Hi Tom,
The FCS2.0 Format is described in Cytometry, (Dean et al.: Cytometry
11:323-332, 1990), FCS1.0 is referenced there. A newer version(FCS3.0) is
being developed at present and a description can be found at ISAC's web
site.
FCS formats describe ways in which flow cytometric data can be stored, and
most manufacturers conform with it to some extent, there are other formats,
such as Coulter's Profile(a description of which is available from Coulter).
Briefly, FCS files are in three major parts:
1) a header section in ascii, the first six characters give the FCS
version(eg "FCS1.0"), there are also ascii numbers giving offsets to the
other parts of the file.
2) a text section, again in ascii this contains keywords (default ones
start with dollar signs), followed by values. This section is used to
describe the machine set-up, and carries descriptive text such as sample
ID. Keywords are separated from values using a special character (this can
be any character, but should be the first character in the text section so
that your program can spot it), B-D uses a slash (solidus), Coulter uses an
exclamation mark.
This part also lets you know what format the actual data is in.
3) the data section, this can be encoded in ascii, binary, or floating
point numbers, I haven't come across any format other than binary. And data
can be organised as list mode, uncorrelated or correlated mode data.
List mode has a value for each parameter in event order (eg cell one
FSC,SSC, FL1, cell two FSC,SSC,FL1 etc).
Uncorrelated mode has data organised as histogram data in parameter order (
eg FSC channel 1 count, FSC channel two count, FSC channel three
count...FSCchannel 1023 count, SSC channel one count etc), note that
cellquest only allows one histogram per file, although other software (and
the format) allows more.
Correlated mode has x-y frequency data for two parameters, allowing
plotting of contour and density plots.
There is also provision for the results of several runs to be included in
the same file, so far I've only come across files from Bio-Rad that use
this feature, Cellquest seems to ignore all data sets other than the first.
I hope you find this useful
Ray
At 5:42 pm -0500 15/3/97, Tom Gallivan wrote:
>hi there. just took a look at the new modfit LT and noticed
>that the old stuff with being able to define file formats is gone
>(offset, composition, etc.) and it mentioned that it uses .FCS
>or Flow Cytometry Standard format. Does anyone know where i can
>get some info on what this file format actuallly is? i'm interested
>writing some software myself. (not quiet of the modfit scale ;)
>
>thanks a bunch. :)
>anders
>anders@pobox.com
>
>(mail me, or i'll check the archive on the website)
Ray Hicks
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