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.

To try out this software, I have been using a data set collected with Ignacio Zuleta that consisted of a portion of the yeast deletion library with a constitute reporter plus a unfolded protein response (UPR) reporter. The cells were initially sampled and then DTT was added to trigger the unfolded protein response. For additional samples were then taken, at roughly equal intervals of time. We would like to see how the response of the cells varied as a function of time across the different deletion strains.

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.

FCS Express

Software by De Novo Software, sold through BD Biosciences. Lite version sells for $300, pro version cells for $800 (standalone license). Windows only.

• Looks fairly full featured. Similar to FlowJo in look and feel.
• Couldn't see how to get the type of plot that I am looking for (no obivous time series functionality)

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.

• http://www.wehi.edu.au/faculty/advanced_research_technologies/flow_cytometry/weasel_for_flow_cytometry_data_analysis/

Flow

"Flow is an open source software tool for flow cytometry analysis that integrates ontology, statistics and visualization for the classification and comparison of multi-color flow cytometry data sets. Together, these provide powerful new tools for the experimentalist or clinician to analyze flow cytometry data in a different way; one we hope will complement and perhaps one day supersede the traditional strategy of sequential gating."

• https://galen.dulci.duhs.duke.edu/flow/

BioConductor

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).
• http://bioconductor.org/

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

Python

• Similar to MATLAB, there appear to be a couple of efforts at interacting with raw data:
  • FlowPy - read FCS files into python and allow data filtering

R

• See description of BioConductor package above.