iCys User Guide

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iCys Cytometric Analysis Software Application Overview iCys Task Bar ❑ Profile—Displays the Profile View window which allows you to display the pixel intensity across a line on the image. For information on creating a profile view, see “Creating a Profile View” on page 3-76. ❑ BrightContrast—The BrightContrast function opens up the following window that allows you to manipulate the Brightness and Contrast of the Field Image. Brightness may be manipulated to bring out dim objects from a dark background. Contrast may be manipulated to better resolve objects that are of close brightness levels. In the histogram in this dialogue box plots the distribution of pixels in the image. The horizontal axis represents expression level or pixel value and the vertical axis plots count of pixels at a given expression level. Adjusting the brightness slider shifts the population of pixels along the horizontal axis. Thus, in the example below the red population represents the shifted pixels. The brightness value, 6553, represents the amount of the shift in expression counts (-16,383 is completely dark, 16,383 is completely white.) All pixels in the field image have become brighter. 3-72 iCys Research Imaging Cytometer User Guide Revision B
May 6, 2005 iCys Cytometric Analysis Software Application Overview The graph in the lower right corner represents the transfer function for the pixel population transformation. The horizontal axis plots the input (or starting) pixel values and the vertical axis plots the output (or finished) pixel values. Comparing the graph immediately above to the original shows a vertical transformation of the transfer function line corresponding to the 6553 pixel value shift. Adjusting the contrast slider broadens or narrows the pixel, population as shown below . Here the red population can be seen to be broader that the original (black) population. This serves to enhance the resolution of objects with similar but distinctly different brightness values. The effect on the transfer function is to increase it's slope. The reset button restores the image to its original state. The binary button makes all the pixels above a certain level completely white and the entire pixel range below that level complete dark. The level of this Revision B iCys Research Imaging Cytometer User Guide 3-73
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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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Appendix A Installing iCys Research
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Appendix B Using the iNovator Toolk
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