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Chapter 5: Analysis Tools
5-31
The Smooth Data function (found in the Data menu) minimizes single pixel
background noise in a lane.
original graph smoothed graph
When this function is selected, the menu option changes to “Unsmooth Data.”
Selecting this undoes the smoothing operation.
The Invert Button
The INVERT function reverses the gray scale assignments, so that zero corresponds to
white and 4,096 corresponds to black. This function can be selected by placing an “X” in
the INVERT checkbox, or by selecting Invert Data from a graph’s Data pull down
menu.
If the image has dark bands and light background, then INVERT should be selected.
If the image has light bands and dark background, the INVERT option should not be
activated.
On the graph, the regions that were peaks are now closer to the baseline and those that
were near the baseline are now peaks.
original graph inverted graph
Since the baseline is determined when the image is initially scanned, it may be necessary
to use the Reset Baseline function to set an accurate baseline for newly-inverted data.
- AlphaImager™ IS-2200 1
- For Windows 2000/XP 1
- AlphaImager 2
- 2200 – 2
- AlphaEaseFC User’s Manual 2
- 1.2.1 System Components 8
- 1.2.2 System Placement 8
- 1.2.3 Cable Connections 8
- 1.5 System Information 15
- 1.6 Acquiring an Image 16
- 1.6.1 Focusing on an Image 17
- Selecting a Filter 21
- Displays 23
- Imaging Functions 32
- 2.1 Contrast Adjustment 33
- Black Level Adjustment 34
- White Level Adjustment 35
- Gamma Setting Adjustment 35
- The Auto Contrast Selection 36
- The Reverse Button 37
- The Grid Button 37
- 2.2 Tool Bar 40
- Sample Printouts 42
- 2.3 Tool Box 43
- 2.4 Status Bar 43
- Chapter 3: Drop Down Menus 46
- File Open 47
- File Overlay 48
- File Close 48
- File Save and Save As 49
- File Types: 50
- Chapter 3: Drop Down Menus 52
- 3.2 The Edit Menu 53
- Reset and Clear 54
- 3.3 The Image Menu 55
- Conversion 56
- Flat Field Calibrate 57
- 3.4 The Setup Menu 59
- Load Defaults 60
- Preferences 63
- 3.5 The Overlay Menu 66
- 3.6 The Utilities Menu 69
- Notepad 70
- 3.7 The View Menu 71
- Zoom Functions 72
- Show Annotations 72
- 3.8 The Help Menu 73
- Chapter 4: The Image 76
- 4.2 The Rotate / Flip Tool 77
- 4.3 Histogram 78
- 4.4 Automatic Enhancement 79
- 4.5 Annotations 81
- Chapter 4: Enhancement Tools 82
- Text Background and Font 83
- Text Angles 84
- The Drawing Tools 84
- The Editing Tools 86
- 4.6 False Color 88
- Palettes 2 through 11 89
- 4.7 Image Filters 90
- Sharpening Filters 92
- 3-D (Contour) Filters 92
- Noise Filters 93
- Smoothing Filters 93
- Edge Filters 93
- Horizontal Edge Filter 93
- Vertical Edge Filter 94
- Custom Filter 94
- The UNDO Button 94
- Examples of Filter Results 94
- 4.8 Movie Mode 95
- Frame Stacking 98
- BLANK PAGE 100
- Tools in the Toolbox 102
- Setting up an ARRAY Template 103
- Aligning the Template 104
- Measuring Density 105
- The INVERT Box 106
- Outputting Data 106
- Output Dialog Box 107
- Introduction 108
- Chapter 5: Analysis Tools 110
- Manually Selecting Bands 111
- Automatic Band Finding 111
- Special Functions: 115
- Snap to Peak 115
- The INVERT Button 115
- Calculating R 116
- Values 116
- The Graph Tool 117
- Auto Grid 118
- Setting up the Lane Template 119
- Specifying the Scan Width 120
- Scanning the Image 121
- Graph Display 122
- The Active Graph 122
- The Data Window 123
- Peak Detection Algorithms 125
- Set parameters dialog box 129
- Reset Base 130
- Base Subtract 130
- Interpreting 1D-Multi Data 130
- V. Line 130
- 3-D View 131
- Smooth Data 131
- The Invert Button 132
- Overlaying Graphs 133
- 1D-Multi 134
- Band Scoring 139
- Outputting Quantitative Data 141
- Exporting Graphs 141
- Exiting 1D-Multi 142
- Auto Lane 142
- Black Bands or White Bands 142
- Sensitivity Adjustment Bar 143
- Area of Interest Drawing 143
- Output Data 146
- Baseline 147
- Options 147
- Editing Peak Boundaries 147
- Auto Lane Editing Features 148
- Manual Band Matching 156
- Band Matching Results 157
- 5.4 Spot Density Tools 161
- Magic Wand and AutoSpot 163
- Magic Wand: 163
- Magic Wand Sensitivity 163
- Area of Interest 165
- Bright Spot vs Dark Spot 166
- Find Spots 166
- Background Threshold 166
- Moving Objects 168
- Deleting Objects 168
- Saving and Loading Objects 168
- Object Libraries 169
- Spot Density Measurements: 169
- Data Definitions 170
- Inverting the Data 170
- No Background 171
- Automatic Background 171
- Manual Background 172
- The Standard Curve Toolbox 173
- Displaying the Curve 175
- Outputting Quantitation Data 176
- Manual Count Tools 177
- Auto Count Tools 177
- Manual Count 179
- Automatic Count 180
- Editing Tools 182
- Displaying Spots 183
- Using the ADD SPOT Tool 183
- Using the Erase Spot Tool 184
- Spot Count Data 184
- Outputting Auto Count Data 185
- 5.6 The Scoring Function 187
- Scoring the Sample 188
- 5.7 The Ruler Function 190
- Appendix A: Opening 192
- AlphaEaseFC Files 192
- Weight Library Files 194
- To Change the Security Setup 196
- Security Features Dialog Box 197
- Instructions 202
- Cabinet Setup 203
- Camera Installation 206
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