FCS data reader

Read FCS 2.0 and FCS 3.0 format flow cytometry files

Description

[fcsdat, fcshdr, fcsdatscaled, fcsdat_comp] = fca_readfcs(filename);

Read FCS 2.0 and FCS 3.0 type flow cytometry data file and put the list mode parameters to the fcsdat array with size of [NumOfPar TotalEvents].
 Some important header data are 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 will calculate the compensated fluorescence
intensities (fcsdat_comp) 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 and Luminex type list mode files.

If you find unsupported LM file type please email me.

You can also find a complex flow cytometry data evaluation toolbox(GUI) at the FileExchane area including this function and containing more specific options:

http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=8480&objectType=file

• MATLAB release: MATLAB 7.10 (R2010a)

[Malcolm McFarland]

I was initially unable to get this code to read BD Influx FCS files created with Sortware software. I found that the mnemonic_separator is 'LF' (line feed) and the data precision is 'uint16'. I modified the get_mnemonic_value subfunction and the section that reads events. It now works well, although I think some header information is missing. Thanks for some very helpful code.

[Avaneesh]

This code can't be used to read Accuri C6 FCS3.0 files. I find that the mnemonic separator is '/'. Made the required changes in the code, works great.
Great code!

[Quanyuan He]

It works well, Thank you.

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[Brian Harms]

Overall nice file. One small error in the code: in line 181 (which converts log-scale FACS data to linear-scale data), the variable "fscdat" needs to be changed from uint16 to double in order for the code to work properly.

[Ivan Cao-Berg]

I find it is an excellent script. But I do have one comment.
In line 64 you can find the following code

fid = fopen(filename,'r','ieee-be');

If you are using a Windows, Matlab will not have a problem. If you are using Linux you should change the line to

fid = fopen(filename,'r','b');

Technically 'ieee-be' and 'b' are to suppose to be the same option. But I had problems and I fixed it that way.