What does MFI do well?
MFI's development was completed before Windows and the World Wide
Web became universal. Its menus operate entirely from the
keyboard. (It doesn't respond to the mouse). Its keyboard-based
menu interface is
unusual in today's icon/mouse-click context, but
easily learned and efficient to use.
- MFI was created to obtain corrected
median fluorescence intensities quickly from large numbers of
flow cytometry listmode data files
(Sample Median Intensity Output).
To the best of my knowledge,
it does this more efficiently
than any commercial software. (If you disagree, please send details
When histograms are multimodal, peaks are automatically detected,
and medians and percentages are given for each peak. (Peak detection
sensitivity is adjustable.) Thus, if you have a large number of files,
you can get results for multiple peaks in histograms quickly and objectively.
- Log fluorescence intensities are converted to a relative
linear scale, corrected
by subtracting the intensity of a designated control (blank), and if desired,
converted to absolute kilomolecules of equivalent soluble fluorochrome (KMESF).
- MFI prints intensities that can be interpreted safely without scrutinizing histograms
and dot-plots for every file. It does this by printing warnings when: multiple
peaks occur, cytometer settings change unexpectedly,
event clouds drift out of the gate, or percentage of events in
gate drops too low.
- MFI can show histograms and dot plots as efficiently
as one data file per keypress (Sample Graphics).
It can overlay two or three
histograms. It can set 1-, 2-, or 3-parameter gates
- MFI can insert labels (that describe the contents of each
sample) into listmode data files (one per file) after
data have been acquired. These appear on all MFI output.
Here are examples of labels in use.
- MFI does time kinetic analysis, even with data where time
isn't recorded as a parameter (see the 3rd snapshot in the
- MFI can add calculated or transformed parameters to the acquired
parameters, and can calculate gate-ratios.
- MFI can create spreadsheet-ready median fluorescence intensities (for
Perhaps the most popular
feature of MFI
in the new millenium
is its ability to
convert listmode data
files and histograms to ASCII text files suitable for
spreadsheets or scientific plotting software (and the A2FSC
program included in the Verification Suite can convert
ASCII files back to Flow Cytometry Standard listmode data files).
- MFI comes with an extensive Tutorial
that teaches some practical principles of flow cytometry.
- Here is the original (pre website)
Why Try MFI?
What does MFI do poorly?
Generally, Joe Trotter's
freeware and MFI do different things well. These two
programs complement each other nicely.
- MFI does not do quadrant-statistics on dot plots, or 3D plots.
Use WinMDI for these.
- The flexibility of MFI's graphics displays is less than
that in most commercial FC software, or
(MFI's emphasis is on printing text listings of median intensities
efficiently, and its graphics are provided primarily to support this goal.)
- MFI's graphics are not publication quality for most purposes,
and its support for printing graphics is limited to printers
common ca. 1996. Nevertheless, graphics printed by MFI are perfectly adequate
for in-house research records purposes.
for printing high-quality graphics.)
MFI is available for
Windows (MS-DOS) only, and works in all
versions of Windows, including Windows on Intel Macintosh OSX.
On x86 linux, it will run in a Windows subsystem with
source code can be made available for porting to other platforms.
MFI is provided free for all users, and without support.
(A statement within the software requiring licensing
by for-profit users is obsolete and may be disregarded.)
Use of MFI for clinical purposes is prohibited.
By the act of using
MFI you agree to accept full responsibility for verifying the accuracy
of MFI's results with your data and its suitability for your
purposes. No warranty is made nor implied. See the
MFI/FCS Verification Suite.
Development of the MFI program stopped in 1996
at version 3.4kb8.
enhancements will be released by MFI's author Eric Martz.
Parties interested in improving MFI should inquire about obtaining
the source code. The Internet in the early
1990's was crucial for distribution of beta-test versions of MFI,
and for exchanging listmode data files for compatibility testing.
All that communication was by email and ftp, as hypertext websites
were not yet common. This website was created in November 2001 to
make MFI more accessible. More about the
development history of MFI is available.
Best MFI Citation (since there is no journal article):
Martz, Eric. 1992-2001. MFI: a flow cytometry list mode data analysis program
optimized for batch processing under MS-DOS. http://www.umass.edu/microbio/mfi
Responses too slow on this website?
Download MFI -- you get this entire website with it! You
will have to wait for the installer to download just once -- after
download is completed and installed, access to the MFI Home Page
and all supporting documents will be immediate!
Revisions to the original November 2001 website about
- October 2012:
- February 2008:
- May 2003: