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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 supports all
common Coulter and BD file formats (including XL, Vantage, FACStation).
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 Windows
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.
/*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor of Immunology emartz@microbio.umass.edu
Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578
Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/
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