 |
 |
 |
 |
> The WinMDI and MFI softwares failed to read my listmode files, generated
> using Profile II. Coulter people pleast take note.
With the Profile series only, Coulter elected to save the listmode files
in non-FCS (Flow Cytometry Standard) format. However, a conversion
program Pro2FCS is available from Verity Software House, Topsham ME,
207-729-6767. Most other cytometers and acquisition software packages
obey the FCS. By the way, this is all clearly explained in the on-line
help within MFI. MFI reads Pro2FCS converted files; I'm not sure about
WinMDI (it probably does also). Here is an excerpt from MFI's on-line
help giving the listmode files supported:
CYTOMETER/SOFTWARE FILES TESTED
MFI is designed to digest FCS1.0 or FCS2.0 standard data files. When first
using MFI, be sure to compare results carefully with those from trusted
software. There is the real possibility of inadvertant errors with some
data file formats; no warranty is made nor implied. MFI appears to work
with list mode files from cytometers and software listed on the following
screen. Be sure to see warnings * thru **** below!
WARNING: Some of the cytometers or software listed below are quite capable of
producing files incompatible with MFI. MFI CANNOT process files which
contain:
- more than 8 parameters,
- log scales with more or less than 4 decades
CYTOMETERS/SOFTWARE CAPABLE OF GENERATING MFI-COMPATIBLE LISTMODE FILES
Becton-Dickinson (800-952-3222)
FACStation 1.0 'CellQuest' MacIntosh System Software 7.1.0 (FACScan) ***
LYSYS II versions 1.0, 1.1, 1.2
(HP 340: FACScan, FACStar-Plus, FACSVantage)
FACScan Research Software (HP 310, 1988)
FACStar PLUS Research Software (HP 310, 1988) * SEE WARNING BELOW
"CellFit" CRDNA Software Version 1.0 5/88
Consort 30 Software (HP 310)
FACS 440 (VAX/VMS or DOS)
Coulter (800-635-3497)
Elite (DOS 4, 5)
Epics XL (DOS)
Epics w/ MDADS/86 DOS
Profile, only if converted with Verity Software's Pro2FCS **
Software Only
Cytomation, Inc.'s CyCLOPS ****
Verity WINLIST 1.0, 2.0 **
* FACStar PLUS Research Software provides an option to save only selected
parameters to the list mode files. This option is called 'list: on/off'
and is found near the bottom of the screen under 'Parameters' on the
'Control Page' accessible from the 'Acquisition' menu. If you turn off
certain parameters, be sure not to leave 'holes' in the sequence. When
holes are left, the resulting file structure cannot be digested by MFI!
For example, it is fine to have on only FSC, SSC, and FL1; but, if you have
on only FSC, SSC, and FL2 (leaving a 'hole' where FL1 would normally be),
the resulting files cannot be processed by MFI (although they can be
processed by FACStar PLUS Research Software).
** The Coulter Epics Profile produces non-standard list mode files
incompatible with MFI. These can be converted to FCS format with
Pro2FCS available from Verity Software (207-729-6767, Topsham ME USA).
*** The FACStation 1.0/MacIntosh files tested do not include instrument
gains, PMV's, threshold, or compensation. Becton-Dickinson promises to
rectify this serious deficiency in a future upgrade. This deficiency
precludes MFI from detecting inadvertant changes in instrument settings.
**** Considerable time has been spent attempting to make MFI correctly
interpret CyCLOPS files provided by Cytomation, Inc. (303-226-2200, Fort
Collins CO USA). However, these files have changed in structure several
times, do not specify which version of the software produced the file (or even
that Cytomation software produced it), and do not provide some critical
information unambiguously. Hence, MFI may remain unable properly to interpret
files from some versions of CyCLOPS.
I will attempt to customize MFI for other formats provided to me. Adaptation
will likely be needed for new formats since adherence to the published Flow
Cytometry Standard is loose at best. Please transmit problem data files by
anonymous FTP to directory /incoming at flowcyt.bio.umass.edu; or UUENCODE
PKZIP'd or ARC'd versions to me. Small files (1,000 to 5,000 events) are
much preferred! Be sure to inform me of the origin of the file(s)
(cytometer, software, computer) at emartz@microbio.umass.edu.
/*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor of Immunology emartz@microbio.umass.edu
Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578
Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/
|
|
|
|