FCS data reader

Read FCS 2.0 and FCS 3.0 format flow cytometry files

Description

[fcsdat, fcshdr] = 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.

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 7.0.4 (R14SP2)

[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.

[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.

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[Quanyuan He]

It works well, Thank you.

[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!

[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.