The default assumption in FCS Express is that users will primarily work with Unmixed data.
As a result, the default visualization in FCS Express is to only view the unmixed data channels and to remove the individual detector channels for visualization to reduce the number of parameters available on any given plot.
For more information, we have a page dedicated to this here.
Application Examples
OMIP-069 is a 40-color flow cytometry-based panel developed by Cytek for in-depth immunophenotyping of the major cell subsets present in human peripheral blood. The panel presented here identifies CD4 T cells, CD8 T cells, regulatory T cells, γδ T cells, NKT-like cells, B cells, NK cells, monocytes and dendritic cells. For each specific cell type, the panel includes markers for further characterization by including a selection of activation and differentiation markers, as well as chemokine receptors. The panel can be used for studies aimed at characterizing the immune response in the context of infectious or autoimmune diseases, monitoring cancer patients on immuno- or chemotherapy, and discovery of unique and targetable biomarkers.
The FCS Express layout provides users with a foundation for data analysis using an optimized panel. You have the ability to customize this OMIP -069 layout to meet your specific analysis needs. Save your customized template and with each new data set you will move quickly and easily from analysis to results.
All the initial gates, plots, and visualizations will automatically populate, after opening the layout and loading your new data files into the data list. Make any adjustments as needed and then click on Run in Batch Processing to generate your desired automatic exports (PDFs, PowerPoint, Excel, etc) to your desktop. Make your analysis reliable, reproducible, and straightforward!
Download the FCS Express OMIP-069 layout template
OR
Download the FCS Express OMIP-069 layout as an example layout with pre-loaded data.
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- OMIP-69 Application Example
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- OMIP-69 Application Example
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- OMIP-69 Application Example
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- OMIP-69 Application Example
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- OMIP-69 Application Example
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- OMIP-69 Application Example
Cytek is an innovative leader in research and is committed to developing cytometry strategies that advance the scientific community. By applying panel design principles, a 35 color Immunophenotyping panel to investigate COVID-19 Immune response was designed using the Cytek Aurora. The teams at Cytek and De Novo Software have constructed an analysis layout to complement the COVID-19: 35 Color Immunophentoyping panel. The analysis layout identifies key populations of the immune system: Monocytes, TCR Gamma Delta T Cells, CD4 T Cells, T Regs, CD8 T Cells, CD4 – CD8- T Cells, NKT-Like Cells, NK Cells, B Cells, and Dendritic Cells.
The layout brings analysis beyond traditional gating and allows for new biological knowledge to be extracted from single-cell data by integrated pipelines and uMap. The use of high dimensional analysis tools found in FCS Express allows users to quickly visualize variables for further data exploration. The inclusion of charting features in the layout helps with the process of identifying differences in expression of immune cells between healthy and unhealthy samples for the user. The COVID-19: 35 Color Immunophenotyping panel makes Identifying populations of interest and extracting important variances streamlined and simple.
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- COVID-19: 35 Color IP Application Example
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- COVID-19: 35 Color IP Application Example
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- COVID-19: 35 Color IP Application Example
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- COVID-19: 35 Color IP Application Example
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- COVID-19: 35 Color IP Application Example
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- COVID-19: 35 Color IP Application Example
The Cytek cFluor™ Immunoprofiling Kit allows for the identification of helper T cells, cytotoxic T cells, B cells, NK cells and monocytes in human peripheral blood mononuclear cells and in whole blood. The reagents in this kit help to distinguish different subsets of T, B and NK cells; including regulatory T cells, naïve T cells, activated T cells, memory T cells, effector T cells, naïve B cell, memory B cells, nonclassical and classical monocytes.
The FCS Express 14C layout provides users with a turn key solution for data analysis of data acquired for the Immunoprofiling kit. Simply open the layout, load your data into the data list, and initial gates, plots, and visualizations will automatically populate awaiting your final analysis changes. Once complete, click on Run in the batch actions for automatic exports to your desktop. What could be easier!
Download the FCS Express 14C cFlour Immunoprofiling Kit layout template
OR
Download the layout as an example layout with pre-loaded data.
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- 14C IP Kit – Application Example
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- 14C IP Kit – Application Example
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- 14C IP Kit – Application Example
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- 14C IP Kit – Application Example
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- 14C IP Kit – Application Example
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- 14C IP Kit – Application Example
When working with highly multi-parametric data sets, having the right tools to perform high dimensional data reduction is key. FCS Express provides cutting edge tools that are directly integrated into FCS Express via "pipelines" which allow users to perform algorthims like tSNE, vSNE, uMAP, SPADE, FlowSOM and more without the need for plugins, without having to program R, and without having to upload and download data sets to an external cloud solution.
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- HD Data Reduction Application Example
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- HD Data Reduction Application Example
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- HD Data Reduction Application Example
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- HD Data Reduction Application Example
Phenotyping of cells is a common application in Flow Cytometry made easier with Cytek's spectral analysis solutions. FCS Express provides a way to conveniently report all cell type subsets, calculate custom statistics, and display data in spectral plots for visualization.
Download the PDF version of the Cytek Spectral Data Analysis layout, or open the published layout with the free FCS Express Reader to see what FCS Express can do for your analysis.
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- 16-C Application Example
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- 16-C Application Example
