Preferences allows the user to select several default WinMDI preferences that get saved in WIN.INI for use the next time WinMDI is started.
With log compressed data, either Geometric or Arithmetic averaging may be selected. Medians my be included in histogram statistics by selecting Medians. If selected, Medians will also be displayed in any histogram statistical screen display.
Histogram Colors allows a choice between RGB color rendering, or the use of a special palette if the installed video driver supports palettes. The maximum number of palette entries is 256. The newer high resolution video boards with 24 bit color/RAMDACs need to use the RGB colors setting in WinMDI. Many color printers need RGB adjustment to get the best results. If you are in doubt, select RGB colors.
Dotplot mode defaults:
1) Kinetics Mode - When selected, allows kinetics experiments to be plotted as dotplots such that 4000 events are drawn from 32K events by showing every 8th event. Otherwise, only the first 4000 events would be shown.
2) Overlay Time vs Y means - enabled only when Kinetics is selected. Allows the mean for each time point (channel) to be plotted against the X axis time parameter. When both Kinetics mode and Overlay Time vs. means are selected, Save As allows output to be save for input to another plotting/spreadsheet program that contains each time point and correlated Y mean for that point as a standard tab delimited text file. The Format dialog should be set to show all the events in the data file.
3) Draw Time vs. Y means only - causes the raw dotplot data to be omitted from the plot so that only the mean line is shown vs. time.
4) Use TIMETICKS (seconds) - causes the output text file created with Save As to be written in seconds as the unit rather than the channel number. The TIMETICKS value in the FCS Text portion of the file is used to convert to time. For example, if TIMETICKS is 200, then each channel is multiplied by 0.2 seconds. In BD’s LYSYS and CellQuest, TIMETICKS is the number of milliseconds per channel.
These defaults may be overridden on a window by window basis from the Format Dotplot dialog box. The suggested Preferences setting for viewing kinetics experiments if you need to use a plot that is other than Time vs. Y is to set the Kinetics Mode in the preferences dialog and select Overlay Time vs. Y means on a window by window basis as desired.
Miscellaneous items
Allow Mixed Mode: Allows the user to override the disallow mixed mode flag for listmode files with 256 and 1024 channel data, for example
Shift 12 bit to 10 bit: Converts 4096 channel (12 bit) listmode data to 1024 channel (10 bit) data .
Force forward byte order: When checked, allows WinMDI to ignore faulty reverse byte order information in the FCS listmode file header. This allows WinMDI to read some files converted into FCS format by conversion programs that assume forward byte order architecture.
2D labels on axes: When checked, causes the parameter labels to be drawn centered on the X and Y axes on all 2D displays (Dotplots, Density plots, Contour plots). WinMDI tries to adjust the window margin based on the size of the current window font.
Short Stats: When checked, results in a short text header to the statistics output that show only the filename and sample ID before the data.
Auto Calculate Stats: When checked, sibling statistical windows are automatically updated as a result of various operations such moving a region. Otherwise, the statistical window must be updated manually.
Windows NT resize flag: When checked, inhibits a redraw during resizing if the left mouse button is still down. Check this if you are running under Windows NT and are annoyed with the redraws during resizing.
Use $PnN not $PnS: BDIS CellQuest allows labels to be saved as text fields in the FCS 2.0 TEXT portion of the file as $PnS, where n is the parameter number. If nothing is there, WinMDI defaults to empty as the label. To use the parameter names instead ($PnN), check this item.
Enable Histogram Export: When checked, enables the DDE server module with WinMDI and sends latest single parameter histogram data via DDE for import by other programs.
I/O Buffer Size: The local memory heap size allocated for Input/Output may be 16K, 12K, or 8K bytes. Since the I/O buffer and any edit window text (Statistics Windows) share the local memory heap space, available local memory may become limiting when there are a large number of statistical windows present. The default I/O buffer size is 16K, with about the same left available for all statistical windows. Several more statistical windows may be present if 12K or 8K is used for the I/O buffer, leaving roughly 19K or 23K respectively available to statistical windows for their contents. A typical WinMDI statistical window uses between 1K and 2K bytes from the local heap space to hold its contents..