Opening an fcs file with multiple tubes

[maaikesangster]

PLATFORM (Mac, PC, Linux, other):

Linux

OPERATING SYSTEM (eg OSX 10.7, Windows 8.1):

Ubuntu

SEVERITY (Critical? Major? Minor? Enhancement?):

Enhancement

DESCRIPTION:

• What were you trying to do?
  Most fcs files contain events from one tube in the experiment, but my flow cytometer spits out fcs files that actually contain all of the measurements. I would like to open such an fcs file that contains multiple measurements/tubes with cytoflow.
• What happened?
  Right now, It only opens the first one.
• What did you expect to happen?
  It would be nice to add a feature in cytoflow that could open all of the tubes in a single fcs file, or split them up in multiple files. A solution was already suggested for the fcsparser package but not yet implemented as far as I know: Unusual multi-FCS files eyurtsev/fcsparser#24

[bpteague]

Thanks for the link to the fcsparser issue. The FCS standard does in fact allow for multiple data sets in a single FCS file, though it's pretty explicit that this usage is deprecated.

Both fcsparser and the cytoflow library support this already. If you are using the modules directly (ie, from a Jupyter notebook), you can set the data_set parameter of the ImportOp operation. I've verified that setting 'data_set = 0' gives me the first dataset, and data_set = 1 gives me the second.

If you're using the point-and-click interface, it's a different story - there's definitely no support for choosing which dataset to use. I'll leave the issue open in case I get a brainstorm for an easy way to support it, but don't hold your breath.

[maaikesangster]

Thank you for your reply. The data_set parameter works indeed!