iCys User Guide

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Using the iNovator Toolkit iNovator-specific Protocol Modules Whole section dynamic scan area Pictured below, on the same Tissue Micro-Array element, are the three types of dynamically generated scan areas (outlined in yellow). The numbers shown are the event IDs generated by the Show event name option. Multi-Scale Association Array Alignment Rectangular dynamic scan area —placed at centroid of element Random dynamic scan area —three scan areas specified The Multi-Scale Association module is analogous to the Association module as described on page 3-58 except that it operates across first and second scale scans whereas the Association module operates within first or second scale scans (or single scale scans.) This is illustrated in Tutorial Exercise 4 where the second scale event component is associated with the first scale Tissue component. There are no parameters for the Multi-Scale Association module. The Array Alignment module is typically used when doing a low resolution scout scan to identify the elements of a Tissue Micro-Array. The module identifies the contoured events for the component to which it is attached, as an ordered pair of numbers. This ordered pair represents the Column and Row for the element within the larger array. This is pictured below. B-26 iCys Research Imaging Cytometer User Guide Revision B
May 6, 2005 Using the iNovator Toolkit Parameters available are: ❑ Max misalignment X & Y—The distance between centers of elements for which adjacent elements are considered to be in the same row or column (relative to the average X or Y dimension.) For example: a 50% X value means that adjacent tissue elements of 2 mm average size are considered to be in the same column if the X value of their centers are no more than 1 mm apart. Use a higher value if elements are not parallel to the X-Y axes and are far apart. Use a lower value if elements are close together and parallel to the X-Y axes. Revision B iCys Research Imaging Cytometer User Guide B-27
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Contents Chapter 1 Introduction Man
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May 6, 2005 Contents Appendix B Usi
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Chapter 1 Introduction This manual
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Chapter 2 iCys Research Imaging Cyt
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Chapter 3 iCys Cytometric Analysis
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Chapter 4 Generating Analytical Dat
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Page 197 and 198: Appendix A Installing iCys Research
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Page 203 and 204: Appendix B Using the iNovator Toolk
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