iCys User Guide

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Glossary Glossary of Terms option button The round buttons in a dialog box that indicate a mutually exclusive choice (for example, a choice between Portrait or Landscape). P palette A grayscale palette containing color definitions for a laser scan image. The palette can be used to adjust the tonal range of the laser scan image. parameter A channel that has been chosen for analysis in a protocol. peak A value that is used to describe the most frequent fluorescence intensity of a population of cells. “Peak mode” is the channel number that is used to describe the largest number of cells in a sample. peripheral contour This contour, along with the integral contour, define a toroidal region of pixels used to calculate the peripheral value or the cytoplasmic fluorescence. photobleaching The result of light altering fluorescent molecules so that they have decreased fluorescence or are no longer fluorescent. photodetector A device that senses light and converts the energy from that light into an electrical signal. photodiode A photodetector used for absorption, extinction, and forward scatter signals. photomultiplier A photodetector used to detect and measure and fluorescence signals. tube (PMT) pixel The smallest logical unit that can be used to build an image on the screen. PMT See photomultiplier tube protocol A description of settings saved from a successful run. probe Any detectable marker that binds to a specific cellular component or molecular sequence. properties Properties refer to the characteristics of a window in the iCys software application. The properties dialog box is used to change the information displayed in a window and how it is displayed. Q quadrant A scattergram that has been divided into four rectangular areas to identify subpopulations for analysis. R RAM (Random Access Memory) Computer memory into which the user can both read and write information. D-8 iCys Research Imaging Cytometer User Guide Revision B
May 6, 2005 Glossary region A user-defined bounded area on a scattergram or histogram. It is used to isolate a subpopulation of events. relocation The process of the iCys software repositioning the microscope stage to the previously saved location of an event on a slide. repetitive scan The process of scanning the same well or scan area multiple times. This allows you to see the change in a single sample over a period of time (which can be especially useful for live samples). report A window which displays selected data windows with additional text and graphics. Acquired data can be displayed in the data windows and the report window can be printed. S sampling rate The frequency at which the laser beam scan occurs. saturation When the detector or display device no longer responds to increase levels of signal. saving The process of placing information in the permanent memory of the computer. scan area The entire area to be scanned. For a well, this is usually the entire well. For samples that reside in other kinds of carriers, the scan area can be defined by the user to encompass all or part of the sample. scan field A single pass of the iCys laser. A scan area is made up of multiple scan fields. Scan View The window in iCys in which scans are displayed. The source of the window’s window data appears in the title bar. When data is coming directly from the iCys cytometer, the window title is Scan View. scanning The process of recording an image on a visual display screen. scattergram A two-dimensional display of data from a scan run or from a cell data file displayed as a plot of two user-selected measured features. scroll A computer term for moving the contents inside a window up, down, right, or left so that more of the contents of the window can be viewed. scroll bar A bar that appears at the side and/or bottom of a window that controls scrolling movement with a mouse action. A rectangular box inside the scroll bar shows the current position relative to the entire contents. segmenting The process of setting boundaries to define events for storage in the computer memory. sensor A device that detects and measures light and converts the energy from that light into an electrical signal. status bar The horizontal bar at the very bottom of the iCys desktop. It contains an assist line, the names of the active files, the cell count, and the power of the objective being used. statistics The calculations that the iCys software makes for cells within regions of the active window of a histogram or scattergram. The data (region number, count, percentage of cells in the region, the mean, full width at half maximum, CV, Revision B iCys Research Imaging Cytometer User Guide D-9
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User Guide DOC190-0037-001 Revision
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Contents Chapter 1 Introduction Man
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May 6, 2005 Contents iCys Status Ba
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May 6, 2005 Contents Appendix B Usi
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Chapter 1 Introduction This manual
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May 6, 2005 Introduction System Ove
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Chapter 2 iCys Research Imaging Cyt
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Chapter 3 iCys Cytometric Analysis
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May 6, 2005 iCys Cytometric Analysi
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Chapter 4 Generating Analytical Dat
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Appendix A Installing iCys Research
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May 6, 2005 Installing iCys Researc
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Appendix B Using the iNovator Toolk
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May 6, 2005 Using the iNovator Tool
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