fca_readfcs

Version 2020.06.22 (6.53 KB) by Laszlo Balkay
Read FCS 2.0, FCS 3.0 and FCS3.1 format flow cytometry files
4.7
(19)
9.7K Downloads
Updated 22 Jun 2020

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[fcsdat, fcshdr, fcsdatscaled, fcsdat_comp] = fca_readfcs(filename);
Read FCS 2.0, FCS 3.0 and FCS 3.1 type flow cytometry data file and creates fcsdat array with the size of [NumOfPar TotalEvents].

Some important header data are also stored in the fcshdr structure:
TotalEvents, NumOfPar, starttime, stoptime and specific info for parameters
as name, range, bitdepth, logscale(yes-no) and number of decades.
[fcsdat, fcshdr] = fca_readfcs;
Without filename input the user can select the desired file using the standard open file dialog box.

[fcsdat, fcshdr, fcsdatscaled] = fca_readfcs(filename);
Supplying the third output the fcsdatscaled array contains also the scaled parameters. It might be useful for logscaled parameters.
[fcsdat, fcshdr, fcsdatscaled, fcsdat_comp] = fca_readfcs(filename);
In that case the script calculates the compensated fluorescence
intensities (fcsdat_comp) as well, if spillover data exist in the header
The program should work also in the case of Becton EPics DLM FCS2.0, CyAn Summit FCS3.0, FACSDiva, BD LSR-II, Partec, Accuri, Luminex, Attune NxT, Biorad ZE5 and BD FACS Melody type list mode files.
If you find unsupported LM file type please email me.

Cite As

Laszlo Balkay (2024). fca_readfcs (https://www.mathworks.com/matlabcentral/fileexchange/9608-fca_readfcs), MATLAB Central File Exchange. Retrieved .

MATLAB Release Compatibility
Created with R2018a
Compatible with any release
Platform Compatibility
Windows macOS Linux
Categories
Find more on Data Import and Analysis in Help Center and MATLAB Answers
Acknowledgements

Inspired: Ratiometric FRET, CytoMAP, Gating-ML, FlowCyLab

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Version Published Release Notes
2020.06.22

Update to read FCS3.1 data from BD FACS Melody.
2020.04.11

Update to read FCS3.1 data from Biorad ZE5
2017.11.1.0

Minor update to read FCS3.1 data from Attune NxT
Minor update to read FCS3.1 data of Attune NxT
2017.6.1.0

The code was modified to read FCS 3.1 file.
1.12.0.0

The FCS 3.0 standard enables the mixture of word lengths in the data, this upgrade modified the code according to. The linefeed (ASCII code 10) as
the mnemonic separator was also added.
Thanks for William Peria /Fred Hutchinson Cancer Researc
1.11.0.0

More accurate compensation correction, gain scaling and appropriate reading for large file size are added. Thanks for Rachel Finck; Garry Nolan's lab at Stanford University and Andrea Pagnani; Politecnico Torino, Human Genetics Foundation.
1.9.0.0

The fluorescence compensation has been implemeted into the code. Thanks for Rick Stanton, J. Craig Venter Institute, La Jolla, San Diego
1.8.0.0

The fluorescence compensation has been implemented into the code. Thanks for Rick Stanton, J. Craig Venter Institute, La Jolla, San Diego
1.6.0.0

Updated to read Luminex 100 data file. Thanks for Ofir Goldberger, Stanford University
1.5.0.0

Additional minor changes on the help section.
1.3.0.0

The help section of the m file was modified.
1.2.0.0

Updated to read the Partec CyFlow format file. Thanks for
Gavin A Price

1.1.0.0

Updated to read the Partec CyFlow format file. Thanks for
Gavin A Price
1.0.0.0

Updated to read the BD LSR II file format and including the comments of Allan Moser (Cira Discovery Sciences, Inc.) Thanks!