WHY TRY MFI?

Why should you consider using the free PC program MFI as an alternative to
your existing flow cytometry listmode file analysis software?  Speed,
convenience for certain tasks, being warned about unexpected problems with
your data, and inexpensive decentralization of certain analysis tasks are the
main reasons.  Another is the ability to view time kinetic results with
cytometers which don't record time.

These benefits are further explained below.  MFI has extensive built-in on-
line help, and comes with a detailed tutorial which walks new users through
its capabilities, using sample data files included.  MFI is in routine use in
flow cytometry facilities in Australia, Germany, Japan, the Netherlands, and
in the USA (Bethesda MD, Madison WI, San Diego CA), as well as its birthplace,
the University of Massachusetts at Amherst.  MFI supports all common Coulter
and BD file formats (including XL, Vantage, FACStation) as well as Winlist,
Pro2FCS, and CyCLOPS.

MFI was designed with these goals: to get fluorescence intensity results
quickly from large numbers of files, including quick, compact viewing/printing
of histograms and dotplots; to provide all necessary corrections to the
intensity data; and to alert the user to situations which might otherwise lead
to inadvertant misinterpretation of the intensity data.  MFI achieves the
first goal by allowing unattended batch runs (without viewing graphics) to
tabulate intensity results. After MFI was well along, another goal was added:
the ability to display time kinetics, even for cytometers which do not record
time as an event parameter.

For large numbers of files, MFI gives you intensity results in closer to final
form, in a more compact table, with less fuss, and faster. It allows you to
scan through histograms or dot plots quickly for large numbers of files, or
skip this entirely if you only need intensity results.  Because of the many
ways in which MFI alerts you to possible problems, you may see things in your
data with MFI that you miss with other software.

MFI fosters decentralization of your data analysis.  You can make as many
copies of MFI as you wish, so there is no reason to confine your analysis to
the flow facility computers.  With MFI, you can analyze or review your data
from your lab or office PC or at home.

MFI's speed and convenience were achieved by sacrificing some of the
flexibility offered by alternative software.  MFI complements other
software, but does not replace it.  MFI does not offer quadrant analysis,
DNA analysis, 3-D plots, contour plots, density plots, different colors for
each gate, complex gating logic, or font control.  With the exception of DNA
analysis, these features are offered by Joseph Trotter's free program
WinMDI (available by anonymous ftp in /pub/pc from flosun.salk.edu).

Getting fluorescence intensity results quickly means printing a compact
table without examining histograms or dot plots for all files.  Doing this
safely means that MFI automatically detects multiple peaks in histograms
when they occur, reports drifting of an event cloud relative to its scatter
gate, and warns when >10% of events are off-scale.  When MFI notices more
than one peak in a histogram, it automatically reports the percentages of
events and intensities for each peak.

Getting graphics results quickly means that MFI shows you histograms for
all parameters on one screen.  You can arrive at this screen for the first
data file as quickly as pressing the Enter key 5 times after starting the
program with new data.  Similarly, all possible dot plots (including kinetic
dot plots if desired) are displayed with one more press of the Enter key.

When graphics are displayed, MFI takes care to offset the axis lines from
the data, so that off-scale data are clearly evident (unlike much other
software).  Although off-scale end-pileups can be clipped for scaling the Y
axis of histograms, a warning is always displayed when this option is
enabled.

MFI deals with large numbers of files by allowing the user to tag a subset of
the files in the current directory for a given run.  The run organization
screen also allows assignment of different gates to different files, marking
of control files for subtraction, and designation of histogram overlay sets. 
Up to 16 runs can be configured for a given directory of files.

MFI provides many convenience features.  A good example is the ability to add
a 1-line sample description or "label" to each list-mode file.  These labels
make organizing an analysis run and interpreting the resulting printed table
much easier.  Did you acquire your control sample last?  No problem, MFI
allows you to rearrange the automated sequence of files from alphanumeric
order.  The control can be marked for subtraction from the intensities of
subsequent files in the run, and its histogram can be overlayed on those for
subsequent experimental files.  Log-acquired intensities are converted to a
linear scale, and intensities can be reported in MESF.  Of course MFI
remembers all of your configuration choices between uses.

MFI is available by anonymous BINARY ftp from flowcyt.bio.umass.edu in
/pub/flowcyt/mfi.  You should get two files: MFIZIP.EXE (the program itself),
and MFITUTOR.EXE (the tutorial with sample data files).  These are
compressed, self-unpacking files.