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Quantity One User Guide
19-12
The Print Report dialog for this report contains special fields for entering a
title for your report.
19.4.b Phylogenetic Tree
Phylogenetic trees are schematic representations of lane similarity. To
compare the similarity of your lanes in a phylogenetic tree format, select
Phylogenetic Tree from the Reports menu. (You can also use the Phylogenetic
Tree Quick Guide under the Help menu to analyze your gel image.)
A dialog box will pop up displaying the different cluster methods for creating
the tree.
Select a method to open the report window. See below for information about
the different methods.
- Quantity One 1
- Table of Contents 3
- Contents 5
- 1. About This Document 9
- 2. Bio-Rad Listens 10
- 1. Introduction 11
- 1.3 About Gel Quality 13
- Acquire Image 14
- Optimize Image 14
- 1.5 Computer Requirements 15
- Macintosh 16
- 1.6 Installing on a PC 17
- 1.7 Installing on a Macintosh 18
- 1.8 Starting the Program 19
- 1.8.a Software License 20
- (If Necessary) 20
- Introduction 21
- 1.8.c Trial Period 22
- 1.8.d Software Registration 24
- Registering by Internet 25
- Registering by Fax or E-mail 26
- Entering a Password 26
- 1.9 Contacting Bio-Rad 27
- 2. General Operation 29
- 2.1.b Main Toolbar 30
- 2.1.c Status Boxes 30
- 2.1.d Secondary Toolbars 31
- 2.1.e Quick Guides 32
- General Operation 33
- 2.2 Mouse-assignable Tools 34
- 2.3 Keyboard Commands 35
- Opening TIFF Images 38
- Close All 39
- Save All 40
- Revert to Saved 40
- Image Info 40
- Change the Image Dimensions 41
- Reduce File Size 42
- 2.5 Preferences 45
- 2.5.a Misc 46
- 2.5.b Toolbar 47
- 2.5.c Application 49
- 2.5.d Display 50
- 2.6 User Settings 51
- 3. Gel Doc 53
- 3.2 Step I. Position Gel 56
- 3.3 Step II. Acquire Image 57
- Manual Expose 58
- Fig. 3-5. Manual Expose 59
- 3.4 Step III. Select Output 60
- 3.5 Image Mode 61
- 3.6 Exposure Status 62
- 3.7 Display 62
- 3.8 Options 64
- DAC Settings 65
- Imaging Area 65
- Auto Exposure Threshold 65
- Reminder 65
- Save Options 66
- 4. Chemi Doc 67
- Chemi Doc 69
- 4.2 Step I. Position Gel 70
- 4.3 Step II. Acquire Image 71
- 4.4 Step III. Select Output 75
- Video Print 76
- Annotate 76
- 4.5 Image Mode 77
- 4.6 Exposure Status 78
- 4.7 Display 78
- 4.8 Options 80
- 5. GS-700 Imaging 83
- 5.1 GS-700 Acquisition Window 84
- GS-700 Imaging Densitometer 85
- 5.3 Step II. Select Scan Area 88
- Selecting an Area 89
- 5.5 Acquire the Image 91
- 5.6 Calibration 92
- 5.6.a Editing the Step Tablet 93
- 5.7 Other Options 96
- 6. GS-710 Imaging 99
- 6.1 GS-710 Acquisition Window 100
- GS-710 Imaging Densitometer 101
- Quantity One User Guide 102
- Choosing Your Own Settings 104
- 6.3 Step II. Select Scan Area 105
- 6.5 Calibration 107
- 6.5.a Editing the Step Tablet 108
- Diffuse Versus Specular O.D 110
- 6.6 Acquire the Image 111
- 6.7 Other Options 112
- Highlight Saturated Pixels 113
- Hide Grid 113
- 7. GS-800 Imaging 115
- Densitometer 115
- 7.1 GS-800 Acquisition Window 116
- GS-800 Imaging Densitometer 117
- 7.3 Step II. Select Scan Area 120
- 7.5 Calibration 122
- 7.5.a Editing the Step Tablet 123
- 7.5.b Calibration Settings 125
- 7.6 Acquire the Image 126
- 7.7 Other Options 126
- Auto Save After Scan 127
- Make Backup Copy 127
- 8. Fluor-S MultiImager 129
- Simulation Mode 130
- Fluor-S MultiImager 131
- Custom Applications 133
- 8.3 Step II. Position/Focus 134
- Position 135
- 8.5 Acquire the Image 138
- 8.6 Options 139
- 8.6.a Dark Subtraction Type 140
- Referenced 141
- Reset Reference 141
- 8.6.b Live Acquire Mode 142
- 8.6.c Save 143
- 8.7 Other Features 144
- File Size of Images 145
- 9. Fluor-S MAX MultiImager 147
- Fluor-S MAX MultiImager 149
- Scan Dimension 152
- 9.3 Step II. Position/Focus 153
- 9.5 Acquire the Image 156
- Live Acquire 157
- 9.6 Options 158
- Reset Reference Button 159
- 9.6.b Live Acquire Mode 160
- 9.6.c Save 161
- 9.6.d Imaging Area Size 162
- 9.7 Other Features 163
- 10.Personal Molecular 165
- Imager FX 165
- Personal Molecular Imager FX 167
- 10.2 Step I. Select Scan Area 168
- 10.4 Acquire the Image 170
- 10.5 Options 171
- 11. Molecular Imager FX 173
- 11.1 FX Acquisition Window 174
- Molecular Imager FX 175
- Standard Applications 176
- Standard FX Applications 176
- Sample Intensity 178
- 11.5 Acquire the Image 183
- 11.6 Options 184
- 12. Viewing and Editing 187
- Zoom Box 188
- Viewing and Editing Images 189
- Zoom In/Zoom Out 189
- Arrow Keys 189
- View Entire Image 190
- Centering an Image 190
- Imitate Zoom 190
- Tiling Windows 190
- 12.2 Density Tools 191
- Density in Box 192
- Plot Density Distribution 192
- Plot Cross-section 192
- Plot Vertical Trace 193
- 12.4 Multi-Channel Viewer 194
- Viewing Options 195
- 12.5 Image Stack Tool 196
- 12.6 Colors 198
- Changing a Color 199
- 12.7 Transform 201
- 12.7.a Transform Subwindows 202
- 12.7.b Transform Controls 203
- Gamma Slider 205
- 12.7.c Other Features 206
- 12.8.a Cropping Images 208
- Flipping 209
- 90° Rotations 210
- Custom Rotation 210
- Auto-scale 214
- Dark Contrast Slider 214
- Background Slider 215
- Background Box 215
- Background Stripe 216
- Completing the Subtraction 216
- 12.10 Filtering Images 217
- 12.10.a Filter Wizard 218
- Step 2: Select Filter Size 219
- Step 3: Begin Filtering 220
- 12.11 Invert Data 222
- 12.12 Text Overlays 223
- Editing a Text Overlay 224
- Line Tool 224
- 12.14 Sort and Recalculate 226
- 13. Lanes 227
- 13.1.a Creating a Lane Frame 228
- Manual Frame Lanes 229
- 13.1.b Editing the Frame 230
- Adjusting the Entire Frame 231
- Adding and Adjusting Anchors 231
- 13.1.c Defining a Single Lane 233
- 13.1.d Adjusting Single Lanes 233
- 13.1.f Deleting Lanes 234
- 13.1.g Lane Width 234
- 13.1.h Creating a Lane Profile 235
- Lanes to Model 237
- Trace Display 237
- When to Apply 237
- Calculation Method 237
- 13.3 Compare Lanes 239
- Magnifying the Graph 240
- Show Gaussian Modeling 240
- Align Band Types 241
- Printing and Exporting 242
- 13.4 Lane-based Arrays 243
- Adjusting the Array Matrix 244
- Analyzing Array Data 246
- 14. Bands 247
- Quantified 248
- 14.2.a Detection Parameters 251
- Shadow Rejection 252
- Band Limit 252
- Sensitivity 252
- Lane Width 253
- Minimum Density 254
- Noise Filter 254
- Shoulder Sensitivity 255
- Size Scale 255
- Saving Parameters 255
- Loading Parameters 256
- Deleting Parameters 256
- Resetting Parameters 256
- In Brackets Mode 257
- In Lines Mode 258
- 14.3.b Adjusting Bands 259
- 14.4 Plotting Traces of Bands 260
- 14.5 Band Attributes 261
- 14.7 Gauss-Modeling Bands 267
- Incorrect Modeling 270
- One pixel enlarged to 271
- 14.8.a Contouring Bands 272
- 14.8.b Drawing Tools 273
- Density in Region 274
- Drawing Band Boundaries 274
- Editing Band Boundaries 276
- 15. Standards and Band 277
- Matching 277
- Standards and Band Matching 279
- Selecting Predefined Standards 279
- Creating New Standards 279
- 15.1.a Standards Form 281
- Entering Standard Values 282
- Showing the Modeling Lines 284
- Standards Regression Models 286
- Display Options 287
- Read-Only Standards 288
- 15.2 Band Matching 289
- 15.2.b Band Set Form 292
- List of Band Types 294
- Band Set Toolbar 295
- Other Band Set Form Functions 296
- 15.2.e Graphs of Match Data 297
- 15.3 Quantity Standards 299
- 15.3.b The Calibration Curve 304
- Checking the Imported Curve 308
- 16. Volume Tools 309
- Volume Contour Tool 310
- Volume Tools 311
- Volume Freehand Tool 311
- Volume Rect Tool 312
- Volume Circle Tool 312
- Volume Labels 313
- Displaying Volumes 314
- 16.3 Volume Standards 315
- Local Background Subtraction 317
- Global Background Subtraction 318
- 16.5 Volume Arrays 319
- What Is a Volume Array? 320
- Creating a Volume Array 320
- Moving an Array 322
- Resizing an Array 322
- Resizing the Array Cells 323
- Copying an Array 323
- Ungrouping an Array 324
- 17. Colony Counting 325
- Colony Counting 327
- 17.2 Counting the Colonies 328
- 17.3 Displaying the Results 329
- Colonies 330
- White and Blue Colonies 331
- 17.8 Saving to a Spreadsheet 334
- Creating/Opening a Batch File 335
- Naming/Saving a Count 336
- Loading Another Image 336
- 18. Differential Display and 337
- Normalization 338
- Displaying the Results 339
- Testing for Ambiguity 341
- 19. Reports 343
- Printing Your Report 345
- Exporting Your Report Data 346
- 19.2 Lane and Match Reports 347
- 19.3 1-D Analysis Report 349
- Comparison Options 350
- Comparison Method 351
- 19.4.a Compare Lane Images 352
- 19.4.b Phylogenetic Tree 354
- Neighbor Joining 356
- Other Methods 356
- Neighbor Joining Only 359
- All Other Methods 359
- 19.4.c Similarity Matrix 360
- 19.5 Volume Analysis Report 361
- 19.5.a Volume Report Options 362
- Background Subtraction Method 363
- 19.6 Volume Regression Curve 364
- 19.7 VNTR Report 366
- 20. Printing and Exporting 369
- 20.1.b Print Actual Size 371
- 20.1.d Video Printing 373
- Analysis Export Mode 374
- Publishing Export Mode 374
- Exporting the Image 375
- Appendix A 377
- Appendix B 379
- B.2 Gel Layout 381
- Appendix B. Other Features 383
- Zoom tools 401
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