BIO RAD Quantity One 1-D Analysis Software manuals

Owner’s manuals and user’s guides for Accessories for water BIO RAD Quantity One 1-D Analysis Software.
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Bio rad Quantity One 1-D Analysis Software User Manual (444 pages)

Brand: Bio-rad | Category: Accessories for water | Size: 8.08 MB |

English

Table of contents

Quantity One

2

Table of Contents

4

Contents

6

1. About This Document

10

2. Bio-Rad Listens

11

1. Introduction

12

1.3 Gel Quality

14

1.4 Quantity One Workflow

15

1.5 Computer Requirements

16

1.6 Installation

18

1.7.a Windows

19

1.7.b Macintosh

20

1.8 Starting the Program

21

1.9 Software License

22

1.9.a Registering by Internet

23

1.9.c Entering a Password

24

1.11 Quantity One Basic

26

1.12 Contacting Bio-Rad

27

2. General Operation

28

2.1.b Main Toolbar

29

2.1.c Status Boxes

29

2.1.d Secondary Toolbars

30

2.1.e Quick Guides

31

2.2 File Commands

33

2.2.a Opening Images

34

Opening TIFF Images

36

2.2.b Saving Images

37

2.2.c Closing Images

37

2.2.d Revert to Saved

37

2.2.e Image Info

37

Changing the Image Dimensions

38

2.2.f Reduce File Size

39

2.4 Exit

42

2.5 Preferences

42

2.5.a Misc

43

Security Mode

44

Use Custom Open Dialog

46

Maximize Application Window

46

Enable DOS Filename Parsing

46

2.5.b Paths

47

2.5.c Display

47

2.5.d Toolbar

48

2.5.e Application

49

2.6 User Settings

50

3. Viewing and Editing

52

Zoom Box

53

Zoom In/Zoom Out

54

Arrow Keys

54

View Entire Image

55

Centering an Image

55

Imitate Zoom

55

Tiling Windows

55

3.2 Density Tools

56

Plot Cross-section

57

Plot Vertical Trace

57

3.4 Multi-Channel Viewer

58

Viewing Options

60

3.5 3D Viewer

61

3.5.a Positioning the Image

62

3.6 Image Stack Tool

63

Fig. 3-8. Image Stack Tool

64

3.7 Colors

65

Selecting a Color Group

66

Changing a Color

67

3.8 Transform

68

3.8.a Transform Subwindows

70

3.8.b Transform Controls

71

3.8.c Other Features

73

3.9.a Cropping Images

75

Advanced Crop Commands

77

Flipping

78

90° Rotations

78

Custom Rotation

78

Auto-scale

82

Dark Contrast Slider

82

Background Slider

83

Background Box

83

Background Stripe

83

3.11 Filtering Images

84

3.11.a Filter Wizard

85

Step 2: Select Filter Size

87

Step 3: Begin Filtering

88

3.12 Invert Data

90

3.13 Text Overlays

90

Editing a Text Overlay

91

Line Tool

91

3.15 Sort and Recalculate

93

3.16 Automation Manager

93

Use Single Image for Template

95

3.16.c Step 3 - Select Images

96

4. Lanes

98

4.1.a Lane Frames

99

Chapter 4. Lanes

100

Manual Frame Lanes

100

4.1.b Editing the Frame

101

Adjusting the Entire Frame

102

4.1.c Single Lanes

103

Adjusting Single Lanes

104

Deleting Lanes

104

4.1.e Lane Profile

105

4.1.d Lane Width

105

Quantity One User Guide

107

4.2.a Profile Trace

108

4.2.b All Lanes Off

109

4.3 Compare Lanes

110

Magnifying the Graph

111

Show Gaussian Modeling

111

Align Band Types

111

Printing and Exporting

112

4.4 Lane-based Arrays

113

Adjusting the Array Matrix

115

Analyzing Array Data

116

5. Bands

118

5.2 Band Detection

120

5.2.a Detection Parameters

122

Shadow Rejection

123

Band Limit

123

Sensitivity

123

Chapter 5. Bands

124

Lane Width

124

Minimum Density

124

Noise Filter

125

Shoulder Sensitivity

125

5.2.b Parameter Sets

126

5.2.c Default Parameters

126

5.4 Plotting Traces of Bands

129

5.5 Band Attributes

130

5.6 Band Information

133

5.7 Gauss-Modeling Bands

135

Reviewing the Results

136

Incorrect Modeling

137

5.8.a Contouring Bands

139

5.8.b Drawing Tools

140

Drawing Band Boundaries

141

Editing Band Boundaries

142

6. Standards and Band

144

Matching

144

6.1.b Creating New Standards

146

6.1.c Standards Dialog

148

Entering Standard Values

149

Standard value

150

Click here to delete

150

Showing the Modeling Lines

152

Standards Regression Models

153

Display Options

154

6.2 Band Matching

156

6.2.b Band Set Dialog

160

List of Band Types

161

Band Set Toolbar

162

Other Band Set Functions

164

6.2.e Graphs of Match Data

165

6.3 Quantity Standards

167

Entering the Quantities

170

6.3.b Calibration Curve

171

Checking the Imported Curve

174

7. Volume Tools

176

Volume Contour Tool

177

Chapter 7. Volume Tools

178

Volume Free Hand Tool

178

Volume Rect Tool

179

Volume Circle Tool

179

Volume Labels

180

Editing Volume Labels

180

Volume Features

181

Displaying Volumes

181

7.3 Volume Standards

182

Local Background Subtraction

184

Global Background Subtraction

185

7.5 Volume Arrays

186

Creating a Volume Array

187

Moving an Array

188

Resizing an Array

189

Resizing the Array Cells

190

Copying an Array

190

Ungrouping an Array

190

8. Colony Counting

192

8.2 Counting the Colonies

194

8.3 Displaying the Results

195

Chapter 8. Colony Counting

196

Doing a Recount

196

Colonies

197

White and Blue Colonies

198

Saving to the Image

200

Resetting the Count

200

8.8 Saving to a Spreadsheet

201

Naming/Saving a Count

202

Loading Another Image

202

9. Differential Display and

204

Outliers

205

Displaying Results

206

Testing for Ambiguity

208

10.Reports

210

Chapter 10. Reports

212

Scrolling

212

Printing

212

Exporting Report Data

213

Reformatting Report Data

213

10.2 Lane and Match Reports

214

10.3 Band Types Report

215

10.4 1-D Analysis Report

217

Comparison Options

218

Comparison Method

219

10.5.a Compare Lane Images

220

10.5.b Phylogenetic Tree

223

Neighbor Joining

224

Other Methods

224

10.5.c Similarity Matrix

228

10.6 Volume Analysis Report

229

10.6.a Volume Report Options

230

10.7 Volume Regression Curve

232

10.8 VNTR Report

234

11.Printing and Exporting

236

11.3 Image Report

237

11.4 Video Print

238

11.5 Export to TIFF Image

239

11.5.a Analysis Export Mode

240

11.5.b Publishing Export Mode

240

11.5.c Exporting the Image

241

Appendix A

242

Simulation Mode

243

Appendix A. Gel Doc

244

A.2 Step I. Position Gel

245

A.4 Step III. Acquire Image

246

Manual Expose

247

A.5 Step IV. Optimize Display

249

A.6 Step V. Analysis

250

A.7 Step VI. Select Output

251

A.8 Exposure Status

252

A.9 Options

252

DAC Settings

253

Simple Acquisition Mode

255

Appendix B

256

Appendix B. ChemiDoc

258

B.2 Step I. Position Gel

259

B.3 Step II. Image Mode

260

B.4 Step III. Acquire Image

260

Auto Expose

261

Live Acquire

263

B.5 Step IV. Optimize Display

265

B.6 Step V. Analysis

267

B.7 Step VI. Select Output

267

B.8 Exposure Status

268

B.9 Options

268

Imaging Area

270

Auto Exposure Threshold

270

Reminder

270

Save Options

271

Appendix C

274

ChemiDoc XRS

274

Appendix C. ChemiDoc XRS

276

C.2.a. Custom Applications

277

C.3 Step II. Position Gel

278

C.4 Step III. Acquire Image

279

C.4.a. Exposure Status

282

Illumination Flat Fielding

282

C.5 Options

284

C.5.a. Imaging Area

285

C.5.b. Reminder

285

C.5.c. Dark Subtraction

286

C.6 Other Features

287

Highlight Saturated Pixels

288

File Size of Images

288

Appendix D

290

D.1 GS-700 Acquisition Window

291

Appendix D. GS-700

292

Choosing Your Own Settings

294

D.3 Step II. Select Scan Area

295

Selecting an Area

296

D.5 Acquire the Image

298

D.6 Calibration

299

D.6.a Editing the Step Tablet

300

Diffuse Versus Specular O.D

302

D.7 Other Options

303

Auto Save After Scan

304

Make Backup Copy

304

Hide Grid

304

Appendix E

306

E.1 GS-710 Acquisition Window

307

Appendix E. GS-710

308

E.3 Step II. Select Scan Area

312

E.5 Calibration

314

E.5.a Editing the Step Tablet

315

E.6 Acquire the Image

318

E.7 Other Options

319

Appendix F

322

F.1 GS-800 Acquisition Window

323

Appendix F. GS-800

324

F.3 Step II. Select Scan Area

328

F.5 Calibration

330

F.5.a Step Tablet Values

331

Reflective Step Tablet

333

F.6 Acquire the Image

334

F.7 Other Options

335

Appendix G

338

Appendix G. Fluor-S

340

Custom Applications

342

G.3 Step II. Position/Focus

343

Position

344

G.5 Acquire the Image

347

G.6 Options

348

G.6.a Dark Subtraction Type

349

Referenced

350

Reset Reference

350

G.6.b Live Exposure Mode

351

G.6.c Save

352

G.6.d Imaging Area Size

352

G.7 Other Features

353

Appendix H

356

Appendix H. Fluor-S MAX

358

Scan Dimension

361

H.3 Step II. Position/Focus

362

H.5 Acquire the Image

365

H.6 Options

366

H.6.a Dark Subtraction Type

367

Reset Reference Button

368

H.6.b Live Exposure Mode

369

H.6.c Save

370

H.6.d Imaging Area Size

370

H.7 Other Features

371

Appendix I

374

Appendix I. Personal FX

376

I.2 Step I. Select Scan Area

377

I.4 Acquire the Image

379

I.5 Options

380

Disable Default Filter

381

Warn on Saturated Pixels

381

Appendix J

382

Molecular Imager FX

382

Family (FX Pro, FX Pro

382

Plus and Molecular FX)

382

J.1 FX Acquisition Window

383

Appendix J. FX

384

J.2.a Selecting a Channel

385

Standard Applications

387

Standard FX Applications

387

Sample Intensity

389

J.3 Step II. Select Scan Area

392

J.5 Acquire the Image

394

J.6 Options

395

Appendix K

398

VersaDoc

398

Appendix K. VersaDoc

400

K.2.a. Selecting a Channel

400

K.3 Step II. Position/Focus

404

Setting an Exposure Time

405

K.5 Acquire the Image

407

Optimize Exposure

409

K.6 Options

411

Reference

412

K.6.b. Save

414

K.6.c. Imaging Area Size

414

K.7 Other Features

415

Appendix L

416

Cross-Platform File

416

Exchange

416

Appendix M

418

Other Features

418

M.2 Gel Layout

419

Appendix M. Other Features

420

Numerics

422

Bio rad Quantity One 1-D Analysis Software User Manual (7 pages)

Brand: Bio-rad | Category: Accessories for water | Size: 0.03 MB |

English

Table of contents

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1

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2

How NetHASP Works

2

410-0201 Rev A Page 3 of 7

3

Configuring Client Computers

5

Using NetHASP.ini

5

License Upgrades

6

Adding Users

6

Troubleshooting Guide

7

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