iCys User Guide

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iCys Cytometric Analysis Software Application Overview Data Structure Data Structure Workspaces and Workspace Files Configuring for an experiment involves setting up the instrument for data acquisition, organizing the data displays for subsequent analysis, and storing selected information about each well on a plate or slide. All of these instrument and display settings are saved in a Workspace file, which always has a.WS.XML extension. The Workspace contains three main sections, as described below. Workspace Protocol Settings The Workspace protocol settings include information about the scan settings and analysis settings, including: ❑ Carrier and scan areas ❑ Protocol settings from the protocol window ❑ Run annotations ❑ Data saving options Note: The protocol settings are also saved in the Raw and Event files. Workspace Display Protocol Settings The display protocol settings, including gating and graph settings such as: ❑ The features for each graph as well as its position and status ❑ The relationships among gating regions of the scattergrams, histograms, 2parameter histograms, and cell analysis windows ❑ Run statistics, galleries, scan field images, and histogram files that you wish to have automatically saved during the scanning process Workspace Desktop Settings Workspace Desktop settings include the size and window positions of the standard windows. The information includes: ❑ Tabs Using Workspaces ❑ Window positions and sizes You can change, delete, or add new analysis windows to your desktop. Any changes can be saved either by overwriting the current Workspace file or saving the Workspace under a new name. 3-86 iCys Research Imaging Cytometer User Guide Revision B
May 6, 2005 iCys Cytometric Analysis Software Application Overview Saving Workspaces When you make changes to the Workspace and then perform any action that closes the current Workspace, prompts you to save your changes as follows: The Save Workspace message indicates that Workspace elements were changed since the last time the Workspace was saved. If no changes were made, the Workspace closes without displaying the Save Workspace message. ❑ If you click No, iCys discards your changes. ❑ If you click Cancel, the action is canceled. ❑ If you click Yes, iCys saves the Workspace. Depending on the action that causes the Workspace to close, iCys takes one of the following actions: ❍ Open Run—Displays the Open Run window to allow you to open a new Run (which includes the Workspace associated with that Run). ❍ Open Workspace—Displays the Open Workspace window to allow you to open an existing Workspace. ❍ Save Workspace—Saves the current Workspace, which remains open. ❍ Save Workspace As—Displays the Save Workspace As window to allow you to save the Workspace under a new name or into a new directory. ❍ Close Workspace—Opens the default.WS.XML Workspace. ❍ Exit—Closes iCys. Note: When you save a read-only Workspace (such as a template or a Workspace associated with a Run file), the Save Workspace As window displays and the new Workspace will be saved in the WorkFiles directory. Any open Raw or Event files remain open. The Save Workspace and Save Workspace As messages inform you of what changes have been made to the Workspace, as follows: ❑ Protocol —Changes to the scan protocol, such as channels, PMTs, and other items, as described in “Workspace Protocol Settings” on page 3-86 and “Workspace Display Protocol Settings” on page 3-86. ❑ Analysis—Changes to scattergrams, histograms, galleries (including window positions), and run statistics. ❑ Layout—Changes to positions for windows such as the Scan View window, Carrier, iNovator, and Well Statistics windows. Revision B iCys Research Imaging Cytometer User Guide 3-87
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Contents Chapter 1 Introduction Man
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Chapter 1 Introduction This manual
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Appendix A Installing iCys Research
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