----->>> On 2-Feb-2001, filipesan@teleweb.pt wrote: > As part of my pos-graduate studies, I am developing a > software cytometer simulator to help high school and college > students in learning flux cytometry. I would like this > simulator to read FCS3.0 files, but unfortunately I can't > find any on the Internet to help me. > > Can you help me on this matter? I would like a file with a > primary and supplemental TEXT segment, so I could see how the > $BEGINSTEXT and $ENDSTEXT keywords work. > > I also can't help notice that when I search Yahoo or > Altavista for "FCS3.0", all I get are discussions that > abruptely end in 1997. What happened? Did the standard died? As I understand it, FCS 3.0 was accepted by ISAC as the current standard, in 1998. Yet, I don't know of any instrument or acquisition system that writes them. The de facto standard remains FCS 2.0. Consequently, I've never run across files that use the $BEGINSTEXT and $ENDSTEXT keywords. I can see that it might be potentially useful for capturing auxilliary information such as instrument settings, or to snap a picture of the operator when the cells are run and hide that in the FCS file, but you probably don't need to use this, so you'd just add $BEGINSTEXT/0/$ENDSTEXT/0/ to your text section, and don't worry about it. And when reading FCS 3 files, just ignore the values you find in those tags. If you do choose to read supplemental text (and more importantly, when you the read primary text section) make sure you use the the END keyword correctly. It points to the LAST byte used, NOT the next byte, as most programmers want it to. The length of the section is (end - begin - 1) I have C++ or Java code for reading/writing FCS files, which you can have, but it relies on all sorts of other libraries and objects, so it might be hard to use once extricated from the rest of FlowJo. But let me know if you're interested, and I'll send you the files. There has been talk for a long time about writing a public domain library for reading and writing files, but it never has come about. The nice thing about there being a few cytometer vendors who are slow to make changes is that data compatibility has never been a big issue. Adam ------------------------------------------------------------ Adam Treister Tree Star, Inc. ph: 1-650-508-9349 fax: 1-650-508-9186 adam@treestar.com <http://www.treestar.com> ------------------------------------------------------------
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