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Thermo Fisher Scientific Attune Cytometric Software User guide

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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.
©2015-2023 Thermo Fisher Scientific Inc. All rights reserved.
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
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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
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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
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20 Attune™ Cytometric Software User Guide
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