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Most of the enhancements concern control of gates. Gate numbers can now be
assigned to input files on the input file selection screen. If an undefined
gate is assigned, the graphic gate-setting screen will come up automatically
after the file is first processed ungated. Multiple gates can now be
displayed on a dot plot.
On the input file screen, tagging is now independent of other marks
(control, histogram overlay, gate assignment). This allows different
subsets to be tagged in different runs without losing other markings.
Also on the input file screen, an input file name can now be duplicated (then
perhaps moved). Among other things, this allows a single file to be gated
with different gates, and the resulting histograms to be overlayed.
This is the end of the enhancement description. A slightly modified
introduction MFI follows.
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INTRODUCTION TO MFI
MFI is an IBM PC-compatible list-mode FACS data analysis program. It is free
for non-profit uses. MFI is advantageous when large numbers of files need to
be analyzed for single-color medians (it has limited support for multi-color
work: no quadrants). It allows rapid batch processing of a hundred or more
files in a few minutes, producing a compact printed table of results. MFI was
designed to be usable without graphics, although substantial graphics have
also been built-in. The graphics can be turned off, or watched, during batch
analysis. MFI warns when cytometer parameters were changed between files.
CYTOMETERS TESTED
MFI has been tested on files from Becton-Dickinson cytometers employing
FACScan, FACStar, LYSYS II, Consort 30, and FACS 440 software, as well as on
files from the Coulter Elite cytometer, and a file generated by Verity
Software's WINLIST. I will attempt to adapt it to files from other sources as
soon as they are supplied to me by interested potential users. The Coulter
Elite Profile produces nonstandard files which require conversion for use with
MFI.
LOG->LINEAR, BLANK SUBTRACTION, PEAK DETECTION, TIME SLICING
MFI calculates median (and mean) fluorescence intensities for
rectangularly-gated events. It automatically converts log-acquired data to a
linear scale, subtracts the 'blank' fluorescence intensities for any number of
arbitrarily tagged control files, and converts to kilo-molecules of equivalent
soluble fluorescein if desired. Multiple peaks are detected automatically by
criteria of adjustable sensitivity; medians and event percentages are
automatically calculated for subpopulations. A single data file can be
time-sliced for kinetic analysis.
PRINTABLE OVERLAYED HISTOGRAMS, DOT PLOTS, GATE SETTING
MFI optionally shows histograms for up to 6 parameters and a dot plot on a
single screen. Each graph can be magnified to full-screen if desired.
2-parameter gates can be set graphically; limits for a third parameter (e.g.
propidium iodide) can be entered manually. All graphics screens can be
printed on a variety of printers. Histograms from up to 2 previous files can
be overlayed on those for subsequent files, and can be smoothed. Gated
histograms (optionally smoothed) can also be written as ASCII data files for
plotting by publication-quality software.
EASE OF USE
MFI is completely menu-driven and easy to use. It has extensive built-in
help. It has many configuration options; all configuration selections,
including arbitrarily ordered input filenames, are automatically saved so that
each session begins with the previous settings. Unnecessary parameters (e.g.
FL2 and FL3 when only fluorescein was used) can be omitted from the output,
and parameters can be put out in any order.
Each run begins by organizing a list of data files. Filenames can be
rearranged if necessary, and a subset of the files present can be tagged for
each run. Files can be marked as control files, for histogram overlays on
subsequent files, and the gate applicable to each file can be indicated.
Filenames can be duplicated on the list; this allows multiple gates or dot
plots to be applied to a single file in a single run.
List mode data files must be available on a PC compatible computer since MFI
does not operate on HP, VAX or other operating systems. A summary of methods
for transferring files from HP's to PC's is available. The C source code for
MFI is available should someone wish to port it to other operating systems.
HOW TO GET IT
MFI version 3.0, released November 1992, is available by anonymous FTP at
flowcyt.cyto.purdue.edu in directory pub/martz. On request, I will transmit
it UUENCODED by internet, or, if absolutely necessary, snail-mail a floppy
diskette. The program uses nearly 500K of memory, and the EXE file is
nearly 160K in size (transparently compressed).
--
/* - - - - - - - - - - - - - - - - - From - - - - - - - - - - - - - - - - - -
Eric Martz emartz@titan.ucc.umass.edu Professor of Immunology
Voice 413-545-2325, FAX 413-545-1578
Morrill IVN Rm 203, Dept Microbiol, Univ Mass, Amherst MA 01003 USA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
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