MFI Home Page (original) (raw)

What does MFI do well?

• 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 efficientlythan any commercial software. (If you disagree, please send details to me.)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 relativelinear scale, correctedby 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 gatesgraphically.
• 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 theSample Graphics).
• 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 unimodal histograms).
• Perhaps the most popular feature of MFIin the new millenium is its ability toconvert 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 Tutorialthat teaches some practical principles of flow cytometry.
• Here is the original (pre website)Why Try MFI? 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.

What does MFI do poorly?
Generally, Joe Trotter'sWinMDIfreeware 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, orWinMDI. (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. (Use WinMDIfor 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 withWin4Lin. MFI'ssource code can be made available for porting to other platforms.

**Agreement:**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 theMFI/FCS Verification Suite.

Development of the MFI program stopped in 1996at version 3.4kb8. No further 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 thedevelopment history of MFI is available.

*** Downloading, Installation and Operation of the MFI Program** *** Converting listmode data files to ASCII with MFI ** *** MFI Tutorial with Sample Data** Includes *** Antibody titration as an introduction to MFI** *** Time kinetics** *** Three-color human leukocytes** *** Quantitation of cell aggregation with Gate Ratios** Supplementary documents: *** Sample Run Organization** *** Sample Median Intensity Results** *** Sample Graphics** *** MFI/FCS Verification Suite** *** Papers That Cite MFI** *** PDF Manuscript on MFI (1993)** *** Figure 2** *** Comments from MFI Users** *** MFI Source Code and development history**

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 1996-MFI:

• October 2012:
  • Verified MFI operation in DOSBox inWindows 7 running in a VMware virtual machine in Intel Mac OSX. Providedinstructions for installing and operating MFI in Windows 7.
• February 2008:
  • Verified MFI operation in virtualWindows XP and Vista on Intel Mac OSXusing Desktop for Mac from Parallels.Com.
• May 2003:
  • Added an entirely new page of instructions aboutconverting listmode data files to ASCII.
  • Improved Installation & Operation, especially the introduction to Running MFI.
  • Added documentation of the (pre-existing) compatibility withWindows 2000 and Windows XP.
  • Updated the list of papers that cite MFI.