Post Wed Nov 02, 2016 7:22 pm

"OTHER" section in Fluidigm FCS files

I have been tinkering around the FCS files generated by the Fluidigm software using hex edit and noticed that they include two "OTHER" segments. The first segment includes an XML file which seems to have channel names and some aggregate statistics and an additional binary section. The second segment is just 0000000.

The Helios normalization tool expects these segments, if you remove them (by importing and exporting the file through flowCore, for example) the normalization tool will crash with an "Sequence contains no elements" error. I tried manually adding these into an FCS file, manually fixing the header appropriately, but I still get the error.

Does anyone have any experience generating Fluidigm-like FCS files? Or could elaborate on the spec that the Helios normalization tool is expecting?