FACS Lab. Software Overviews & Tips

Last updated 31st January 1996

CELLQuest WinMDI Verity Winlist Verity Modfit PC-LYSYS

CELLQuest 1.0

Overview

CELLQuest is commercial flow cytometry data acquisition and analysis software for the MacIntosh computer, produced by Becton Dickinson.
This software has a multi document interface allowing the user to set up one or more document windows, each of which may contain data acquistion or analysis plots, a combination of both, or acquisition to analysis plots.
Analysis plots can be of any of the standard types: dotplot (2 or 3 parameter), density plot, histogram, contour, or isometric. One of the nicest features of this software is the ability to select all the plots, even if they are of different types, and then increment (or decrement) all the selected plots with a simple key combination.

Tips

For a detailed list of CELLQuest tips connect to The Scripps Research Institute, USA. : CELLQuest Help

Text Tip: Initially when "Free Text" is applied to an active window, the default text box background is opaque (i.e. white) with black text. As the text box is rather large you'll probably want to change the background to transparent, but make sure you also change the text colour to something other than black, otherwise you won't be able to see your text box or text so that it can be repositioned, even though it will still print.
Layout Tip: To get the display boxes within a document the same size, first drag out a display window to the required size using the appropriate tool from the palette, then choose subsequent plots of the same kind by going to the appropriate option under the "Plots" menu. Remember this method works for the display size as set when you stop dragging, and ignores any minor alterations you may have made after that time.
Region Tip: To delete a region you must delete it not only from the display window in which it appears, but also from the region list. To do this, highlight the region in a display window, and then either choose "cut" under the "Edit " menu, or easier still just press the delete key on the keyboard. Next you need to choose "Region list" under the "Gates" menu, select the region number you deleted, then again either "cut" or delete via the keyboard.

It's also recommended that you set aside a little time and work your way through some of the training tutorials, which can be found in the FACS Applications / Training folders on both Mac's within the Flow facility.

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WinMDI

Overview

WinMDI (Multiple Document Interface) is an excellent Windows based public domain flow cytometry data analysis package written by Joseph Trotter (trotter@scripps.edu). WinMDI allows the user to draw analysis plots of any of the standard types: dotplot, density plot, histogram, contour, or isometric. Particularly useful are the density plot options for publication. All bivariate displays can have a reference grid applied so it's easy to see if one population shifts, relative to another. Click

for a larger (22k) example, showing various density plots
. The program is essentially very intuitive with most commonly used functions available from a small pop-up menu. Fairly extensive help is available on-line, should you get stuck at any point.

Tips

"How do I overlay one histogram on another?"

Draw a histogram by choosing the "Display" menu, "Histogram", and selecting a file and an appropriate parameter.
Choose the "File" menu, "Open" and select a file, and the appopriate parameter, then choose "overlay", NOT "read".
Tip You can use this feature to good advantage if used in conjunction with the "Increment all" and "Set file increment" menu options.

"How do I use control histogram overlays with the "Increment all" option?"

Draw up the number of displays you want, say 9 windows with the parameter you want to increment.
Click on the menu bars of the various windows in the REVERSE order to that which you want them displayed i.e. 9 to 1.
Choose "Screen stats" now if you want them.
Go to the "Window" menu and "tile".
Open and overlay on each window the file you wish to use as your non incrementing control file e.g. 1.
Tip you can quickly jump between windows using the Ctrl-Tab key combination, which decreases the likelihood of you ruining the window tiling by accidentally moving the window when making a window active by clicking on the menu bar.
Set file increment to correspond to the number of screen windows you've created, in this case 9.
Increment windows, noting that the overlayed histograms, in this case the control file #1 stays on each window.
Tip You can speed up your data throughput by using the key combination of Alt-Page Dn to increment all files, then Alt-F9 to print the screen. If you choose the option of screen stats, as recommended earlier, each display will also have stats applied.

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Verity Winlist 2.0

Overview

Winlist is one of the most powerful flow cytometry data analysis package available for the PC. This package can display histograms or dotplots, with options of density dotplots, or 3 parameter dotplots. Note that contour plots, or 3D isometric displays cannot be displayed using this package, and that 3 parameter dotplots have only one viewing angle, as opposed to say WinMDI, or CELLQuest (isocontour).
Winlist can create and handle artificial parameters within a file, a powerful and unique feature. An example of the application of this capability is the creation of an artificial parameter contain SSC data with a 3rd order polynomial applied thus increasing the spread of data points in the lower part of the data scale, at the expense of separation of populations further out on the SSC scale.
Click

to download a 30K an example of artificially created parameters, in this case, time, and a polynomial, being used in data analysis.
Histogram overlays can be done with greater flexiblity with other packages in our opinion, and for this purpose we recommend either CELLQuest, WinMDI, or PC-LYSYS.

Tips

When first starting to use Winlist it is recommended to you work your way through the tutorial section, which appears in the users manual while using the computer. This will provide a good grounding in most of the basics, and allows you to work at your own pace, or come back to a section at a later date.

Verity Modfit

Overview

Modfit is the main DNA / Cell cycle analysis package used in the school. It has powerful modelling capabilities with models built from gaussian, rectangular and other components. If these models do not suit the data, new models can be created, or existing models customised. Data analysis can be done on either a manual basis or automatically.
Click

to download an 19K example of data taken in the lab and analysised using Modfit.

Tips

PC-LYSYS

I'll get to this one sometime . . .

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