
Analysis Software Manual
Contents
1 Introduction............................................................................................ 1
1.1 Abstract.............................................................................................. 2
1.2 Technical Support.............................................................................. 2
2 Main User Interface................................................................................ 3
2.1 General .............................................................................................. 4
2.2 General Settings ................................................................................ 6
2.3 The scan^R Data Structure................................................................ 7
2.4 Managing Histograms and Scatter Plots............................................ 7
2.4.1 The Histogram Context Menu .......................................................... 9
2.4.2 The Region Context Menu ............................................................. 10
2.5 Using the Image Viewer................................................................... 11
2.6 Adjusting the Image Displays........................................................... 12
2.7 Selecting Wells for analysis ............................................................. 13
3 Assays.................................................................................................. 15
3.1 General ............................................................................................ 16
3.2 Object Finder: Detecting Main Objects ............................................ 16
3.3 Sub-object Finder: Detecting Sub-objects ....................................... 18
3.4 Object Finder Modules..................................................................... 20
3.4.1 Entire Image................................................................................... 20
3.4.2 Intensity Threshold......................................................................... 20
3.4.3 Edge Detection............................................................................... 21
3.5 Measurement Parameters ............................................................... 25
3.6 Derived Parameters......................................................................... 26
3.7 Image Processing ............................................................................ 27
3.7.1 Background Correction .................................................................. 28
3.7.2 XY Shift .......................................................................................... 29
3.7.3 Inversion......................................................................................... 29
3.7.4 Cut Image....................................................................................... 30
3.8 Virtual Channels............................................................................... 31
3.8.1 Simple Math ................................................................................... 31
3.8.2 Spectral Unmixing.......................................................................... 33
3.9 Tracking – Analyzing Time-Lapse Data........................................... 35
3.9.1 Tracking Configuration................................................................... 37
3.9.2 Track Analysis Parameters ............................................................ 38
3.9.3 Trace Viewer.................................................................................. 43
4 Analysis Results.................................................................................. 45
4.1 Running an Analysis ........................................................................ 46
4.2 Managing Gates............................................................................... 47
4.2.1 Gates and Regions. ....................................................................... 47
4.2.2 The Gate Manager......................................................................... 47