Here are downloads and documentation for MATLAB code routinely used in the Springer Lab. Each of the following “toolkits” is independent, so you can download one without having to download others. Individual functions will require other functions from its toolkit and should not be distributed by themselves.

At the bottom of the page, there are tutorials to demonstrate basic usage of the code. Details on each function is included in the code itself and can be accessed via MATLAB’s built-in help system. In particular, you can see a full function list for each toolkit by typing “doc” followed by the name of the toolkit. For example: doc Flow-Cytometry-Toolkit.


Here are links for downloading each code package. To “install”, just unzip the code and add the folder to your MATLAB path.

  • Flow Cytometry Toolkit (Latest version zip) – A set of basic functions for manipulating flow cytometry data and segmenting cell populations, developed by Bo and Jue. Designed to be modular but low-level, so elaborate analyses must be designed by the user.
  • Utility (Latest version zip) – Miscellaneous helpful MATLAB functions. Includes csv2cell.

Pending: The code for analyzing double gradients from Renan and Yoni will be posted here when it has been completed.

NOTE FOR PROGRAMMERS: To contribute changes to this code, clone the toolkit’s repository from the Springer Lab Github instead of downloading the zip files above. To push back your changes, you will need a GitHub account and permissions from an admin (Jue, Kayla, or Chiara).


Flow Cytometry Toolkit
Tutorial (Also available as interactive .m file)- Demonstrates basic functionality of the toolkit: load .fcs files, plot histograms and scatterplots, filter subpopulations of events, manual segmentation, automatic segmentation.

Function Reference: Type doc Flow-Cytometry-Toolkit at the MATLAB command-line after installing the code.