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Perform Area Density Analysis
159
Grey Level calculations are used when the sample is imaged using reflective light. Grey level of an area
is simply the sum of grey levels of all pixels in the area. Changes are reflected on the curve after the
window is closed.
Types of Calibration Curves
Two types of curves options can be defined using the Intensity Calibration Curve button:
• Standard Optical Density - Use this type if the sample is excited through transmitted light (such
as the FirstLight uniform UV Illuminator by UVP). Also useful when imaging colorimetric samples.
• Free Form - Use this type when fine-tuning input and output intensity values or when imaging
fluorescent/luminescent samples to produce results in Grey Levels.
Apply Pre-Defined Intensity Calibration Curve
• To apply a pre-defined intensity calibration curve to a previously defined region of interest, click
the Area Density Action Tab > Calibration menu button > Intensity Calibration.
• An Intensity Calibration Curve window opens. To select a previously defined intensity curve,
click the down arrow next to Edit List in the upper right hand corner of the window. A list of
intensity curve options will appear.
• Select the appropriate curve from the list. (For example: choose Black Band Intensity Curve if
black bands are captured in the image)
• Based on the user selection, Free Form or Std. Optical Density will be automatically selected.
• Click OK.
Add New Intensity Calibration Curve
• Click onto Edit List in the Intensity Calibration Curve window.
• A Point List Collection window will appear. Click onto Add to add a new curve. Name the curve,
then select OK.
• The new user-created curve will appear in the drop down menu list. This new curve can be
deleted and edited in the Point List Collection window, if desired.
• With the new curve selected, choose Free Form or Std. Optical Density.
- Life Science Software 1
- Table of Contents 3
- LS Software User Guide 13
- Welcome 15
- Capturing Images 16
- Minimum System Requirements 17
- Registering the Software 18
- Offline Activation 19
- Single-User License 21
- Network-User License 22
- Additional Network Users 26
- User Administration 28
- Users Rights 30
- Configure User Accounts 31
- Add a New User 32
- Edit a User 32
- Technical Support 35
- License Agreement 36
- Limitation of Liability 37
- Navigate the Software 38
- Navigating the Software 38
- Image Windows 40
- Fit the Image to the Window 41
- Context Menu Commands 41
- Status Bar 41
- Obtain Image Information 42
- Menu Buttons 44
- Main Menu Buttons 44
- Action Menu Tabs 44
- File Menu Overview 46
- FTP Transfer 50
- Edit Menu Button Overview 52
- Copy an Entire Image 53
- Paste an Image 54
- Paste Special 54
- Undo and Redo 56
- Region of Interest (ROI) 57
- Select a Region 58
- Adjust a Region 58
- Cancel a Region 58
- Image Enhancement Filters 59
- Sharpen 61
- Remove Noise 63
- Adjust the Image 64
- Rotate Function 65
- Align the Image 67
- Flip Image 68
- Resize Image 70
- Reduce Image to Monochrome 71
- Change Image Depth 72
- Advanced Menu Overview 73
- Log Viewer 74
- Display Loaded Modules 79
- Configure Application 80
- Rulers 81
- Using Macros 82
- Edit Macros 83
- Play a User-Defined Macro 83
- Help Menu Overview 84
- Display Help Topics 85
- Application Information 86
- Acquire Images 87
- Image Acquisition 89
- Emission Filters 91
- Magnification 92
- Fine Focus 93
- Bookmarks 93
- Lighting/Darkroom/Lens 95
- Using the BioLite Functions 95
- Darkroom Control 97
- Lens Control 99
- Camera Functions 100
- Exposure Time 101
- Post Processing 102
- Binning 102
- Saturation Preview 102
- Preferences 102
- CCD Temperature 103
- Camera Integration 104
- Dynamic Integration 106
- Binning Modes 107
- Perform 1D Analysis 108
- Finding Lanes and Bands 111
- Lane and Band Information 114
- Add Lanes and Bands 117
- Delete Lanes and Bands 120
- Edit Lanes and Bands 121
- Place Bands Exactly 122
- Lane Profile Overview 124
- Overview 126
- Calibrate a Lane 127
- Stretch Factor 128
- Manual Placement of Weights 129
- Exact Placement of Bands 129
- Background Correction 132
- Joined Valleys 133
- Rolling Disc 134
- Area Between Lanes 134
- Lane Profile Graph 136
- Axis Options 137
- Display Options 137
- Display Options for Details 138
- Selecting Background Color 138
- Concentration Calibration 140
- Change Unit Type 141
- Select Unit Type 141
- Select Data Points 142
- Select Curve Type 143
- Adjust an Automatic Rf Line 145
- Add Rf Lines Manually 146
- Move Rf Lines 146
- Delete Rf Lines 146
- Remove All Rf Lines 147
- Dendrogram Analysis 148
- Generate Dendrogram Graphs 148
- Modify Dendrogram Graphs 149
- Dendrogram Standards 149
- Create Clusters 150
- Linkage Rules 151
- 1D Analysis Settings 153
- Results 155
- Results Data Explorer 156
- Print Data Explorer Reports 157
- Report Types 158
- Perform Area Density 163
- Modify Regions in the Image 165
- • Define Image Scale 166
- Area Density Settings 167
- Define Background 168
- Delete Background Region 169
- Estimate Region Volume 170
- Calibration Curves 172
- Types of Calibration Curves 173
- Save the Results 178
- Print the Results 178
- Export the Results 178
- Perform Colony Counting 179
- Colony Counting Settings 181
- Colony Marking 182
- Label Color 182
- Circle Radius 182
- Counting Colonies - Options 183
- Automatic Counting 184
- Click and Add Counting 186
- Add Colonies 193
- Delete Colonies 194
- Split Colonies 195
- Auto Split Colonies 196
- Merging Colonies 197
- Identify by Color Counting 198
- Classes 200
- Spiral Counting 205
- Adjust Grid Size and Volume 206
- User Tips 208
- Zone Analysis 209
- Colony Counting Reports 210
- Exporting to Excel 211
- Printing Colony Results 211
- Modify Images 218
- Image Action Tab Overview 218
- Image Corrections 219
- Change Brightness 220
- Change Contrast 220
- Change Gamma 221
- Invert Image 221
- Histogram Controls 222
- Pseudocolor 224
- 3D Plots 226
- Viewpoint Tab 227
- Output Tab 227
- Annotations 229
- Annotation Tools 230
- Create Annotations 231
- Create Line Annotations 233
- View or Hide Annotations 235
- Modify Annotations 236
- Rotate Text Annotations 237
- Format Annotations 237
- Delete Annotations 238
- Synchronize Annotations 239
- Measurement Tools 240
- Angle Measure 241
- Layer Actions 242
- Multi-Image Actions 243
- Image Compositing 244
- Player (Image Sequences) 245
- Merge Functions 246
- Player Features 247
- Player Options 247
- Saving .AVI Files 249
- Create Templates 250
- Edit a Template 252
- Synchronize a Template 252
- Delete a Template 252
- Open and Save Images 253
- Image File Types 254
- Print Reports 256
- File Print Command 257
- Print Image History 258
- Print an Image 259
- Purpose 260
- Features 260
- Image History 263
- Glossary 264
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