Installing and Operating MFI
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This document was updated in October, 2012 for Windows 7.
Downloading and Installing MFI
  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.

  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.
Running MFI with Your Data Files

Windows 7 (For Windows XP, Vista, and earlier Windows version, see below.)
  1. Install and configure DOSBox. DOSBox is a small free utility that enables old MS-DOS programs such as MFI (1996) to display their graphics in newer Windows systems. If you attempt to run MFI in Windows 7 without DOSBox, MFI's text output will work. However, when you get to the first graphics screen, you will see
    1. Download DOSBox (free).
    2. Run the DOSBox installer.
    3. Run DOSBox from the DOSBox shorcut on your Desktop. Two windows will open. Keep both of these windows open.
    4. Enter these 3 commands at the DOSBox Z:\ prompt:
        mount c: c:\flowcytm
        c:
        setup
      [They (i) set a virtual C disk drive in DOSBox to be the flowcytm directory, (ii) make it the working directory, and (iii) run setup.bat which puts the MFI program on the DOS path.]

    5. Optional: DOSBox is designed for old games that expect old slow computers. By default it runs slowly. If you want it to run faster, use Notepad (do not use Word!) to edit the file c:\Users\Your_Name\AppData\Local\DOSBox\dosbox-0.74.conf. About a third of the way into the file (or use Edit, Find) is the line "core=auto". Two lines farther down, you will see "cycles=auto". Change "cycles=auto" to "cycles=max". Save the file.

  2. Running MFI in DOSBox.
    1. You will be using MFI in DOSBox, which is similar to MS-DOS. After entering the commands in the previous step, you will need to use only these 4 commands (you might like to print this page):
      • dir to list the files and directories in the current location.
      • cd to change directories. For example, if dir lists a directory named "mfihelp", you can change to work in that directory with the command "cd mfihelp". If you need to change to the parent of the current directory, the command is "cd ..".
          Shortcut: instead of typing the full directory name after "cd", you can type only the first letter and then hit the Tab key to complete the name. If more than one name begins with the same letter, hitting Tab repeatedly scrolls through the matching names that are shown by "dir".
      • mfi to run the MFI program. This command should be given after you have changed to a directory containing flow cytometry listmode data files.
      • exit when you are done with MFI and DOSBox.
    2. Note that the above commands work only when you are at the DOSBox prompt, for example C:\mfitutor\. When you are running MFI (blue background), you must use one-key commands. Those MFI commands are shown in green in every MFI screen.
    3. The terms "directory" or "subdirectory" means the same as "file folder".
    4. Although you cannot access the "Z:" disk drive used by DOSBox outside of DOSBox (it is a virtual disk), you can access its "C:" disk drive in Windows Explorer as c:\flowcytm. You can add and delete files and directories there, and edit text files there, in the normal manner.
    5. Instructions for printing text and graphics are below.

  3. Quick Start:
    1. Using "dir" and "cd", change to the folder c:\flowcytm\mfitutor\1titrat.
    2. Enter the command mfi.
    3. Simply press the Enter key repeatedly and observe what happens after each press.
    4. When you want to quit, press Q.

  4. Printing from MFI in DOSBox.

      PRINTING TEXT
    1. While running MFI in DOSBox, go to the Configuration Menu, and direct the primary output to a disk file.
    2. Using Windows Explorer, open the output file RESULTS.MFI with a text editor (such as Notepad or Wordpad) or a word processor. Right click on RESULTS.MFI and choose Open with....
    3. Make sure the font for the entire document is a fixed width or monospace font such as Courier. Otherwise, the columns will not line up properly.
    4. The table is wide. To prevent having lines wrap around, you may adjust the font size, or you may want to use Page Setup to set the paper to landscape instead of portrait.
        Despite the table being wide, if your MFI configuration specifies results from more than four parameters, the results for parameters 5-8 will be in a second line for each listmode data file, the line labeled par 5-8:.
    5. Now you are ready to print normally.

      PRINTING GRAPHICS: METHOD I
    6. Because it is such an old program (1996), printing directly from MFI (METHOD II below) is fussy. If you are familiar with a graphics editor such as Adobe Photoshop, you may prefer this METHOD I. If you are not familiar with graphics editors, go ahead to METHOD II below.
    7. Use the Snipping Tool provided with Windows 7 (Start, All Programs, Accessories, Snipping Tool). Lasso the MFI graphic that you want to print, and save it to a .png file. (Do not use a .jpg file. Compression will make it smudgy.)
        If you double click this saved .png file, Windows attempts to display it in Windows Photo Viewer, which does not work. Instead, to view the saved file, drag it into any web browser.
    8. You could try printing the graphic directly, but with the very thin colors on a black background, it may not be very satisfactory. The steps below convert it to black graphics on a white background.
    9. These steps are for Adobe Photoshop Elements 9. Open the .png file.
      1. Enhance, Adjust Color, Remove Color. Now you have a grayscale image on the original black background.
      2. Filter, Adjustments, Invert. Now you have a grayscale image on a white background.
      3. Enhance. Adjust Lighting, Levels. On the "Input Levels" graph, slide the bottom (black) marker up from 0 to about 200. This should make the gray lines black.
      4. Now you are ready to save/print the file. For example, you could drop the saved file into Word and print the resulting page.

      PRINTING GRAPHICS: METHOD II
    10. MFI is designed to print only graphics screens that you select by hand -- not all graphic screens for an entire run. This contrasts with the text output, where the expectation is that you will print the results for an entire run as one multi-page text document.
    11. MFI's printer drivers are old and limited. In theory, Postscript output would be good, but MFI appears to have a bug that omits the dots from dot plots in its Postscript output. The best I have found is HP Laserjet. The resulting file can be viewed and printed (on any printer that you have installed on your Windows 7 system) using free software OpenPCL Viewer. Therefore, you should download and install OpenPCL Viewer.
    12. OpenPCL Viewer requires Java. Go to java.com and make sure you have installed the current java.
    13. Run MFI and get to a graphics screen that you want to print. Now we'll configure MFI's printer driver.
      1. At the graphics screen, press 'O' for Options.
      2. At the MFI GRAPHICS OPTIONS MENU, press 'P' for Print.
      3. Type 'Y' (Yes) to change the printer selection.
      4. At the MFI PRINTER SELECTION MENU, choose '3' for H-P Laserjet. (Do not choose 13.)
      5. Type 'N' to answer the question "Is your H-P Laserjet a Series II or older?".
      6. At the MFI PRINTER MODE MENU, you have two choices. If you want the graph to be in portrait mode, and occupy about a half of a sheet of paper, choose '3' for 300 dpi. If you want the graph to be in landscape mode, and occupy about one quarter of a page, choose '2' for 150 dpi.
      7. At SELECT PRINTER PORT, choose '5' for Disk File.
      8. For portrait/300 dpi, choose 2 figures per page. For landscape/150 dpi, choose 1 figure per page. (You'll get 1 per page regardless, but this affects the size of the figure.)
      9. Select 'Y' Yes for thick lines.
      10. Press Enter to accept the new printer configuration.
      11. Press Enter until you are told "There will be a short pause while the graph is reconstructed for the printer". (This should take less than 15 sec.) Notice the filename generated by MFI, such as MFIPRINT.001. You are now ready to view or print this file.
          You do not have to repeat this printer configuration for other experiments. When running MFI, press F1 to get the COMPREHENSIVE HELP SYSTEM. You may have to press another number to get it depending where you start. You want the whole HELP directory with all 20 numbered chapters. Enter '16', Saving a customized initial configuration on the DOS PATH.

          Basically, you should copy the file MFI.CFG from the directory where you configured the printer, into c:\flowcytm\program. Since that directory is on the DOS PATH (as a result of the 'setup' command you entered to start up DOSBox) MFI will use this configuration as its default, regardless of where you run MFI within DOSBox.

    14. Run "OpenPCL Viewer", the program that you installed above: "Start/All Programs/OpenPCL Viewer/OpenPCL Viewer (local install)".
    15. Open the file created by MFI, for example MFIPRINT.OO1. You will need to change "Files of type" to "All files" since MFI does not create the expected type. In a few seconds, you should see the graphic in black on white. Now you can print it.

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

  6. For your own data, you must create a new folder (subdirectory) to contain your data files. You should make a separate folder for each experiment.
    1. For convenient access within DOSBox, it will work best to make a directory "my-data" within "c:\flowcytm". Then for each experiment, or group of experiments, make a subdirectory within "my-data". Thus, the list mode data files for "expt1" would be placed with Windows Explorer into "c:\flowcytm\my-data\expt1". Then to run MFI for expt1, inside DOSBox, use "cd" to change to "c:\my-data\expt1" and enter the command "mfi".
    2. Note that DOSBox is limited to filenames with 8 characters or less (plus, optionally, a period followed by 3 characters). This is why we suggest the directory name "expt1". If you name it "experiment1", you will not see the full name in DOSBox and this may make it difficult to manage your work.
    3. After you have created directories and added files to the c:\flowcytm directory tree, you will probably need to exit from DOSBox and restart it in order for those new directories and files to be accessible within DOSBox.
    4. 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.)
    5. 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.
    6. Depending on how many files you have in an experiment, it is often helpful to separate sets of files for different cell types.

Windows Vista, XP, and earlier Windows versions (For Windows 7, see above.)

  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.

  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.


Shortcuts to MFI

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.
Copy the shortcut into each folder containing FCM data files, and use the copy to start MFI within the folder containing the data files you wish to analyze.


 
Compatibility with Windows Versions:

MFI is an MS-DOS program.

For Windows 7, MFI operates within the small, free DOXBox environment, as explained above.

MFI 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.

MFI also operates on Intel Macs in OSX within a Windows virtual machine (using VMWare, or Parallels Desktop for Mac).

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.)