FCS Express 6 Manual

Welcome to FCS Express 6
- About the Manual
- System Requirements
  - Supported File Formats
- Purchasing and Installing FCS Express
- New Features in FCS Express 6
- Upgrading From Version 5
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
Working with Layouts
- Introduction to the Layout
- Introduction to Docking
- Navigators
- Layout Page Features
- 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
- Resizing Text Boxes
- Adding a Text Box to a Plot
- Formatting Text Box Features
- Adding Tokens to Text Boxes
- Exporting a Text Box to Excel
Working with Plots
- Data Display Plot Types
- Inserting Plots
- The Current Data File
- Changing Data Files
Formatting Objects
- Overview
- Customizing Default Options
- Formatting Options Shared by All Objects
  - General
  - Background
  - Border
  - Size
  - Authorizations
- Formatting Features Shared by All Plots
- Formatting Single Parameter Histograms
- Formatting 1D Spectrum Plots
  - Overlays
  - Spectrum Options
- Formatting 2D Plots
- Formatting Heat Maps
- Changing the Parameter on Plot Axes Using Keyboard Shortcuts
- Formatting Data Grids and Custom Data Grids
Analysis of Flow and Image Cytometry Data Files
- Using Gates
- Using Markers
- Using Quadrants
- Snapshots
  - Creating and Applying Snapshots
  - Iteration Snapshots
- Statistics
- Axis Scalings
Creating and Using Parameter Label Sets
Spreadsheets
- Creating a Spreadsheet
- Working with Spreadsheets
- Analyzing Files from the Data List with Spreadsheets
- Spreadsheet Formula Definitions
- Renaming Spreadsheets
- Deleting Spreadsheets
- Exporting Data in Spreadsheets
- Graphing Data with Pie Charts, Bar Plots, and Scatter with Regression Plots
The Concentration Calculator
- Calculating a Single Concentration
- Calculating Concentrations on the Statistics Page
The Histogram Subtraction Tool
Publishing Layout Tools
- 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
- Extra Hosting Plans
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
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 Data Grids
- Formatting Data Grids to Display Only Images
- Applying Gates to a Data Grid
- Backgating on a Data Grid
- Creating Cell Number Gates on a Data Grid
- Using Data Grids as Image Galleries
- Viewing Compensated and Transformed Values in Data Grids
Using 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
Batch Processing
- Working with the Data List
- 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
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
- 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
Spectrum Analysis
- Inserting a Spectrum Plot
- Formatting a Spectrum Plot
- Gating and Backgating on Spectrum Plots
- Overlaying Spectrum Plots
Transformations
- Parameter Math
  - Defining Parameter Math
  - Applying Parameter Math
- Principal Component Analysis
  - Defining a PCA Transformation
  - Applying a PCA Transformation
- K means (Cluster Analysis)
- R Integration
- tSNE (viSNE)
- SPADE
- Sampling Options
  - Target Density Downsampling
  - Weighted Density Sampling
Working with Amnis .DAF files
Picture Plots
- Working with Picture Plots
Heat Maps
- Working with Heat Maps
- Working with Index Sort Data in Heat Maps
Electronic Signatures
- Maintaining Signatures
- Signing Layouts
- Unsigning Layouts
- Displaying Signature Information
  - Signature Status
Layout History
Standard Operating Procedures
- Accessing and Docking SOP Navigator
- Creating the SOP
- Changing Order of SOP Steps
- Deleting SOP Step
- SOP Permission Rules and Authorizations
- Running SOP
- Displaying SOP Information and SOP tokens
Permission Rules
- Creating a Permission Rule
- Organizing Permission Rules in folders
- Save and Load Permission Rules Action List
- Editing a Permission Rule
- Deleting a Permission Rule
- Permission Rules Options
- Available Permission Rules
Formatting Authorizations
- Accessing and Docking Formatting Authorizations Navigator
- Working with Authorizations
- Overriding Authorizations
Security
- User-Based Security
- Layout-Based Security
- Working with User-Based Security
- Working with Security Groups
- 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
- Layout and Data Security
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
- 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
- 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 Pie, Bar, and Scatter Plots - 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 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
  - 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 6 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
- 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