Flow cytometry software

This page contains notes on flow cytometry software that I found while trying to analyze some data from UCSF. Mainly for internal usage, but figured I would put it online in case others needed it.

Commercial packages

FlowJo

This is a very well-designed package that has a lot of analytical tools built in. Simple things it can do:

• Load lots of different data sets and choose various subsets of the data for analysis
• Plot histograms, scatter plots, time series, etc

Things that don't look so easy:

• Scripting or other more complicated programming functions

The software costs about $1500 for a node-locked license or key-based license.

Open source/free packages

Weasel

This is a basic package that has a variety of plotting tools, but doesn't seem to have nearly as much functionality as FlowJo. The user interface was pretty crude.

BioConductor "flow cytometry" workflow

The BioConductor software suite is a set of R packages that includes a number of tools for reading and manipulating flow cytometry data. The basic libraries handle reading FCS files, maintaining dataframes consisting of collections of FCS data, and a variety of analysis and plotting tools.

• The plot at the right shows an example of a series of histograms at different timepints. SSC-A is (roughly) the cell volume, FITC-A is the UPR response reporter and mCherry-A is a constitutive fluorescent protein. Produced using the densityplot() function in the flowViz library.
• The iFlow package is a more visual interface with some basic functions for loading and plotting data (roughly comparable to Weasel).

Toolboxes

MATLAB

• There are several routines for loading FCS files and plotting standard flow cytometry plots:
  • Flow Cytometry Data Reader and Visualization - basic reading and plotting
  • FCA toolbox - a bit more functionality, including some ability to define gates [doesn't appear to work in MATLAB 2009a]
  • FCS data reader - read FCS 2.0 and 3.0 data files