Alternative to the commercial BD Diva or FlowJo to open and analyze flow cytometry data in FCS 2.0, 3.0, or 3.1 format.
Updated 12 Mar 2023

View License

FlowCyLab v1.1 was developed using App Designer and R2022b.
  • If you have Matlab Run Time 2022b, double click on .exe. This was only tested on Windows 11.
  • If you have Matlab, double click on .mlapp. The .mlapp file can be opened within Matlab to examine and modify.
There are three tabs in the App:
Tab #1: Navigate to a folder and browse the content. Double click on a file in order to load. Or select multiple files (either shift or control key) and press “Open”.
Tab #2: Manage loaded files. Enter abbreviated (or mnemonic) names under “Abbrev” to refer to each uploaded data. Press “Update”. “Delete” removes highlighted data from the workspace. Move “Up” or “Down” to rearrange the files.
Tab #3: Analysis of loaded data.
  • Rearrange the data using ‘Up” or “Down”. “Open” new data or “Delete” loaded data.
  • Double click displays 2D scatter and 1D histogram in a single figure.
  • Press “2D Plot” or “1D Plot” to display 2D scatter plot or 1D histogram of selected channels.
  • Use “<” or “>” to navigate through the data set (1D or 2D).
  • Create “2D Gate” by drawing a polygon. Or move the sliders in the “1D Control” panel to define the lower and upper limits and create a “1D Gate”.
  • Selecting the checkboxes next to loaded data allows 2D scatter or 1D histogram of multiple files to be displayed in a single figure.
  • Selecting the checkboxes next to 1D or 2D gates will apply these gates in 2D and 1D plots.
  • Checking “Show Ungated” next to 2D or 1D will show both gated and ungated data.
  • Moving the slider in the 2D panel will create quadrants by drawing vertical and horizontal lines.
  • Moving the “Density” slider will reduce the density of scatter plot (20 – 100%).
  • Selecting “Show Stat” will show the stats for the quadrants as well as displayed gated data points.
  • Multiple Windows” will open separate figures for 1D, 2D, Overlay.
  • Checking “1D/2D” in the 1D panel will show both 2D scatter and 1D histogram while navigating with “<” and “>”.
  • Overlay” in the 1D panel will superimpose selected data sets.
  • Fit” in the 1D panel will fit the histogram with an exponential Gaussian, thus generating a smooth curve through data points. Checking “Data” will include data points with the fit.
  • New Wind” will open new figures when repeatedly pressing “Overlay”.
  • Smooth knob” will change the bin size for 1D in order to smooth the curve.
  • Save Fig” will save a figure (e.g. in “.jpg”).
  • Compensation can be introduced by adjusting the slider in the “Compensation” panel to compute: Target = Target + Origin * (compensation percentage). (Currently not implemented).
The session can be saved by pressing “Save Session” at the top and can be restored from a stored file by pressing “Restore Session”. “Reset” will clear the workspace by deleting data and gates.

Cite As

Sheldon Park (2024). FlowCyLab (https://www.mathworks.com/matlabcentral/fileexchange/125660-flowcylab), MATLAB Central File Exchange. Retrieved .

MATLAB Release Compatibility
Created with R2022b
Compatible with any release
Platform Compatibility
Windows macOS Linux

Inspired by: fca 2.2, fca_readfcs

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!
Version Published Release Notes

Added a few additional features. Fixed bugs.

Included the mlapp file, which can be run within Matlab.

Updated summary.

Updated the image.

Changed the Description.

Changed the image.

Packaged Matlab executable that can be run directly without installation.