FCS Express 5 Manual

Opera Bug

Contents | Index

• Welcome to FCS Express 5
  • About the Manual
  • System Requirements
  • Purchasing and Installing FCS Express
  • New Features in FCS Express Version 5
    • Speed Improvements
    • General Usability Improvements
    • Data Loading and Data List Features
    • Plot Types and Enhancements
    • Batch Processing Features
    • Gate, Quadrant, and Marker Features
    • Statistics, Tokens and Custom Token Features
    • Compensation and Transformation Features
    • Audit Trails, Logging, and Security
  • Upgrading From Version 4
• Learning How to Use FCS Express
  • Recorded Webinars and Tutorial Videos
  • Written Tutorials
  • Integrated Help System
  • Comprehensive Manual
  • Online Discussion Forum
  • Email Support
• A Quick Tour of FCS Express
  • Getting Started with FCS Express
  • Startup Screen
  • A Quick Walk through the Ribbon
    • The File Tab
    • The Quick Access Toolbar
    • The Home Tab
    • The Insert Tab
    • The Gating Tab
    • The Batch Tab
    • The Format Tab
    • The Text Tab
    • The Data Tab
    • The Multicycle Tab
    • The View Tab
    • Customizing the Ribbon
• Working with Layouts
  • Introduction to the Layout
    • Creating a New Layout
    • Saving a Layout
    • Opening a Previously Created Layout
    • Closing Layouts
    • Working with Pages
    • Printing Pages from a Layout
    • Exporting a Page as a Picture from a Layout
    • Exporting a Layout as a PowerPoint® Presentation
    • Exporting a Layout as a PDF File
    • Navigating through the Layout
    • Viewing Pages
    • Zooming the Layout
    • Auto Recovery Files
    • Working with Multiple Layouts
    • Layout and Layout Performance Options
  • Introduction to Docking
    • Opening a Dockable Window
    • Docking a Window
    • Pinning a Docked Window
    • Undocking a Window
    • Closing a Dockable Window
  • Navigators
    • Layout Navigator
    • Data Navigator
    • Gate Navigator
  • Layout Page Features
    • Inserting Items onto a Page
    • Selecting Items on a Page
    • Grouping Items on a Page
    • Cutting, Copying, Deleting, Duplicating, and Pasting Items on Pages
    • Moving Objects
    • Resizing Objects
    • Aligning Objects
    • Ordering Objects
    • Undoing and Redoing Changes
    • Page Layout Using Predefined Placeholders
  • Using the Master Page
    • Changing Background Color and Design
  • FCS Express Short Cut Keys
• Working with Pictures
  • Inserting Pictures
  • Formatting Inserted Pictures
• Working with Text Boxes
  • Inserting Text Boxes onto a Page
  • Quadrant Label Text Boxes
  • Entering and Formatting Text in a Text Box
    • Inserting Tables
    • Formatting Tables
      • Table Properties
  • Resizing Text Boxes
  • Adding a Text Box to a Plot
  • Formatting Text Box Features
  • Adding Tokens to Text Boxes
• Displaying Plots
  • Data Display Plot Types
  • Inserting Plots
  • The Current Data File
  • Changing Data Files
• Formatting Objects
  • Overview
  • Customizing Default Options
    • General Options
    • Plot Options
      • Axis Options
      • Background Options
      • Legend Options
      • 1D Plot Options
      • 2D Plot Options
      • Text Boxes Selection Options
      • DNA Options
    • Statistic Options
      • 1D Plot Statistics
      • 2D Plot Statistics
      • DNA Cycle Statistics
      • DNA Model Statistics
      • DNA Experiment Statistics
      • Proliferation Fit Statistics
      • Proliferation Population Statistics
    • Startup Options
    • Gate Options
    • Files/Directories
    • Data List
    • Dialogs Options
      • Keyword Dialog
      • Dont Show Again
    • Save Preferences
    • Security Preferences
    • Text Box Preferences
    • User Information
    • Advanced Publishing Preferences
    • Data Saving
    • Data Loading
      • FCS File Options
      • Image XPress Velos Options
      • CellProfiler Options
      • ICE Format Options
      • PerkinElmer Acapella Options
      • Building Blocks Options
      • MDC Store Options
      • Life Technologies Tali Options
      • Nexcelom Options
      • ImageJ Options
      • IDEAS Options
  • Formatting Options Shared by All Objects
    • General
    • Background
    • Border
    • Size
  • Formatting Features Shared by All Plots
    • Specific Options
    • Title
    • Legend
    • Axes
    • 3D Display Options
    • Magnifying a Plot
    • Changing Plot Type
    • Plot Names
  • Formatting Single Parameter Histograms
    • Overlays
    • Histogram Markers
    • Histogram Specific Options
  • Formatting 2D Plots
    • Overlays
    • Quadrants
    • Color Levels
    • Gate Display
    • Specific Options
  • Changing the Parameter on Plot Axes Using Keyboard Shortcuts
  • Formatting Data Grids and Custom Data Grids
    • General
    • Gate Display
    • Parameters to Display
    • Image Options
• Analysis of FCS Data
  • Using Gates
    • Live Updating Gates
    • Creating Gates
    • Using Boolean Logic to Create Combination Gates
    • Adding a Combination Gate Matrix
    • Moving Gates
    • Resizing Gates
    • Deleting Gates
    • Hiding Gates
    • Using Snapshots with Gates
    • Gate View Object
    • Saving and Loading Gates
    • Gates and the Clipboard
    • Linking Gates
    • Applying Gates to Plots
    • Hierarchical Gating
  • Using Markers
    • Creating Markers
    • Moving Markers
    • Resizing Markers
    • Deleting Markers
    • Using Markers and the Clipboard
    • Linking Markers to Gates
  • Using Quadrants
    • Showing Quadrants
    • Moving Quadrants
    • Hiding Quadrants
    • Linking Quadrants to Quadrants
    • Creating Gates from Quadrants
    • Linking Quadrants to Gates
    • Using Quadrants and the Clipboard
  • Snapshots
    • Creating and Applying Snapshots
    • Iteration Snapshots
  • Statistics
    • Histogram Statistics
    • 2D Plot Statistics
    • Using Statistics and the Clipboard
    • Formatting Statistics
    • Percent Gated - Parent and Percent Gated - Grandparent
  • Axis Scalings
    • Data Display
    • Gating and Axis Scalings
    • Quadrants and Axis Scaling
• Creating and Using Parameter Label Sets
• Custom Data
  • Adding Custom Data
  • Working with Custom Data
    • Adding Rows or Columns
    • Deleting Rows or Columns
    • Reordering Columns
  • Renaming Custom Data
  • Deleting Custom Data
  • Graphing Custom Data
    • Pie Charts
      • Inserting Pie Charts
        • Populating Pie Charts by Drag and Drop
        • Populating Pie Charts from Custom Data Grids
      • Formatting Pie Charts
    • Bar Plots
      • Inserting Bar Plots
        • Populating Bar Plots by Drag-and-Drop
        • Populating Bar Plots from Custom Data Grids
      • Formatting Bar Plots
    • Scatter With Regression
      • Scatter With Regression Plots
      • Scatter with Regression Tokens
    • Scatter Plots
      • Inserting Scatter Plots
        • Populating Scatter Plots from Custom Data Grids
      • Formatting Scatter Plots
      • Regression Analysis (Manually fitting data)
        • Manual Regression Analysis Example
        • Available Equations
• Using Parameter Math
  • Performing Parameter Math
  • Creating a Parameter Math Sequence
  • Running a Parameter Math Sequence
• The Concentration Calculator
  • Calculating a Single Concentration
  • Calculating Concentrations on the Statistics Page
• The Histogram Subtraction Tool
• The Channel Calibration Tool
  • Creating a New Channel Calibration
  • Using a Channel Calibration
  • The Channel Calibration Window
• The Compensation Tool
  • Software Compensation Caveats
  • Setting Up Compensation Definitions
  • Editing a Compensation Definition
  • Automatically Calculating Compensation Definitions
  • Applying Compensation Definitions
  • Selecting the Default Compensation
  • Adjusting Compensation Definitions from a 2D Plot
  • Working with Individual Compensation Files
  • Saving Compensation Definitions
  • Loading Compensation Definitions
  • Principal Component Analysis 
    • Defining a PCA Transformation
    • Applying a PCA Transformation
• Working with FCS Data Files
  • Viewing and Changing FCS File Headers
  • Extra Keywords
  • Keyword Anonymizer
  • Exporting FCS File Data
    • Exporting FCS File Data from a Single File
    • Exporting FCS File Data from Multiple Files: Batch Export
• Data Grids
  • Formatting Data Grids
  • Applying Gates to a Data Grid
  • Backgating on a Data Grid
  • Creating Cell Number Gates on a Data Grid
  • Image Galleries
• Using Tokens
  • Inserting Tokens
  • Common Token Properties
    • Display Text Token Property
    • Data Source Token Property
  • Token Descriptions and Editing Tokens
    • Editing Statistic Tokens
      • 2D Plot Statistic Token Options
      • Histogram Statistic Token Options
    • Editing Keyword Tokens
    • Layout Tokens
      • Inserting a Page Layout Token
    • Gate Tokens
    • Signature Tokens
    • Compensation Tokens
    • Batch Processing Tokens
    • System Tokens
    • Plot Tokens
    • Data Parameter Tokens
  • Custom Tokens
    • Creating Custom Tokens
    • Custom Token Example 1: Mathematical Calculation
    • Custom Token Example 2: Mathematical Calculation with a Token
    • Custom Token Example 3: Appending Text
    • Custom Token Example 4: Conditional Statements
    • Custom Token Example 5: Hiding Signature Tokens
    • More Complex Custom Token Examples
    • Inserting Functions into Formulas
    • Editing Custom Tokens
    • Custom Token Formatting
    • Using Boolean Values in Custom Tokens
    • Using Array Formulas in Custom Tokens
    • Deleting Custom Tokens
    • Custom Token Display Types
      • Edit Box Custom Tokens
      • Check Box Custom Tokens
      • Dropdown Custom Tokens
  • Custom Token Formula Reference
• Batch Processing
  • Working with the Data List
    • Data List Actions
    • Adding Files to the Data List
    • Sorting in the Data List
    • Using the Data List to Change the Data Set in a Plot or Token
      • Next/Previous
      • Dragging and Dropping
      • The Change File Button
      • Defer Layout Changes
  • Adding Batch Processes
    • Batch Processing Actions
      • Print
      • Save Layout
      • Save To PowerPoint
      • Save To PDF
      • Save As Picture
      • Folders (Action Containers)
    • Batch Processing Reports
      • Working with Reports
      • Creating Templates for Reports
      • Adding Items to Reports
        • Configuring a Report Item's Report Specific Property
      • Adding Pictures to a Report
      • Reordering and Copying Items in Reports
  • Batch Processing Options
  • Running the Batch Process
  • Rerunning and Reviewing the Batch Process
    • Using Flags
    • Snapshots and Batch Iteration Navigation
• Using Panels
  • Working with Panels
• Using Templates
• Importing External Documents and File Types
  • BD FACSDiva Files
    • How to Import FACSDiva Experiment Files
    • Tips for Importing FACSDiva Experiments
  • BD Accuri CFlow and C6 Files
    • How to Import CFlow Experiment Files
    • Tips for Importing CFlow Experiments
  • Comma Separated Value / Delimited (.csv) Files
• DNA Analysis
  • Multicycle
  • Inserting a DNA Histogram
  • Formatting a DNA Histogram
    • General Options
    • Cycle Options
    • Background Options
    • DNA Position Markers
  • Setting Default DNA Options
  • The Multicycle Tab
  • DNA Statistics
  • DNA-Specific Tokens
  • DNA Cycle and Model Summary Reference
• Proliferation Analysis
  • Obtaining the Proliferation Add-on
  • Inserting a Proliferation Histogram
  • Formatting a Proliferation Histogram
    • The Fit Parameters Option
    • Proliferation Position Markers
  • Proliferation Statistics
  • Proliferation-Specific Tokens
• Kinetics Analysis
  • Inserting a Kinetics Plot
  • Formatting a Kinetics Plot
  • Kinetics Statistics
  • Kinetics-Specific Tokens
• Heat Maps and Picture Plots
  • Working with Heat Maps
    • Setting the Parameter to Display
    • Choosing a Color Scheme
    • Well Gates
  • Working with Picture Plots
• Collaboration Tool
  • Opening, Joining, and Reserving a Session
  • Conducting a Meeting
• Security
  • User-Based Security
  • Layout-Based Security
  • Working with User-Based Security
    • Creating a User
    • Editing a User
    • Deleting a User
    • Editing Security Configurations
      • Managing Password Configurations
      • Mail Notifications
      • SMTP Server
  • Working with Security Groups
    • Creating a User Security Group
    • Editing a Security Group
    • Duplicating a Security Group
    • Deleting a Security Group
    • Loading and Saving Security Group and Layout Status
  • Working with Layout Security Groups
  • Managing the Databases
  • Available Security Group Permissions
  • Security Database Options
  • Configuring MS SQL Server to host Security Databases
  • Backing up the Databases
  • Preparing for Database Updates
  • Security Reports
    • Report All Events
    • Report Failed Logins
    • Report Full Sessions
    • Report Remote Logouts
    • Arranging, Grouping, and Filtering Reports
      • Arranging Columns in Reports
      • Grouping and Filtering Reports
      • Filtering on a Date Range
    • Exporting Reports
  • Layout and Data Security
• Electronic Signatures
  • Maintaining Signatures
    • Adding Signatures
    • Modifying Signatures
    • Deleting Signatures
  • Signing Layouts
  • Unsigning Layouts
  • Displaying Signature Information
    • Signature Status
• Layout History
• Publishing Layouts
  • Publishing a Layout to the De Novo Software Publishing Site
  • Advanced Publishing
  • Default Publishing Options
  • Managing Your Published Layouts
  • Sharing Published Layouts with Others
  • FCS Express Reader
    • Obtaining the FCS Express Reader
    • FCS Express Reader Limitations
    • Upgrading from FCS Reader to FCS Express
  • Extra Hosting Plans
• Tutorials
  • Using Objects
    • Inserting an Object
    • Selecting and Deselecting Objects
    • Resizing an Object
    • Moving an Object
    • Deleting an Object
    • Undoing and Redoing Changes
    • Duplicating Objects
    • Selecting Multiple Objects
    • Copying Objects
    • Pasting Objects
    • Grouping Objects
    • Aligning Objects
    • Ordering Objects
  • Inserting Plots
    • Inserting a 2D Plot
    • Inserting a Histogram
    • Inserting from the Data Tab with the Open Command
    • Always Display Selection Dialog
    • Inserting Plots from Windows Explorer
  • Formatting Plots
    • Formatting Plots Using the Pop-up Menu
      • Formatting Multiple Plots
    • Formatting Plot Titles
    • Formatting Plot Axes
    • Formatting Plot Background
    • Formatting the Legend
    • Changing Histogram Overlays
    • Formatting 3D Options
  • Gating
    • Creating Gates
    • Creating a 1D Gate on a 2D Plot
    • Creating a Gate from a Marker
    • Creating a Gate from a Quadrant
    • Creating Combination Gates
    • Moving Gates
    • Resizing Gates
    • Deleting Gates
    • Applying Gates
  • Text Boxes and Tokens
    • Inserting Text Boxes
    • Formatting Text in a Text Box
    • Formatting Text Box Properties
    • Inserting and Modifying a Table
    • Inserting and Modifying a Token
    • Creating a Custom Token
    • Using Custom Token Display Types
      • Creating an Edit Box Custom Token
      • Creating a Check Box Custom Token
      • Creating a Dropdown list Custom Token
  • Quadrants
    • Rectangular and Floating Quadrants
    • Percentile Quadrants
  • Quadrant/Marker to Gate Linking
    • Quadrant to Gate Linking
    • Marker to Gate Linking
  • Compensation
    • Manual Compensation
    • Automatic Compensation
      • Automatic Compensation- Optional Steps 3 and 4
      • Automatic Compensation and Batch Processing
    • Compensation Digitization Error
  • Snapshots
    • Snapshots Window
    • Iteration Snapshots
    • Batch Processing Snapshots
  • Batch Processing
    • Exporting Plots to PowerPoint
    • Excel Report (Cell Mode)
    • Excel Report (Column Mode)
    • Exporting to LabKey
    • Snapshots
  • Creating and Using Panels
    • Setting Up the Panel
    • Creating the Layout
    • Using the Panel
    • Saving and Loading Panels
  • Docking
    • Features of a Docked Window
    • Docking Features (Multiple Windows)
    • Undocking a Window
  • Data Navigator
    • Opening and Docking
    • Data Navigator Features
  • Gate Navigator
    • Opening and Docking
    • Gate Navigator Features
  • Layout Navigator
    • Opening and Docking
    • Layout Navigator Features
  • Creating and Using Custom Data
    • Loading a Layout for Custom Data
    • Inserting a Data Grid
    • Creating Custom Data
    • Create Custom Tokens
    • Create Token Classifiers
  • Working with Pie, Bar, and Scatter Plots
    • Creating Bar and Scatter Plots and Pie Charts
      • Creating Bar Plots
      • Creating Pie Charts
      • Creating Scatter Plots
    • Formatting Bar and Scatter Plots and Pie Charts
      • Adding Error Bars
      • Adding Highlighting or Exploding
      • Displaying Additional Datasets
        • Overlays on Bar and Scatter Plots
        • Ring on Pie Chart
  • Titration
    • Define Custom Tokens
    • Create a Custom Data Table
    • Insert a Scatter with Regression Plot
  • High Content Flow
    • Load, Insert, and Format Heat Maps
    • Analyzing Data in Heat Maps
    • Using Batch Analysis
    • Using the Z-Prime Function
  • DNA Analysis
    • Autofit Selection (1 Cycle Analysis)
    • Expanded Analysis with Autofit
    • Formatting a DNA Histogram
    • Analysis of 3 Cycle Data
  • Proliferation
    • Inserting Proliferation Plots
    • Fitting Proliferating Cells
    • Formatting a Proliferation Histogram
    • Batch Processing Proliferation Data
  • Kinetics
    • Using Parameter Math
    • Applying Gating and Statistics
    • Plotting Values
    • Overlay and Format Kinetics Plots
    • Format to Change Resolution
  • Cell Concentration
    • Setting up the Bead Gates
    • Concentration Calculator (Beads)
    • Concentration Calculator (Time/Flow Rate)
    • Showing the Concentration in a Statistics Window
    • Showing the Concentration as a Token
  • Channel Calibration
    • Setting Bead Gates and Markers
    • Channel Calibration Tool Setup
    • Channel Calibration Demonstration
    • Saving/Loading Channel Calibrations
    • Channel Calibration Defaults
  • CellProfiler Export
    • CellProfiler for FCS Express Knowledge Base
    • Exporting 96 Well Format Images
    • Import and Analyze 96 Well Images
    • Exporting Single Images
    • Importing Single Image Data
    • Exporting Numeric Data (96 Well)
    • Importing Numeric Data (96 Well)
    • Exporting Single Image Numeric Data
    • Import Single Image Numeric Data
    • Selecting Individual Parameters for CellProfiler Export
    • Exporting Tiled Images From CellProfiler
    • Importing Tiled Images
    • Exporting Plate Based Data That Contains Multiple Fields Per Well
    • Importing Plate Based Multiple Field Location Imaging Data
  • ImageJ Export
    • ImageJ Macros Overview
      • DNS Macro Example Overview
      • DNS Analysis Creator Macro Overview
    • Creating a .ijx Analysis Configuration File
      • Macro-enabled Excel method for creating ijx file
      • Creating an analysis configuration file using the DNS Analysis Creator Macro
        • Editing an .IJX file in ImageJ
        • Editing an .IJX file in Excel
    • Analyzing and Exporting Individual Image Results with ImageJ
    • Analyzing and Exporting Multi Channel Image Results with an .ijx file
    • ImageJ for FCS Express Knowledge Base
  • Exporting from Image Xpress Velos
    • Export an Image Xpress Velos Experiment
    • Import Image Xpress Velos Data with Images
    • Export in Numeric Form (Data Only)
    • Import Numeric Form Data
  • Picture Plots
    • Insert and Format Picture Plots
    • Gating with Picture Plots
    • Using Data Grids for Analysis
  • Regression Analysis
    • Complete a Custom Data Grid and Insert a Scatter with Regression Plot
    • Working with Regression Tokens and Fit Equations
    • Create a Regression Overlay
    • Apply Regression to an FCS File
    • Save a Regression
  • Introduction to FCS Express 5 Image Cytometry
    • Getting Started with Image Cytometry
    • Using The High Content Module with Image Data
    • Batch Processing and Reporting for Image Data
  • Immunophenotyping
    • Building your layout
    • Adding statistics to your layout
    • Batch processing your analysis
  • Changing Common Preferences
    • Displaying Filenames Without Path in Data List
    • Changing Axis Labels
    • Creating Gates Hierarchically and Adding Statistics to Gate Text Boxes

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