WinList User Guide Copyright 2021 Verity Software House All rights reserved. Updated 4 August 2021 This guide is intended for WinList 10.0 and minor version updates. Table of Contents WinList™ 10 User Guide ..................................................................................................... 1 License and Warranty ......................................................................................................... 3 Latest Versions .................................................................................................................. 5 What's new? ...................................................................................................................... 7 System Requirements ......................................................................................................... 9 Installing and Running WinList ...........................................................................................11 Registering Your Software .................................................................................................13 Contacting Verity Software House.......................................................................................17 Tutorials ...........................................................................................................................19 WinList Basics ...................................................................................................................19 Cascade Gating and Boolean Gates .....................................................................................29 Using Interactive N-Color Compensation ™ .........................................................................41 Compensation Review Mode ..............................................................................................51 Creating Reports ...............................................................................................................60 Using Overlays ..................................................................................................................73 Using FCOM to enumerate phenotypes ...............................................................................80 Population Identification with Cen-se' and t-SNE ..................................................................88 Sticky Regions and Magic Contours ................................................................................... 105 Kinetic Analysis with Excel ............................................................................................... 112 Enhanced Proliferation Analysis ........................................................................................ 124 Remote connection to ModFit LT ...................................................................................... 137 Using MultiGraphs ........................................................................................................... 142 Reference ....................................................................................................................... 147 i Table of Contents Main Window .................................................................................................................. 147 Ribbon Bar ..................................................................................................................... 149 Toolbar .......................................................................................................................... 155 Status Bar ...................................................................................................................... 157 Open Protocol ................................................................................................................. 158 Open Bundle................................................................................................................... 159 Save Protocol ................................................................................................................. 160 Save Protocol As... .......................................................................................................... 161 Save Bundle ................................................................................................................... 163 Data Source Windows ..................................................................................................... 164 Data Source Toolbar........................................................................................................ 166 Data Source Context Menu .............................................................................................. 168 Open FCS File ................................................................................................................. 171 Open Dialog Box ............................................................................................................. 172 Choose Dataset............................................................................................................... 173 Next FCS File .................................................................................................................. 174 Previous FCS File ............................................................................................................ 175 Duplicate Data Source ..................................................................................................... 176 Edit Data Source ............................................................................................................. 177 Add Parameters .............................................................................................................. 180 Edit Calculated Parameter ................................................................................................ 182 FCOM Background and Usage .......................................................................................... 186 Edit Transformations ....................................................................................................... 188 Names and Resolutions ................................................................................................... 191 ii WinList User Guide Quantitation ................................................................................................................... 193 Using the Quantitation Spreadsheet .................................................................................. 196 Compensation Toolbox .................................................................................................... 201 Compensation Toolbox dialog........................................................................................... 202 Compensation: Setup Tab ................................................................................................ 204 Compensation: AutoComp Tab ......................................................................................... 207 Compensation: Transforms Tab ........................................................................................ 209 Compensation: Miscellaneous Tab .................................................................................... 211 Compensation Trace Lines ............................................................................................... 214 Compensation Notice dialog ............................................................................................. 215 Edit Properties for Compensation ...................................................................................... 217 Advice on Compensation dialog ........................................................................................ 220 Normalization Targets ..................................................................................................... 221 Histogram Windows ........................................................................................................ 224 Histogram Toolbar .......................................................................................................... 226 Histogram Context Menu ................................................................................................. 229 Create Histogram ............................................................................................................ 233 Create Multiple Histograms .............................................................................................. 235 Edit Histogram ................................................................................................................ 238 Edit Remote ................................................................................................................... 240 Edit 1P Graphics.............................................................................................................. 244 Edit 2P Graphics.............................................................................................................. 247 Edit 3P Graphics.............................................................................................................. 253 Subtract Histogram ......................................................................................................... 257 iii Table of Contents Information Windows ...................................................................................................... 262 Index Analysis ................................................................................................................ 263 Edit Index Analysis .........................................................................................................