The MFI (Median Fluorescence Intensity) free analysis software I authored
was last mentioned on this list in 1993. (I can tell because of the
excellent Kelly/Robinson history search!) Development continued into 1996,
but ended before Windows and the WWW became universal. Since I continue to
get new requests, I have made a new MFI Home Page,
http://www.umass.edu/microbio/mfi with a new method of installation, more
suited to current versions of Windows.
MFI's forte is extracting median intensities from large numbers of listmode
data files quickly and efficiently. Because MFI reports many checks and
warnings, and a range of values at the end of each run, you can tell whether
to rely on the medians it tabulates WITHOUT examining graphics for every
file. If the event cloud drifts relative to the scatter gate (or partially
out of it), or you have large pileups of off-scale events in end channels,
MFI indicates for which files, so you know which graphics need scrutinizing.
MFI is ideal for antibody titrations. When histograms are multimodal, MFI
automatically detects and objectively separates the peaks, giving
percentages of gated events and blank-subtracted linear intensities (when
log-acquired) for each peak. Optionally, intensities can be reported in KMESF.
Also often praised is MFI's ability to convert raw listmode FCM files to
plain text (ASCII). Such plain text lists of numbers are digestible by
common scientific plotting, spreadsheet or statistics software. In addition,
MFI can emit spreadsheet-ready tables of median intensities.
For those still using older acquisition software that does not record time
as an event, MFI enables kinetic studies of calcium fluxes, antibody binding
rates, etc. by slicing listmode files by order of events recorded.
MFI can calculate gate ratios (e.g. cells/bead) and transform parameters.
MFI comes with an extensive tutorial with sample data files, covering
titrations, kinetics, 3-color work, and quantitating cell aggregation (by
loss of single cell density relative to plastic beads). The tutorial not
only teaches how to use MFI, but teaches some important cytometry principles
as well. The new web-browser version of the tutorial is lavishly
illustrated with screenshots.
Because MFI is unsupported freeware, by the act of using it, you accept
responsibility to verify suitability for your purposes. Enter the "MFI/FCS
Validation Suite" (can be used with ANY analysis software!). This is a set
of synthetic data files, and programs to generate them, with known medians
etc. One of the programs can convert plain text lists of numbers into FCS
listmode files -- so you can make any data into "flow" data (hmmmm). At one
point I generated a synthetic two-million event file, and MFI processed it
correctly. Want to send your colleagues a listmode file that displays "[your
name] was here!" in the scatter dot plot? To be honest, you'll have to do a
little C programming for that, but you can see MY name :-)
The new downloadable installer includes the entire MFI website, tutorial,
and sample data files (it will take about 4 megabytes on your hard disk),
and ready-to-click shortcuts to run the program.
For those, like myself, who use Joe Trotter's fabulous WinMDI, MFI is not a
_competing_ alternative. MFI does different (and fewer!) things well. The two
programs complement each other nicely.
-Eric Martz
Former immunology researcher, current immunology teacher, and
now ...
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
The Protein Explorer: http://proteinexplorer.org
Workshops: http://www.umass.edu/molvis/workshop
World Index of Molecular Visualization Resources: http://molvisindex.org
PDB Lite molecule finder: http://pdblite.org
Molecular Visualization EMail List:
http://www.umass.edu/microbio/rasmol/raslist.htm
Eric Martz, Professor (Immunology), Dept Microbiology
U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532
http://www.umass.edu/molvis/martz
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