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How-To’s of Managing Flow Cytometry Data

How-To’s of Managing Flow Cytometry Data


Flow cytometry data is widely used across diverse set of research areas including drug discovery and personalized medicine. Ongoing improvements to instrument technology allow scientists to generate more and more targeted reagents which in turn leads to increasing amounts of high-dimensional flow cytometry data. As the application of flow cytometry in immune monitoring becomes more prevalent, many scientists are finding themselves asking “what is the best way to manage flow cytometry data?”

As teams evaluate software tools for managing flow cytometry data, there are several things to keep in mind. Instrument-generated fcs files from cytometers are generally not useful to scientists on their own. Typically, users interrogate their data by creating an analysis file, either with manual gating through commercially-available tools like FlowJo and FCS Express, or by performing computational analyses via free software packages like Bioconductor. Ensuring that data provenance is maintained between fcs files and analysis is vital, and provides valuable information for groups looking to validate or re-analyze the raw data in the future.


Best practices for maintaining comprehensive flow cytometry records using LabKey ServerMaintaining Comprehensive Data Records

The LabKey Server software platform help groups ensure data provenance and maintain comprehensive flow cytometry records by:

  • Allowing for import of raw fcs files as well as analysis files
  • Validating all fcs files are present when linking data to a FlowJo workspace file
  • Auditing file upload for analysis data used in a LabKey study
  • Surfacing run parameters and compensation values for further quality control

Add value to flow cytometry analysis runs using LabKey Server

Adding Value to Runs

LabKey Server’s flow cytometry tools can also helps add value to runs by:

  • Providing mechanisms to insert keywords and adding metadata
  • Ensuring gate naming is consistent across workspaces
  • Allowing administrators to merge gating strategies when necessary
  • Visualizing statistics in Levy-Jennings plots for valuable quality control metrics


Using LabKey Server visualization tools to interrogate flow cytometry analyses

Improving Data Analysis Workflows

Using LabKey Server, scientists can achieve further improvements to their analysis workflow by:

  • Integrating flow cytometry statistics and 2D plotting within the LabKey Server platform
  • Creating easy integration mechanisms across flow cytometry runs, panels, and projects
  • Providing built-in visualization tools for users to interrogate their data

With the right tools, scientists can maximize the insight derived from their flow cytometry data. To learn more about using LabKey Server to manage flow cytometry analysis, check out the flow cytometry documentation library or request a demo.

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