FCS Express 7 Manual

Welcome to FCS Express
- About the Manual
- System Requirements
  - Supported File Formats
- Purchasing and Installing FCS Express
- New Features in FCS Express 7
- Upgrading From Version 6
Learning How to Use FCS Express
- Recorded Webinars and Tutorial Videos
- Written Tutorials
- Integrated Help System
- Comprehensive Manual
- Email Support
A Quick Tour of FCS Express
- Getting Started with FCS Express
- Startup Screen
- A Quick Walk through the Ribbon
Layouts
- Introduction to the Layout
- Introduction to Docking
- Navigators
- Layout Page Features
- Using the Master Page
  - Changing Background Color and Design
- Using Templates
Plots and Other Objects
- Plot Types and Formatting
- Pictures
  - Inserting Pictures
  - Formatting Inserted Pictures
- Text Boxes
- Gate View
- Data Grids
- Spreadsheets and Charts
- Multi Plot
- Formatting Options
Loading and Organizing Data Sets
- Working with the Data List
- Panels
  - Working with Panels
Gating
- Gates
- Quadrants
- Markers
Batch Processing
- Adding Batch Processes
  - Batch Processing Actions
  - Batch Processing Reports
- Batch Processing Options
- Running the Batch Process
- Rerunning and Reviewing the Batch Process
  - Using Flags
  - Snapshots and Batch Iteration Navigation
Tools
- Compensation and Spectral Unmixing
- Transformations
- Parameter Label
- Snapshots
  - Creating and Applying Snapshots
  - Iteration Snapshots
- Channel Calibration
- Concentration Calculator
  - Calculating a Single Concentration
  - Calculating Concentrations on the Statistics Page
Quality
- Standard Operating Procedures
- Permission Rules
Statistics
- Histogram Statistics
- 2D Plot Statistics
- Using Statistics and the Clipboard
- Formatting Statistics
- Percent Gated - Parent and Percent Gated - Grandparent
- Spreadsheet Statistics from Data Files
Tokens
- Inserting Tokens
- Common Token Properties
  - Display Text Token Property
  - Data Source Token Property
- Token Descriptions and Editing Tokens
- Custom Tokens
- Custom Token Formula Reference
Publishing Layout Tools
- Publishing a Layout
- Advanced Publishing
- Default Publishing Options
- Sharing Published Layouts with Others
- FCS Express Reader
Working with FCS Data Files
- Viewing and Changing FCS File Headers
- Extra Keywords
- Keyword Anonymizer
- Merging / Concatenating Multiple Files
  - Adding Merged Files to the Data List
- Exporting FCS File Data
  - Exporting FCS File Data from a Single File
  - Exporting FCS File Data from Multiple Files: Batch Export / Merging/ Concatenation
    - Merging / Concatenating FCS Files Via Batch Export - Use Case Example
Working with Other 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
- Working with Amnis .DAF files
Electronic Signatures
- Maintaining Signatures
- Signing Layouts
- Unsigning Layouts
- Displaying Signature Information
  - Signature Status
Layout History
Security
- Security Package for Network Licenses
- Internet Dongle and Site License Security and User Management
  - Internet Dongle and Site License Access and Security
  - User Administration
- Editing Security Configurations
- Security Reports
- Layout and Data Security
User Default Options
- General Options
- Plot Options
- Statistic Options
- Startup Options
- Gate Options
- Files/Directories
- Data List
- Dialogs Options
- Save Options
- Security Options
- Text Boxes Options
- User Information
- Performance
- Customer Experience Program
- Advanced Publishing Preferences
- Data Saving
- Data Loading
FCS Express Keyboard Shortcuts
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
  - Inserting from the Data List
  - Inserting from Windows Explorer
  - Always Display Selection Dialog
- Formatting Plots
  - Formatting Plots Using the Pop-up Menu
  - Formatting Multiple Plots
  - Formatting Plot Titles
  - Formatting Plot Axes
  - Formatting Plot Background
  - Formatting the Legend
  - Formatting 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
  - Data Specific 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
- 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 4 and 5
    - Automatic Compensation and Batch Processing
  - Compensation Digitization Error
  - NxN Plots
- 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
- 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
- Layout Navigator
  - Opening and Docking
  - Layout Navigator Features
- Data Navigator
  - Opening and Docking
  - Data Navigator Features
- Gate Navigator
  - Opening and Docking
  - Gate Navigator Features
- HLA Cross Matching - Spreadsheets Use Case 1
  - Loading a layout for analysis
  - Creating a Spreadsheet for analysis
  - Populating a Spreadsheet with data
  - Working with Custom Tokens and Formula References in spreadsheets
  - Create Token Classifiers
  - Using Conditional Formatting to Classify Data
- Antibody Titration - Spreadsheets Use Case 2
  - Creating an analysis Spreadsheet
  - Creating a regression curve from a Spreadsheet
  - Interpolating values from the regression
- Calibration via Regression Analysis - Spreadsheets Use Case 3
  - Complete a Spreadsheet and Insert a Scatter with Regression Plot
  - Working with Regression Tokens and Fit Equations
  - Apply Regression to an FCS File
  - Save a Regression
- Working with Bar, Pie, and Scatter Charts - Spreadsheets Use Case 4
  - Creating Bar and Scatter Plots and Pie Charts
  - Formatting Bar and Scatter Plots and Pie Charts
- High Content Flow
  - Load, Insert, and Format Plate 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 Multicycle DNA Plot
  - Analysis of 3 Cycle Data
- Proliferation
  - Inserting Proliferation Plots
  - Formatting a Proliferation Histogram
    - Fitting Proliferating Cells
  - 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)
  - Concentration Calculator ($VOL keyword)
  - 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
  - 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
  - CellProfiler for FCS Express Knowledge Base
- 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
    - Import Numeric Form Data
  - Export in Numeric Form (Data Only)
- Picture Plots
  - Insert and Format Picture Plots
  - Gating with Picture Plots
  - Using Data Grids for Analysis
- Introduction to FCS Express 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
- Cluster Analysis
  - Defining a k-means clustering
  - Applying a k-means clustering
  - Working with k-means using 1D-2D plots
  - Working with k-means parameters
- Changing Common Preferences
  - Displaying Filenames Without Path in Data List
  - Changing Axis Labels
  - Creating Gates Hierarchically and Adding Statistics to Gate Text Boxes
- Cytek Aurora Spectral Data
  - Loading Data and Creating Plots, Gates, and Statistics
  - Working with Spectrum Plots