Table of Contents Standalone Application (MATLAB not required) Software Prerequisites Installing the Single Cell Debarcoder Running the Single Cell Debarcoder in MATLAB

The Single Cell Debarcoder (SCD) for mass cytometry data is distributed as a standalone MATLAB application. That means that it requires installing the MATLAB Compiler Runtime (MCR), but an installation or license for MATLAB itself is not required. It is important to install corresponding releases of the MCR and the Normalizer; v0.2 of the Normalizer requires

• MCR Release R2013b (8.2) for Mac OSX
• MCR Release R2013a (8.1) for 64-bit Windows

Instructions for download and installation of the MCR are available here.

The SCD is available here.

Simply download and unzip the version corresponding to your operating system. You are now ready to debarcode FCS files.

Download the source code, and also download the FCS reader and writer available in the MatlabCytofUtilities repository. To run the debarcoder, at the prompt type

>> single_cell_debarcode_gui

You are now ready to debarcode FCS files.