Convert Accuri .c6 flow cytometry files to .fcs

A command line program for the conversion of Accuri .c6 flow cytometry data files to the standard .fcs format, has been released today via github and PyPi.


Someone in our lab recently needed to convert a large number of files (>500) and processing each one manually in the c6 software wasn't going to be much fun. This script is the result of trying to automate that process, and it works. Usage is not exactly straightforward, however it is quite powerful. In it's standard configuration it will find all .c6 files in the current directory, match every sample name outputting .fcs files named [filename.c6]_[row|column].fcs. This is probably perfectly fine for most uses.

However, it also supports the use of regular expressions to extract data from your .c6 Sample Name fields, and then saving the resulting .fcs into named files and folders built from that data. Have fun!

Download & Installation

You can install accuri2fcs via the PyPi Python package system. You can install via the command line with:

pip install accuri2fcs

Alternatively the code (and issue tracker) is available on github.

Once installed, using is as simple as entering on the command-line:


…to convert everything in the current folder. You'll end up with a folder named fcs containing the output. For more options type accuri2fcs --help.


Accuri2fcs is licensed under a Modified BSD 2 clause (i.e. completely free), my license of choice for interoperability software.


This software is not under active development (I don't do flow cytometry) but any suggestions or bug reports are still appreciated.

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