This file contains SELECTED PORTIONS of MFI's on-line documentation.
Run MFI and select HELP to write all/selected documentation to this file.
(This file can be deleted; MFI will re-write it on request.)

MFI (Median Fluorescence Intensity) ver. 3.4I (c) 1992-95 by Eric Martz.
.............................................................................
WARNING: Testing has been minimal.  Check results carefully vs. trusted soft-
ware.  Report problems to emartz@microbio.umass.edu.  Use anonymous FTP to
put problem data files in directory /incoming at flowcyt.bio.umass.edu.
           >>   FOR RESEARCH USE ONLY; NOT FOR CLINICAL USE.  <<
.............................................................................

SHORT OVERVIEW OF MFI
 
MFI is an IBM PC-compatible program for analyzing flow cytometry list-mode
data files.  It is free for non-profit uses.  MFI is advantageous when large
numbers of files need to be analyzed for corrected median fluorescence
intensities (it does not do quadrant analysis).  It is also useful for
visualizing kinetic changes, even when time is not recorded as an event
parameter.  MFI 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, or when the
event cloud shifts away from the scatter gate.  Many features are designed to
avoid inadvertant misinterpretation of data.

                           CYTOMETERS TESTED
 
MFI can process files from Becton-Dickinson cytometers employing FACStation,
FACScan, FACStar, FACSVantage, LYSYS II, Consort 30, and FACS 440 software,
as well as Coulter Elite, Epics, XL, Verity Software's WINLIST 2.0, and
Cytomation's CyCLOPS.  The Coulter Elite Profile produces nonstandard files
which require conversion with Verity's Pro2FCS for use with MFI.  I will
attempt to adapt MFI to files from other sources when supplied to me by MFI
users.

  LOG->LINEAR, BLANK SUBTRACTION, PEAK DETECTION, GATE RATIOS, FILE 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.  Ratios of
events in different gates can be reported.  A single data file can be sliced
for quantitative kinetic analysis.

    HISTOGRAMS, DOT PLOTS, TIME GRAPHS, GATE SETTING, ASCII CONVERSION
 
MFI optionally shows histograms for up to 6 parameters plus a gating dot
plot, all on a single screen.  It can also show 3 additional screens of up
to 9 dot plots each.  MFI can draw kinetic line graphs when X is time or
event number.  Each graph can be magnified to full-screen if desired.  2- or
3-parameter gates can be set graphically.  Up to 8 gates can be remembered
simultaneously.  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) or list mode data can also be written as ASCII data files for
spreadsheets or plotting by publication-quality software.

                               EASE OF USE
 
MFI is completely menu-driven and easy to use.  It has extensive built-in
help, and comes with a detailed tutorial plus sample data files.  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.  Up to 16 runs (tagged subsets) are remembered, each with a
description.  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.  A one-line
descriptive label can be inserted into each file.
 
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 on email request.

                              HOW TO GET IT
 
MFI is available by anonymous FTP from flowcyt.bio.umass.edu in directory
/pub/flowcyt/mfi.  The C source code for MFI is available on request
(emartz@microbio.umass.edu).
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