1. The MFI program, documentation and tutorial sample data package requires 4 megabytes of disk space on a Microsoft Windows system (not counting disk space for your own FC data files). It is an MS-DOS program and is compatible with all versions of Microsoft Windows (including Windows under linux, and Virtual PC on a Macintosh, see below).

2. Download the file MFISETUP.EXE. Save the file to any convenient location on your C: hard drive, such as the Desktop, or C:\temp.

3. Double click MFISETUP.EXE.
   • If you did not place it on the Desktop, you may need to open Windows Explorer (Start, Programs, Windows Explorer), to find MFISETUP.EXE.

   • MFISETUP is configured to install MFI on your C: disk drive. If that is OK, simply click the Unzip button in the WinZip Self-Extractor dialog that appears. When the message "unzipped successfully" appears, click OK, then Close the Winzip dialog.

   • You may install MFI on a different disk drive. Double click MFISETUP.EXE, and in the WinZip Self-Extractor dialog, change the disk in the slot "Unzip to folder" before you click on the Unzip button.

4. Open your favorite web browser, pull down its File menu, select Open, click the Browse button, and open the file c:\flowcytm\mfihelp\index.htm. This is your local copy of the MFI Home Page.

5. Add a Favorite/Bookmark to this file in your browser!

6. Start with the MFI Tutorial by clicking its link on the above MFI Home Page. At this point, you have the entire MFI Home Page website and all documentation installed on your hard disk, so you no longer need to go to the on-line version of the Tutorial. It will be quicker to use the favorite/bookmark (previous step) to your local copy for all future work.

7. Optionally, you may delete the file MFISETUP.EXE once you have completed the above steps.

1. Quick Start: (Read this entire set of steps A-E before you run MFI because once you start MFI, you won't be able to see this page, unless you print it first. See #2 below for an explanation.)
   1. Open Windows Explorer.
   2. Find the folder c:\flowcytm\mfitutor\1titrat.
   3. In that folder, double click the Shortcut to MFI.exe.
   4. Simply press the Enter key repeatedly and observe what happens after each press.
   5. When you want to quit, press Q.

2. When MFI's first graphics screen appears, it will force your monitor into 640 x 480 resolution and occupy the full screen. It will not be in a Window, so your Desktop will not be visible. Don't be alarmed -- just proceed with your MFI session until it is completed. You may need to adjust your monitor's horizontal and vertical positions in order to see MFI's complete graphics screen. This will not affect your display at your usual working resolution (e.g. 1024 x 768 pixels). When you Quit from MFI, it will disappear, and your Desktop will reappear. MFI works this way in all versions of Windows that I have tested.
   Generally, after the first graphics screen is displayed, MFI will not operate within a window. (You can try forcing the full-screen view of MFI into a window with Alt-Enter. If MFI then fails to respond to keystrokes, again use Alt-Enter to restore it to full screen.)

3. Do the first section of the MFI Tutorial (Antibody Titration) in order to learn how to use MFI.

4. For your own data, you must create a new folder (subdirectory) on your hard disk to contain your data files. You should make a separate folder for each experiment. For large experiments, it is best to make subfolders for parts of the experiment. If you have more than 40 data files consider separating the files into logical subsets. (40 files is the maximum that shows on one run organization screen in MFI. If you prefer, you can process many more files (hundreds) in one folder by using PgUp/PgDn to move from screen to screen.) In particular you should separate into different folders sets of files containing different parameters (e.g. one set contains FL3, another does not), or acquired with different lasers or excitation wavelengths. Depending on how many files you have in an experiment, it is often helpful to separate sets of files for different cell types.

5. Copy the Shortcut to MFI into the new folder that now contains your data files. The master copy of the Shortcut is in c:\flowcytm. To copy it, in Windows Explorer, right click and select Copy. Then change to the folder containing your data files, and in the blank white space in this folder, right click and select Paste. Alternatively, you can right-click and drag the shortcut into the target folder -- when you release the mouse, a menu will pop up and you can select Copy. (If you left-click and drag, you may move the shortcut instead of copying it, thereby losing the master copy.)

6. Start MFI by double clicking the Shortcut to MFI in the folder containing your data files.

7. Most-Legible Font Sizes
   Font Size	Screen Pixels
   8 x 12	640 x 480
   10 x 18	800 x 600
   TT 12 x 20	1024 x 768
   TT 13 x 22	1280 x 1024 or more

   Windows 98

   Windows 98: Adjust the font size in the MFI text window for optimal legibility. Use the pull-down menu in the upper left. The optimum depends on your screen resolution. Simply try different sizes and choose the one you like best. It will be remembered the next time you use the same shortcut, or a copy of it.

   Windows 2000, XP: Adjusting the font size is not necessary.

Printing on an IEEE-488 PaintJet Printer

PaintJet printers with an IEEE-488 (GPIB) interface (as distinct from the now common Centronics parallel port interface) were provided with Becton-Dickinson flow cytometers in the late 1980's and early 1990's. If you have a PC with an IEEE-488 card, you can print from MFI to your PaintJet. Here are instructions.

Using MFI with the DOS Prompt

This section is for DOS experts only! If you work in Windows but not at the DOS prompt, and if you like the mouse, then the Windows Shortcut method described in the previous section is for you -- so skip this section! MFI is a DOS program. If you are thoroughly familiar with DOS commands and the DOS working environment (including the DOS PATH, file and directory management under DOS), you may prefer to run MFI from the DOS prompt rather than using the Windows Shortcut method described above. There is no fundamental advantage to using MFI from the DOS prompt vs. a Windows Shortcut -- personal preference should be the deciding factor. Instructions for this mode of use are available in the document dossetup.txt and some abbreviated instructions are built-into MFI. Run MFI and in its HELP SYSTEM, see especially #2 "How to use MFI for the first time", and #16 "Saving a customized initial configuration on the DOS PATH". For DOS users only, we strongly recommend several Free Martz-Authored DOS Utilities that will improve your DOS working environment.

You must already have downloaded and installed MFI before you can do the steps below. MFI comes with a master Shortcut in c:\flowcytm which you can simply copy. The information below is therefore usually unnecessary, but is provided in case you accidentally delete the master shortcut. (If you deleted the master Shortcut after you made a copy of it in another folder, you could copy the copy back to the master location, instead of creating a new Shortcut.)

Creating a New Shortcut:
1. Find the file MFI.EXE. (It should be in c:\flowcytm\mfitutor\program. If not, use Start, Find, Files or Folders. If it is missing, you will need to reinstall it -- see above.)
2. Run Windows Explorer and display the folder containing MFI.EXE.
3. Right click on MFI.EXE, and select Create Shortcut.
4. Right click on the new Shortcut to MFI, and click Properties.
5. In Properties, Program, delete everything in the slot labeled "Working". This is critical: it makes the shortcut look for data files in the current folder from which each copy of the shortcut is started.
6. In Properties, Program, check "Close on exit".
7. In Properties, Misc, under Mouse, check QuickEdit. (This allows you to block and copy MFI text to paste into another application.)
8. In Properties, Misc, under Background, Always Suspend should not be checked. (This allows MFI to run when its window is not in the foreground.)
9. In Properties, click OK.
10. Right-click and drag the shortcut into the c:\flowcytm folder.
11. Double-click the Shortcut, and adjust the font size to be optimal (see above). Press Esc repeatedly until MFI quits.

MFI is an MS-DOS program. It has been verified to run with MS-DOS versions 5 or 6, 4DOS, and in MS-DOS ("Command Prompt") under MS Windows 3.1, 95, 98, 2000, XP, and Vista*. No problems are anticipated under Windows NT or Me, although I have not had an opportunity to verify operation there.

* As of February, 2008, I have tested MFI in Vista Business only in a virtual machine on an Intel Mac.

MFI also operates on Intel Macs in OSX (Leopard) within a Windows virtual machine, installed on the Mac using Desktop for Mac from Parallels.Com. MFI has been verified to run on a MacBook Pro in virtual Windows 98, XP, and Vista Business.

MFI is expected to run in a Windows subsystem supported by Win4Lin under x86 linux, and in Virtual PC on a PPC (non-Intel) Macintosh. (If you can verify operation in one of these untested platforms, please tell me.)