Thermo Fisher Scientific Attune Cytometric Software User guide

For Research Use Only. Not for use in diagnostic procedures.

Attune™ Cytometric Software

USER GUIDE

For data acquisition and analysis using the Attune™ NxT and

Attune™ CytPix™ Flow Cytometers

Publication Number MAN0026553

Revision B.0

Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256

Revision history:MAN0026553 B.0 (English)

Revision Date Description

B.0 27 April 2023 Add Process Images dialog and Attune Image Processing Dashboard chapters; add Attune Cytometric SW Image

processing parameters appendix; update Ribbon tabs, Image View, Experiment Explorer, Customize panel, Image

Capture Settings panel, Options dialog, File dialogs, Dialogs, Attune Database Utility chapters and the Data

Management appendix with information about image processing and data processing; convert the UG to CCMS

and change the formatting and style.

A.0 25 April 2022 Change Pub. No. from 100024236 to MAN0026553, add Autogating section to WS tab and to Gate options, add

Autogate controls to Customize Gates panel, update UI screens to include Autogating tools and revised icons,

update Cloud sign in and Enable SAE mode workﬂows.

L.0 (Pub.

No.

1000242

36)

21 June 2021 Change the name of the SW to Attune™ Cytometric Software and update the title of the user guide. Add

information about Attune™ CytPix™ Flow Cytometer. Update the UI screens to reﬂect the new instrument and

software functions.

K.0 (Pub.

No.

1000242

36)

21 April 2020 Add information about the CytKick™ Autosampler, SAE Administrator Console, sign in information in the SAE

mode, SAE tab to Ribbon tabs, SAE signing dialogs, information about SAE mode in Administrator and User

Management options. Update the sections of the user guide to include revised UI screens relevant to CytKick™

Autosampler controls and the SAE module. Add software installation information.

J.0 (Pub.

No.

1000242

36)

1 May 2019 Add Appendix B: Data management in Attune™ Cytometric Software, add Cloud sign in to Quick Access toolbar,

add Thermo Fisher Cloud status to Application status bar, update Valve positions, add Adjust plots, add Export

Logs for Service, Device Registration Options, Cloud Sign in, Switch Accounts, and Cloud Storage dialogs, update

UI screens.

H.0 (Pub.

No.

1000242

36)

20 September

2018 Add Bent Quadrant Gates to Gates topic in Workspace view, add Sample List view chapter, Map Sample

List Data dialog, Update Sample Information dialog, Create/Edit Keyword dialog, Experiment Keyword dialog,

and Keyword options sections, update Experiment Explorer context menus, update Collection panel chapter,

Customize Experiment options, and Conﬁguration options sections.

G.0 (Pub.

No.

1000242

36)

8 August 2017 Update Collection panel, add Save as Template, Manage Templates, Plate Mapping, and Select Template dialogs,

update Import FCS Files dialog, update Instrument Ribbon tab and Overlay Ribbon tab sections, and add

Automation Group to Instrument Ribbon tab.

F.0 (Pub.

No.

1000242

36)

29 December

2016 Update Experiment tab, Statistics tab, and Collection panel functions, update various context menus; add Overlay

tab, Overlay View, Attune™ Database Utility sections.

E.0 (Pub.

No.

1000242

36)

20 May 2016 Add new instrument functions and ﬁlter conﬁgurations.

D.0 (Pub.

No.

1000242

36)

13 November

2015 Basis for this revision.

The information in this guide is subject to change without notice.

DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE

LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR

ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.

Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these

products, you accept the terms and conditions of all applicable Limited Use Label Licenses.

TRADEMARKS: All trademarks are the property of Thermo Fisher Scientiﬁc and its subsidiaries unless otherwise speciﬁed.

Contents

■About thisguide ..................................................................... 28

Conventions ................................................................... 28

Text and keyboardconventions .............................................. 28

Clicking .................................................................. 29

User attentionsymbols ..................................................... 29

Other Attune™ userguides ...................................................... 29

Safetyinformation .............................................................. 30

Safety alert words ......................................................... 30

SDSs ..................................................................... 30

■CHAPTER1Attune™ Cytometric Software ...................................... 31

Attune™ Cytometric Software overview ........................................... 31

About the software ......................................................... 31

System requirements ....................................................... 32

Supportedﬁles ............................................................ 32

Software layout and ribbon bar menu system ...................................... 32

Softwarelayout ............................................................ 32

Ribbon bar menu system ................................................... 32

Contextmenus ............................................................ 33

Keyboard shortcuts ........................................................ 33

Attune™ Cytometric Softwareinstallation .......................................... 33

Guidelines forinstallation ................................................... 34

Install the Attune™ Cytometric Software ...................................... 34

Update the instrumentﬁrmware ............................................. 35

■CHAPTER2Startup, login, and mainmenu .................................... 36

Main application startup ........................................................ 36

Main application startup .................................................... 36

End user license agreement(EULA) .......................................... 36

SAEmodule .............................................................. 37

Login screen .................................................................. 37

Sign in – standardmode .................................................... 38

Sign in – SAEmode ........................................................ 38

SAE accountrules ......................................................... 40

Attune™ Cytometric Software User Guide 3

Invalid username or password ............................................... 40

Expired password ......................................................... 41

Accounttypes ................................................................. 42

Default local Attune™accounts .............................................. 42

MainMenu .................................................................... 46

LogOut .................................................................. 47

Main Menu ribbon bar ..................................................... 47

Experiment Explorer ....................................................... 48

■CHAPTER3Attune™ Desktop ................................................... 49

Attune™ Desktop overview ..................................................... 49

Attune™ Desktoplayout .................................................... 50

Application titlebar ............................................................. 51

Quick Access toolbar .......................................................... 52

Default buttons ............................................................ 52

Sign in toCloud ................................................................ 53

Ribbonbar .................................................................... 55

Ribbontabs ............................................................... 55

Ribbon contextmenu ...................................................... 55

Main application workspace .................................................... 56

Application area ........................................................... 56

Applicationpanels ........................................................ 57

Dockinglocations .......................................................... 58

Docking and undockingpanels .............................................. 59

Docking and undockingtabs ................................................ 61

Floatingpanels ............................................................ 61

AutoHide ................................................................ 61

Application status bar ......................................................... 64

Instrument status and alerts ................................................. 64

Camerastatus ............................................................. 67

Connectstatus ............................................................ 67

Tube and Platemodes ...................................................... 67

Time ..................................................................... 69

Coordinates ............................................................... 69

Workspace and InstrumentSettings .......................................... 70

Acquisitionstatus .......................................................... 70

Analysisstatus ............................................................ 70

Sizeslider ................................................................ 71

Contents

4Attune™ Cytometric Software User Guide

■CHAPTER4Ribbontabs ......................................................... 72

Overview ...................................................................... 72

Ribbontabs ............................................................... 72

Filetab ....................................................................... 73

Filemenu ................................................................. 73

Hometab ..................................................................... 75

Create group .............................................................. 75

Templates group ........................................................... 75

General group ............................................................. 76

Clipboard group ........................................................... 76

Editing group .............................................................. 77

Refresh group ............................................................. 77

Viewtab ...................................................................... 78

Experiment group .......................................................... 78

Show Panels group ........................................................ 79

ShowColors .............................................................. 80

Other Options group ....................................................... 81

Workspacetab ................................................................ 82

Save as Default Workspace ................................................. 82

Plots group ............................................................... 83

Gating Tools group ......................................................... 84

Autogating Tools group ..................................................... 85

Cell Image Analysis group .................................................. 86

Other group ............................................................... 86

Size and Position group .................................................... 87

Instrumenttab ................................................................. 89

Setup group .............................................................. 89

System History group ...................................................... 90

Functions group ........................................................... 90

Service group ............................................................. 93

Automation group ......................................................... 94

Experimenttab ................................................................ 95

Experimentlimits .......................................................... 95

Experiment tab controls .................................................... 95

Hot keys .................................................................. 98

Compensationtab ............................................................. 99

Setup group .............................................................. 99

Apply group .............................................................. 100

Adjustment group ........................................................ 101

Statisticstab ................................................................. 103

Statistics tabbehavior .................................................... 103

Results group ............................................................ 105

Tools group .............................................................. 106

General group ............................................................ 107

Contents

Attune™ Cytometric Software User Guide 5

Event Statistics group ..................................................... 108

Intensity group ........................................................... 108

Variation group ........................................................... 109

Overlaytab ................................................................... 110

Create group ............................................................. 110

Gating Tools group ....................................................... 111

Galleries View group ...................................................... 111

Image Settingstab ............................................................ 112

Setup group ............................................................. 112

Analysis group ........................................................... 113

Image Processing group ................................................... 113

SAEtab ..................................................................... 114

Signing group ............................................................ 114

Other group .............................................................. 115

■CHAPTER5Workspaceview ................................................... 116

Overview .................................................................... 116

Workspacebehavior ...................................................... 117

Workspaceselection .......................................................... 118

Workspacelevels ......................................................... 118

Workspace viewlabel ..................................................... 118

Workspace selectionmenu ................................................ 118

Workspaceobjects ............................................................ 120

Create Workspaceobjects ................................................. 120

Select Workspaceobjects ................................................. 121

Resize Workspaceobjects ................................................. 123

Move Workspaceobjects .................................................. 124

Delete, format, or duplicate Workspace objects .............................. 124

Paste Workspaceobjects .................................................. 125

Workspace viewlayout ........................................................ 126

Resize the Workspaceview ................................................ 126

Workspace viewmodes ................................................... 126

Freeformmode ........................................................... 126

Auto Layoutmode ........................................................ 127

Previews ..................................................................... 132

Overview ................................................................ 132

Access the Previewpanel .................................................. 132

Preview panel titlebar ..................................................... 133

Previewplots ............................................................ 134

Resize Previewplots ...................................................... 134

Add Plots to Workspace – Single Plot selection .............................. 134

Add Plots to Workspace – Group selection .................................. 135

Mouse overbehavior ...................................................... 136

Contents

6Attune™ Cytometric Software User Guide

Plots ........................................................................ 138

Overview ................................................................ 138

Histogramplot ........................................................... 139

Dotplot ................................................................. 140

Densityplot .............................................................. 141

Precedence densityplot ................................................... 142

Adjustplots .............................................................. 143

Gates ....................................................................... 145

Overview ................................................................ 145

Create and delete gates ................................................... 145

Gatename ............................................................... 146

Gatecolor ............................................................... 147

Move and resize gates .................................................... 148

Rectangular Gate ......................................................... 149

Oval Gate ................................................................ 150

Polygon Gate ............................................................ 151

Quadrant Gate ........................................................... 152

Bent Quadrant Gate ....................................................... 153

Histogram Gate .......................................................... 155

Contour Autogate ......................................................... 156

Ellipse autogate .......................................................... 159

Autogate gatingrules ..................................................... 162

Derived gate ............................................................. 163

O-plot gates ............................................................ 164

Gatebehavior ............................................................ 166

Workspacestatistics .......................................................... 168

Overview ................................................................ 168

Workspacestatistics ...................................................... 169

Plot statistics (singleplot) .................................................. 170

Plot statistics (multipleplots) ............................................... 170

Workspace images and text .................................................... 171

Workspaceimages ....................................................... 171

Workspace text .......................................................... 171

Imagebackgating ............................................................. 172

Cell imagecontainer .......................................................... 174

Overview ................................................................ 174

Populationmenu ......................................................... 175

Navigation ............................................................... 176

Measure Image tool ....................................................... 177

Workspace view contextmenu ................................................. 178

Overview ................................................................ 178

Insert ................................................................... 178

Paste and Selectall ....................................................... 179

Send All Plots ToOverlay .................................................. 180

Plot titlehyperlink ............................................................. 181

Contents

Attune™ Cytometric Software User Guide 7

Plot contextmenu ............................................................ 182

Overview ................................................................ 182

Customize ............................................................... 182

Scale ................................................................... 183

Set Population ........................................................... 184

Add gate ................................................................ 185

Insert plotstatistics ....................................................... 185

SwapAxis ............................................................... 185

Cut, Copy, and Delete ..................................................... 185

Send tooverlay .......................................................... 186

Saveas ................................................................. 186

Gate contextmenu ............................................................ 187

Overview ................................................................ 187

Customize ............................................................... 187

Create daughterplot ...................................................... 188

Export FCSﬁle ........................................................... 188

Cut, Copy, and Delete ..................................................... 189

Edit gates ............................................................... 189

Plot axis contextmenu ........................................................ 190

Overview ................................................................ 190

Customize ............................................................... 190

Scale ................................................................... 191

Parameter ............................................................... 192

Set Population ........................................................... 194

Add gate ................................................................ 195

Insert plotstatistics ....................................................... 195

SwapAxis ............................................................... 195

Cut, Copy, Paste, and Delete ............................................... 195

Send tooverlay .......................................................... 196

Saveas ................................................................. 197

Plot parameterhyperlink ....................................................... 198

Statistics contextmenu ........................................................ 200

Overview ................................................................ 200

Customize ............................................................... 200

Cut, Copy, and Delete ..................................................... 200

Exportstats .............................................................. 200

Image contextmenu .......................................................... 201

Overview ................................................................ 201

Cut, Copy, and Delete ..................................................... 201

Text box contextmenu ........................................................ 201

Overview ................................................................ 201

Customize ............................................................... 202

Cut, Copy, and Delete ..................................................... 202

Contents

8Attune™ Cytometric Software User Guide

Text box text contextmenu ..................................................... 202

Overview ................................................................ 202

Cut, Copy, and Delete ..................................................... 202

Cell Image Container contextmenu ............................................. 203

Overview ................................................................ 203

Customize ............................................................... 203

Cut, Copy, and Delete ..................................................... 203

Measure ................................................................. 203

■CHAPTER6Heat Map View .................................................... 204

Overview .................................................................... 204

Display ofsamples ............................................................ 205

Overview ................................................................ 205

TubeExperiment ......................................................... 206

PlateExperiment ......................................................... 207

Navigation andselection ....................................................... 208

Set up anExperiment ......................................................... 209

Experiment/Grouplabels .................................................. 209

Compensationwells ...................................................... 209

Manualwells ............................................................. 210

Run Protocol ............................................................. 210

Legend .................................................................. 211

Analyze results ............................................................... 213

Display of results ......................................................... 213

Tooltips ................................................................. 213

Indicators ................................................................ 214

■CHAPTER7Sample Listview .................................................. 215

Overview .................................................................... 215

Sample List properties ......................................................... 217

Edit values in the SampleList .............................................. 217

Rules for editing the SampleList ........................................... 217

Navigation in the Sample List with the keyboard ............................. 218

Selection in the SampleList ................................................ 218

Multiselection in the SampleList ........................................... 219

Copy and Paste .......................................................... 219

Print the SampleList ...................................................... 220

Sample List contextmenu ..................................................... 220

Sample List contextmenus ................................................ 220

Contents

Attune™ Cytometric Software User Guide 9

■CHAPTER8Resultsview ....................................................... 221

Overview .................................................................... 221

Resultstable ................................................................. 222

Resultstable ............................................................. 222

Primarytable ............................................................. 222

Select rows .............................................................. 223

Group results ................................................................. 223

Group results by columnheaders ........................................... 223

Add and remove columnheaders ........................................... 224

Moving versus copyingheaders ............................................ 225

Examples of grouped results ............................................... 225

Results table column header context menu ...................................... 226

■CHAPTER9Overlays ............................................................ 227

Overview .................................................................... 227

Overlaystab ............................................................. 227

Overlays area ............................................................ 228

Galleries area ............................................................ 229

Overlayplots ................................................................. 230

Overlay plotmodes ....................................................... 230

Overlay plot characteristics ................................................ 231

Galleryplots .................................................................. 234

Gallery plot characteristics ................................................. 234

Controlplot .............................................................. 234

Overlaycalculations ...................................................... 236

Display ofstatistics ....................................................... 237

Gates ................................................................... 238

Overlay properties ............................................................ 239

Overlaysettings .......................................................... 239

Add plots toOverlays ..................................................... 240

Compare Plots with dierent Scale and Range settings ....................... 240

Selectplots .............................................................. 241

Move and copy plots betweenOverlays ..................................... 243

Copy plotimages ......................................................... 244

Resizeplots .............................................................. 244

Overlay plot links to Sourceplot ............................................ 244

Auto-Refresh ............................................................. 244

Overlay plot contextmenu ..................................................... 246

Overview ................................................................ 246

Overlay plot context menuoptions .......................................... 246

Contents

10 Attune™ Cytometric Software User Guide

Gallery plot contextmenu ...................................................... 249

Overview ................................................................ 249

Gallery plot context menuoptions .......................................... 249

OverlayBuilder ............................................................... 253

Overview ................................................................ 253

Select and ordersamples .................................................. 255

SelectPlots .............................................................. 257

PageSetup .............................................................. 259

Printoverlays ............................................................ 261

■CHAPTER10Image View ....................................................... 262

Overview .................................................................... 262

Image viewtab ........................................................... 263

Activeimage ................................................................. 264

Image gallery ................................................................. 265

Navigation andselection .................................................. 266

Image capture gate ........................................................... 269

Imagebackgating ............................................................. 271

Measure image tool ........................................................... 273

Image view contextmenus ..................................................... 275

Active image contextmenu ................................................ 275

Image Gallery contextmenu ............................................... 276

Measure image tool contextmenu .......................................... 277

■CHAPTER11Experiment Explorer ............................................. 278

Overview .................................................................... 278

Experiment Explorericons ................................................. 279

Filesview .................................................................... 280

Organization ............................................................. 280

Storage and Size .............................................................. 281

Experiment hierarchy .......................................................... 284

Plate hierarchy ........................................................... 284

Tube hierarchy ........................................................... 285

Experiment Explorerbehavior .................................................. 287

Selection indicators ....................................................... 287

Selection ................................................................ 287

Drag and drop ............................................................ 288

Instrument Settings (IS) badge identiﬁcation ................................. 290

Drag-and-drop from Experiment Explorer to Overlays ......................... 291

Contents

Attune™ Cytometric Software User Guide 11

Drag-and-drop FCSﬁles ................................................... 291

DisplayID ............................................................... 292

Experiment Explorer contextmenus ............................................. 294

Overview ................................................................ 294

Validation of nameﬁelds ................................................... 294

User and Shared folder contextmenus ...................................... 295

Plate contextmenu ....................................................... 297

Experiment contextmenu ................................................. 303

Group contextmenu ...................................................... 311

Sample contextmenu ..................................................... 317

Compensation node contextmenu ......................................... 324

Compensation control contextmenu ........................................ 328

Deleted itemsdialog ...................................................... 332

■CHAPTER12Collectionpanel .................................................. 333

Overview .................................................................... 333

Acquisitionstatus ............................................................. 337

Acquisition status indicators ............................................... 337

Sample remaining indicator ................................................ 338

Collection controls ............................................................ 339

Overview ................................................................ 339

Collection controls – tube and manualwells ...................................... 340

Overview of collection controls for tube and manual wellsamples .............. 340

Buttonsdisplayed ........................................................ 341

Collection controls – plate ...................................................... 344

Overview of plate collection controls ........................................ 344

Buttonsdisplayed ........................................................ 347

Buttonavailability ......................................................... 349

Current well indicator ..................................................... 350

Set up compensationworkﬂow ............................................. 350

Collect and displayoptions .................................................... 351

Collect group overview .................................................... 351

Collectoptions ........................................................... 352

Record and savedialogs .................................................. 357

Run protocol ................................................................. 363

Overview ................................................................ 363

Settings buttons .......................................................... 366

Optimize for high throughputcollection ...................................... 368

Set up compoptions ...................................................... 368

Flow/Recording ﬂowoptions ............................................... 369

Stopoptions ............................................................. 372

Otheroptions ............................................................ 374

Rinse reminderdialog ..................................................... 377

Contents

12 Attune™ Cytometric Software User Guide

■CHAPTER13Instrument settingspanel ....................................... 378

Overview .................................................................... 378

General panel properties .................................................. 379

Default and loadoptions ....................................................... 379

Overview ................................................................ 379

Automatic updateoption .................................................. 379

Set as experimentIS ...................................................... 380

Save as default split button ................................................ 380

Parameters ................................................................... 381

Overview ................................................................ 381

Conﬁguration dropdown ................................................... 383

Update allsamples ....................................................... 384

Parameter selector ........................................................ 385

Target textbox ............................................................ 386

Fluorophore textbox ...................................................... 387

Notiﬁcationbadge ........................................................ 387

Threshold .................................................................... 388

Overview ................................................................ 388

Logic selector ............................................................ 389

Channel selector ......................................................... 389

Threshold adjustment sliderbar ............................................ 390

Threshold textbox ........................................................ 390

Exclude coincident events check box ....................................... 391

Voltage ...................................................................... 392

Overview ................................................................ 392

Voltage adjustment sliderbar .............................................. 393

Voltage value textbox ..................................................... 393

Advanced™settings ........................................................... 394

Overview ................................................................ 394

Width thresholdsetting .................................................... 395

Area scaling factor(ASF) .................................................. 396

Window extensionsetting ................................................. 397

Notiﬁcation button ........................................................ 397

System instrumentsettings .................................................... 397

Overview ................................................................ 397

Area scaling factor(ASF) .................................................. 399

Window extensionsetting ................................................. 400

Notiﬁcationicon .......................................................... 400

Contents

Attune™ Cytometric Software User Guide 13

■CHAPTER14Heat map setuppanel ........................................... 401

Overview .................................................................... 401

Apply, save, and loadoptions .................................................. 403

Overview ................................................................ 403

Applychanges ........................................................... 403

Set as default split button .................................................. 404

Experiment ................................................................... 404

Overview ................................................................ 404

Experiment dropdown ..................................................... 405

Experiment color button ................................................... 405

Statistic dropdown ........................................................ 406

Gate dropdown .......................................................... 407

Parameter dropdown ...................................................... 407

Displaymode ................................................................. 408

Overview ................................................................ 408

Display modeoptions ..................................................... 408

Sample mode – threshold ...................................................... 410

Overview ................................................................ 410

Transitioncolors .......................................................... 411

Transitionvalues .......................................................... 411

Create additional transitionpoints .......................................... 412

Sample mode – heatmap ...................................................... 413

Overview ................................................................ 413

Transitioncolors .......................................................... 414

Transitionvalues .......................................................... 414

Create additional transitionpoints .......................................... 415

■CHAPTER15Customizepanel ................................................. 416

Overview .................................................................... 416

Customize panelbehavior ................................................. 416

Customize plotoptions ........................................................ 417

Overview ................................................................ 417

Plottypes ............................................................... 417

Customize panel behavior forplots ......................................... 420

General group ............................................................ 423

General group – plot-speciﬁcoptions ....................................... 430

X-axis group ............................................................. 432

Y-axis group ............................................................. 437

Text group (plotsonly) ..................................................... 438

Customize text boxoptions .................................................... 440

Text boxoptions .......................................................... 440

Customize statistics boxoptions ................................................ 441

Statistics boxoptions ..................................................... 441

Contents

14 Attune™ Cytometric Software User Guide

Customize gateoptions ........................................................ 443

Overview ................................................................ 443

Customize panel behavior for gates ......................................... 443

Gate type group .......................................................... 444

Gate type buttons ........................................................ 450

Nameoptions ............................................................ 455

Coordinates group ........................................................ 457

Autogatingoptions ....................................................... 460

Customize experiment (Plate or Tube)options .................................... 462

Overview ................................................................ 462

Customize panel for plate experiments ...................................... 463

Customize panel behavior fortubes ......................................... 464

Plateinformation ......................................................... 464

Experimentinformation .................................................... 466

Groupinformation ........................................................ 467

Sampleinformation ....................................................... 469

Customize Overlayoptions ..................................................... 470

Overview ................................................................ 470

Generaloptions .......................................................... 471

3DOptions .............................................................. 475

Calculations ............................................................. 477

Text ..................................................................... 479

Customize Imageoptions ...................................................... 480

Overview ................................................................ 480

ImageAdjustment ........................................................ 481

MaskSettings ............................................................ 486

SAE object properties ......................................................... 487

Overview ................................................................ 487

■CHAPTER16Image Capture Settingspanel .................................. 488

Overview .................................................................... 488

Settingsoptions .............................................................. 490

Automatically update ...................................................... 490

Set as Experiment Level ................................................... 490

Set asDefault ............................................................ 490

CaptureSettings .............................................................. 491

Image Gate .............................................................. 491

Image Frequency ......................................................... 492

Total Images and Storage Size ............................................. 492

Camerasettings .............................................................. 494

Focus ................................................................... 494

Illumination .............................................................. 495

Contents

Attune™ Cytometric Software User Guide 15

Image Size and PositionSettings ............................................... 496

Size and Position ......................................................... 497

Advanced .................................................................... 499

■CHAPTER17FCS informationpanel ........................................... 500

Overview .................................................................... 500

FCS ﬁleinformation ........................................................... 502

Sample information group ................................................. 502

Parameters group ......................................................... 504

Compensation group ...................................................... 505

System information group ................................................. 506

Data format group ........................................................ 507

Other group .............................................................. 508

■CHAPTER18Filterconﬁguration ............................................... 509

Filter conﬁguration (FC)module ................................................. 509

Overview ................................................................ 509

Launch the FCmodule .................................................... 510

Conﬁguration ribbontab ....................................................... 510

General group ............................................................ 511

Conﬁguration management group .......................................... 511

Edit ﬁltersdialog .......................................................... 516

View group .............................................................. 521

Default ﬁlter labellist ...................................................... 522

Filter conﬁgurationview ........................................................ 523

Overview ................................................................ 523

Default instrumentconﬁgurations ........................................... 524

Conﬁgurationoptions ......................................................... 534

Overview ................................................................ 534

Hardware/Virtual laserconﬁguration ........................................ 535

■CHAPTER19Performance testing ............................................. 536

Overview .................................................................... 536

Performance tests ........................................................ 536

Performance testdata ..................................................... 536

Baseline and performance test (BL/PT)module ................................... 536

Launch the BL/PTmodule ................................................. 537

Set up and run abaseline ...................................................... 538

Baseline setup screen ..................................................... 538

Set up and run abaseline .................................................. 539

Baseline screen .......................................................... 540

Contents

16 Attune™ Cytometric Software User Guide

Baseline results ............................................................... 542

Baseline completion without errors ......................................... 542

Baseline completion with errors ............................................ 542

Run a performance test ........................................................ 543

Performance test setup screen ............................................. 543

Set up and run a performance test .......................................... 545

Performance test screen ................................................... 547

Performance test results ....................................................... 548

Performance test completion without errors .................................. 548

Performance test completion with errors ..................................... 549

Performance test reports .................................................. 549

■CHAPTER20Performance Test reports ....................................... 550

Overview .................................................................... 550

Performance tests ........................................................ 550

Performance testdata ..................................................... 551

Performance test reports .................................................. 551

Performance History Report .................................................... 551

View the performance history report ........................................ 551

Resultsplot .............................................................. 553

Print the performance history report ......................................... 554

Baseline test results ........................................................... 554

View the baseline test results .............................................. 555

Baseline results report .................................................... 556

Baseline resultstable ..................................................... 557

Print the baseline results report ............................................. 558

Current PT results ............................................................. 558

View the current PT results ................................................ 558

Current PT results report .................................................. 559

PT resultstable ........................................................... 561

Print the PT results report .................................................. 562

Levey-Jennings report ......................................................... 562

View the Levey-Jennings report ............................................ 562

Levey-Jenningsplots ..................................................... 564

Print the report ........................................................... 566

Contents

Attune™ Cytometric Software User Guide 17

■CHAPTER21Compensation .................................................... 569

Overview .................................................................... 569

Compensation ........................................................... 569

Compensation controls .................................................... 569

Compensationsetup .......................................................... 570

Initiate compensationsetup ................................................ 570

Compensation setupdialog ................................................ 571

Compensation control source – Tubes ........................................... 571

Measurement ............................................................ 572

Select background ﬂuorescencemode ...................................... 573

Select compensation parameters ........................................... 574

OK and cancel buttons .................................................... 574

Compensation control source –wells ............................................ 575

Measurement ............................................................ 576

Select background ﬂuorescencemode ...................................... 576

Select compensation parameters ........................................... 578

OK and cancel buttons .................................................... 580

Compensationworkspace ..................................................... 580

Overview ................................................................ 580

Customize the compensationworkspace .................................... 580

Plot contextmenu ........................................................ 582

Plot axis contextmenu .................................................... 582

Gate contextmenu ....................................................... 584

Compensation workspace for histogramview ................................ 584

Gatingplot ............................................................... 586

Histogram compensation plot without negative gate .......................... 587

Histogram compensation plot with negative gate ............................. 588

Unstained controlworkspace .............................................. 589

Matrixdialog ................................................................. 589

Overview ................................................................ 589

Matrix dialogtable ........................................................ 590

OK, reset, and cancel buttons .............................................. 591

On-Plot compensationadjustment .............................................. 592

Overview ................................................................ 592

Manual on-plot compensationadjustment ................................... 593

Compensation acquisitionworkﬂow ............................................. 593

Overview ................................................................ 593

Compensation acquisition fromtubes ....................................... 593

Compensation acquisition fromwells ....................................... 594

Compensation of instrumentdata .......................................... 594

Contents

18 Attune™ Cytometric Software User Guide

■CHAPTER22New Experiment and Groupdialogs ........................... 596

New Experimentdialog ........................................................ 596

Open the New Experimentdialog ........................................... 596

Create a Tube-only experiment ............................................. 597

Create a plate experiment ................................................. 599

New experiment from templatedialog ........................................... 603

Launch the new experiment from templatedialog ............................. 604

Select template .......................................................... 605

Create experiment ........................................................ 608

New groupdialog ............................................................. 609

Launch the new groupdialog .............................................. 609

Create a group ........................................................... 610

■CHAPTER23Process Imagesdialog .......................................... 612

Overview .................................................................... 612

Open the Process Imagesdialog ................................................ 613

SelectSamples ............................................................... 614

Select Population ............................................................. 616

Image ProcessingOptions ..................................................... 618

Image processingqueue ....................................................... 620

Completion of image processing ................................................ 622

Reprocessimages ............................................................ 624

■CHAPTER24Attune™ Image Processing Dashboard ........................ 626

Attune™ Image Processing Dashboard ........................................... 626

View image processing queue, status, and progress .......................... 628

Reprioritize the image processing queue .................................... 628

Cancel image processing requests .......................................... 628

Pause or resume image processing ......................................... 628

■CHAPTER25Optionsdialogs .................................................. 629

Overview .................................................................... 629

General ...................................................................... 631

Overview ................................................................ 631

New ExperimentDefaults .................................................. 632

NamingOptions .......................................................... 634

Colors andThemes ........................................................... 637

Overview ................................................................ 637

Colors and Themesoptions ................................................ 637

Contents

Attune™ Cytometric Software User Guide 19

Fonts and Styles .............................................................. 639

Overview ................................................................ 639

Plot Title and Axis Label Style .............................................. 640

Text Box Style ............................................................ 641

Previews ................................................................ 642

PlotOptions .................................................................. 643

Overview ................................................................ 643

UngatedColor ........................................................... 643

HistogramOptions ........................................................ 644

Dot PlotOptions .......................................................... 644

Density PlotOptions ...................................................... 645

Precedence Density PlotOptions ........................................... 645

GateOptions ................................................................. 646

Overview ................................................................ 646

Autogating ............................................................... 647

Gate Style ............................................................... 649

Gate Label Style .......................................................... 649

Gate LabelNaming ....................................................... 650

ExportOptions ............................................................... 652

Overview ................................................................ 652

Plot ExportOptions ....................................................... 653

Plot export preview ....................................................... 653

Default Plot Image Format ................................................. 653

Export Size (scaled towidth) ............................................... 654

StatsOptions ................................................................. 655

Overview ................................................................ 655

Header .................................................................. 656

Statistics ................................................................ 656

Stats Box Style ........................................................... 657

DecimalSettings ......................................................... 657

KeywordOptions ............................................................. 659

Overview ................................................................ 659

KeywordManagement .................................................... 659

ImageOptions ................................................................ 663

Image BackgatingColor ................................................... 663

MaskOptions ............................................................ 664

Image ProcessingModels ................................................. 664

PlateOptions ................................................................. 665

Administrator ................................................................. 667

Overview ................................................................ 667

Data ManagementOptions ................................................ 668

OtherSettings ............................................................ 670

SAEConﬁguration ........................................................ 671

Rules for enabling the SAEmode ........................................... 673

Enable the SAEmode ..................................................... 673

Contents

20 Attune™ Cytometric Software User Guide

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Thermo Fisher Scientific Attune Cytometric Software User guide

Thermo Fisher Scientific Attune Cytometric Software User guide

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