FCS Express 7 Manual
Opera Bug
Contents
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Index
Welcome to FCS Express
System Requirements
Supported File Formats
Purchasing and Installing FCS Express
Learning How to Use FCS Express
A Quick Tour of FCS Express
Getting Started with FCS Express
A Quick Walk through the Ribbon
The Quick Access Toolbar
Customizing the Ribbon
The File Tab
The Home Tab
The Insert Tab
The Design Tab
The Gating Tab
The Batch & Export Tab
The Text Tab
The Data Tab
The Tools Tab
The Quality Tab
The View Tab
The Help tab
The Format Tab
The Multicycle Tab
The Multi Plot Tab
The Spreadsheets Tab Group
The Layout Tab
The Formulas Tab
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
Startup Script
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
Notes
Layout Page Features
Inserting Items onto a Page
Selecting Items on a Page
Overlaying 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
Page Layout Using Predefined Placeholders
Using the Master Page
Using Templates
Plots and Other Objects
Plots
Inserting Plots
1D Plots
Histograms
Multicycle DNA Plots
Inserting a DNA Histogram
Formatting a DNA Histogram
DNA Fit
DNA Background
Position Markers
Setting Default DNA Options
The Multicycle Tab
DNA Statistics
DNA-Specific Tokens
DNA Cycle and Model Summary Reference
Proliferation Plots
Inserting a Proliferation Histogram
Formatting a Proliferation Histogram
Proliferation Fit Options
Position Markers
Proliferation Statistics
Proliferation-Specific Tokens
Subtraction Plots
Formatting Options Shared by All 1D Plots
Overlays
Markers
Specific Options
Parameter Overlays
2D Plots
Dot Plots and Color Dot Plots
Dot and Color Dot Plot Overlays
Density and Contour Plots
Color Levels
Density and Contour Plot Overlays
Surface Plots
Surface Plot Overlays
Kinetics Plots
Inserting a Kinetics Plot
Formatting a Kinetics Plot
Overlays
Kinetics Statistics
Kinetics-Specific Tokens
Formatting Options Shared by All 2D Plots
Quadrants
Gates To Display
Specific Options
Resolution Overview
Charts
Special Plots
Spectrum Plots
Inserting a Spectrum Plot
Formatting Spectrum Plots
Overlays
Spectrum Plot Specific Options
Color Levels
Gates to Display
Gating and Backgating on Spectrum Plots
Picture Plots
Gates Heat Maps
Creating Gates Heat Map Overlays
Gates Heat Map Overlays
Gates Heat Map Color Levels
Gates Heat Map Specific Options
Plate Heat Maps
Working with Plate Heat Maps
Choosing Parameters and Statistics
Well Gates
Creating Plate Heat Map Overlays
Working with Index Sort Data in Plate Heat Maps
Influx Index Sorting Data Files
Summit Index Sorting Data Files
Diva Index Sorting Data Files
Chorus Index Sorting Data Files
Formatting a Plate Heat Map
Formatting Plate Heat Map Overlays
Formatting Plate Heat Map Color Levels
Formatting Plate Heat Map Specific Options
Parameters Heat Map
Creating Parameters Heat Map Overlays
Parameters Heat Map Overlays
Parameters Heat Map Specific Options
Parameters Heat Map Color Levels
Parameters to Display
Formatting Options Shared by All Plots
Title
Legend
Axes
Axis Scalings
Axis Scalings and Statistics
Gating and Axis Scalings
Quadrants and Axis Scaling
Biexponential Scaling Implementation in FCS Express
Axis Min/Max
Changing Plot Type
Plot 3D Options
The Current Data File
Changing Data Files on Plots
Changing the Parameter on Plot Axes Using Keyboard Shortcuts
Pictures
Text Boxes
Inserting Text Boxes onto a Page
Quadrant Label Text Boxes
Text Box Selection
Gate, Quadrant and Marker Text Boxes
Entering and Formatting Text in a Text Box
Inserting Tables
Formatting Tables
Exporting a Table to Excel
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
Gate View
Formatting the Gate View
Data Grids
Formatting Data Grids and Custom Data Grids
General
Gates To Display
Parameters to Display
Formatting Data Grids to Display Only Images
Data Image Options
Applying Gates to a Data Grid
Creating Cell Number Gates on a Data Grid
Viewing Compensated and Transformed Values in Data Grids
Spreadsheets and Charts
Creating a Spreadsheet
Working with Spreadsheets
Formatting
Formatting Spreadsheet Cells
Conditional Formatting
Spreadsheet Cells
Find and Replace
Supported Keystrokes
Analyzing Files from the Data List with Spreadsheets
Spreadsheet Formula Definitions
ANOVA - Analysis of Variance
Tukey's Test
Renaming Spreadsheets
Deleting Spreadsheets
Exporting Data in Spreadsheets
Graphing Data with Pie Charts, Bar Plots, Scatter with Regression, and Box and Whisker Plots
Pie Charts
Inserting Pie Charts
Populating Pie Charts by Drag and Drop
Populating Pie Charts from Spreadsheets
Formatting Pie Charts
Bar Plots
Inserting Bar Plots
Populating Bar Plots by Drag-and-Drop
Populating Bar Plots from Spreadsheets
Formatting Bar Plots
Scatter Plots
Inserting Scatter Plots
Populating Scatter Plots from Spreadsheets
Formatting Scatter Plots
Regression Analysis (Manually fitting data)
Manual Regression Analysis Example
Available Equations
Scatter With Regression
Scatter With Regression Plots
Formatting Scatter With Regression Plots
Scatter with Regression Tokens
Interpolating values from Scatter with Regression Plots
Levey Jennings Plots
Summary Charts
Inserting Summary Charts
Formatting Summary Charts
Multi Plot
Formatting Options
General
Background / FIll
Border / Line
Size
Formatting Authorizations
Working with Authorizations
Overriding Authorizations
The Data List
Adding Files to the Data List
Adding Merged Files to the Data List
Adding Gated Data to the Data List
Organizing data files into Iterations and Controls
Sorting in the Data List
Load Data files and Iterations in the Layout
Load a specific Data file into one or multiple plots
Load an Iteration into all plots on the layout
Panels
Working with Panels
Defer Layout Changes
Gating
Gates
Gate Types
Live Updating Gates
Creating Gates
Formatting Gates
Data Specific Gates
Using Data Specific Gates
Using Data Specific Gate Groups
Using Boolean Logic to Create Combination Gates
Adding a Combination Gate Matrix
Moving and Resizing Gates
Deleting Gates
Showing and Hiding Gates
Using Snapshots with Gates
Gates and the Clipboard
Linking Gates Together
Hierarchical Gating
Applying Gates to Plots
GatingML
Quadrants
Type of Quadrants
Creating Quadrant Gates and Compound Quadrant Gates
Showing and Hiding Quadrants
Formatting Quadrant Sets and Quadrant Gates
Formatting Quadrant Sets
Formatting Individual Quadrant Gates
Moving Quadrants
Linking Quadrants to Quadrants
Linking Gates to Quadrants
Using Quadrants and the Clipboard
Markers
Creating Markers
Moving Markers
Resizing Markers
Resizing marker boundaries using the mouse
Resizing the marker boundaries via the Formatting Marker dialog
Resizing marker boundaries by dragging and dropping tokens
Resizing and linking marker boundaries by dragging and dropping marker bounds
By dragging and dropping a gate
By dragging and dropping a plot
Deleting Markers
Using Markers and the Clipboard
Linking Markers to Gates
Batch Processing
Adding Batch Processes
Batch Processing Actions
Print
Save Layout
Save To PowerPoint
Save To PDF
Custom Grid Options
Save As Picture
Save Gating ML
Folders (Action Containers)
Prism Project
Save Spreadsheet to Excel
Batch Processing Reports
Export to Luma
Internal Spreadsheet
Prism XY Table
Prism Column Table
Prism Grouped Table
Export to Excel (Column Mode)
Export to Excel (Cell Mode)
Word Report
PDF Form
Text Report
Adding Items to Reports
Configuring a Report Item's Report Specific Property
Adding Pictures to a Report
Reordering and Copying Items in Reports
Display Text Options
Running Options
Batch Processing Options
Running the Batch Process
Reviewing the Batch Process
Snapshots and Batch Iteration Navigation
Using Flags
Snapshots
Iteration Snapshots
Manual Snapshots
Tools
Compensation and Spectral Unmixing
The Compensation and Unmixing Window
Creating and Modifying a Compensation Definition
Manually Editing a Compensation Matrix via the Compensation Window
Manually Editing a Compensation Matrix from a 2D Plot
Automatically Calculating Compensation Matrices
Compensation Options
Creating and Modifying an Unmixing Definition
Creating an Unmixing Definition Using Single Stained Controls
Visualized Mixing Matrix
Spectral Unmixing Detection, Caveats, and troubleshooting
Note on Virtual Bandpass Filter pipeline step for unmixing
Creating or Modifying an Unmixing Definition by Importing Endmembers via CSV files
EasyPanel
Spillover Spreading Martrix
Cross Stain Index Matrix
Using Definitons
Applying Definitions to Existing Plots
Selecting the Default Definiton to Use When Loading Data
Import and Export Definitions
Reporting a definition into the layout and into Excel
Transformations
Transformation Navigator
Sampling Options
Target Density Downsampling
Weighted Density Sampling
Parameter Math
Defining Parameter Math
Applying Parameter Math
Principal Component Analysis
Defining a PCA Transformation
Applying a PCA Transformation
K means (Cluster Analysis)
Defining a k-means cluster analysis
Applying a k-means cluster analysis
Working with k-means parameters
R Integration
Enabling R integration in FCS Express
Installing R packages on the MAC version of FCS Express
Introduction to R integration in FCS Express
R Add Parameters
R Cluster Transformation
tSNE (viSNE)
tSNE performance in FCS Express
Defining a tSNE transformation
Applying a tSNE transformation
Working with tSNE transformations
Saving tSNE results with an FCS File
SPADE
Defining a SPADE transformation
Working with SPADE transformations
Saving SPADE results with a DNS file
Pipelines
Setting Up Pipelines
Pipeline Steps
Pre-defined Algorithms
Downsampling
Dimensionality Reduction
Clustering
Visualization
Mathematical
Random Parameters
Quality Controls
Feature Extraction
Miscellaneous
Python Transformation
Python Transformation Training Scripts
Python Transformation Example Scripts
Parameter Labels
Channel Calibration
Creating a New Channel Calibration
Using a Channel Calibration
The Channel Calibration Window
Concentration Calculator
Calculating a Single Concentration
Calculating Concentrations on the Statistics Page
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
Quality
Alerts
Creating Alerts
Running Alerts
Statistics
1D Plot Statistics
2D Plot Statistics
The Statistics table and its associated plot
Using Statistics and the Clipboard
Formatting Statistics Table
Percent Gated - Parent and Percent Gated - Grandparent
Spreadsheet Statistics from Data Files
Tokens
Inserting Tokens
Viewing the Source of Tokens and the Formula of Custom Tokens
Token Properies
Common Token Properties
Display Text Token Property
Font Token Properties
Data Source Token Property
Number Format
Editing Statistic Tokens
2D Plot Statistic Token Options
Histogram Statistic Token Options
Data File Statistic Token
Token Multiplication Grouping
Editing Keyword Tokens
Statistic Classifier Tokens
Layout Tokens
Inserting a Page Layout Token
Gate Tokens
Signature Tokens
Compensation/Unmixing Tokens
Batch Processing Tokens
SOP Tokens
System Tokens
Plot Tokens
Data Parameter Tokens
Spreadsheet Cell Value 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
Creating A Token Report
Publishing Layout Tools
Publishing a Layout
Advanced Publishing
Default Publishing Options
Sharing Published Layouts with Others
FCS Express Reader
Obtaining the FCS Express Reader
FCS Express Reader Limitations
Upgrading from FCS Reader to FCS Express
Working with FCS Data Files
Viewing and Changing FCS File Headers
Extra Keywords
Group Parameter Extra Keywords
Keyword Anonymizer
Merging / Concatenating Multiple Files
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
Adding Signatures
Saving and Loading Signatures
Modifying Signatures
Deleting Signatures
Signing Layouts
Unsigning Layouts
Displaying Signature Information
Signature Status
Layout History
Security
Security Package for Network Licenses
User-Based Security
Layout-Based Security
Working with User-Based Security
Creating a User
Editing a User
Deleting a User
Exporting User List
Setting Default User Options
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
Report Security Group Permissions
Working with Layout Security Groups
Managing the Databases
Available Security Group Permissions
Security Database Options
Configuring MS SQL Server to host Security Databases
MS SQL Server Database User Permissions
Backing up the Databases
Preparing for Database Updates
Internet Dongle and Site License Security and User Management
Editing Security Configurations
Managing Password Configurations
Mail Notifications
SMTP Server
Online Registration
LDAP and Single Sign On
Creating and Administering LDAP Users
System Level Audits
Internet Dongle and Site License Access and Security
User Administration
Creating an Internet Dongle or Site License User
Editing an Internet Dongle or Site License User
Deleting an Internet Dongle or Site License User
Exporting User List
Setting Default User Options
Security Reports
All Events Report
Failed Logins Report
Full Sessions Report
All Remote Logouts Report
Report Unique Users
All System Level Audits Report
Billing Report
User Billing Report
Arranging, Grouping, and Filtering Reports
Arranging Columns in Reports
Grouping and Filtering Reports
Filtering on a Date Range
Exporting Reports
Layout and Data Security
Proxy Support
User Default Options
General Options
Plot Options
Borders
Title
Axis Options
Background Options
Legend Options
1D Plot Options
2D Plot Options
Text Boxes Selection Options
DNA Options
Multi Plot Options
Statistic Options
Statistics Naming Options
1D Plot Statistics
2D Plot Statistics
2D Plot Quadrant Statistics
DNA Cycle Statistics
DNA Model Statistics
DNA Experiment Statistics
Proliferation Fit Statistics
Proliferation Population Statistics
Kinetics Statistics
Regression Fit Statistics
Startup Options
Gate Options
Quadrant Options
Files/Directories
Data List
Dialogs Options
Keyword Dialog
Open Data Dialog
Accessing the Open Data Dialog
Advanced Open Data Dialog Tabs
Do Not Show Again
Save Options
Security Options
Spreadsheet Data
Text Boxes Options
User Information
Performance
Customer Experience Program
Advanced Publishing Preferences
Data Saving
Data Loading
FCS File Options
Instrument Specific Settings
ICE Format Options
PerkinElmer Acapella Options
Life Technologies Tali Options
Nexcelom Options
ImageJ Options
Amnis DAF Reader Options
Perkin Elmer Vectra Options
Thermo Cytpix ACS Options
FCS Express Keyboard Shortcuts
Canned Comments
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 Combination Gates
Moving and Resizing Gates
Deleting Gates
Applying Gates
Data Specific Gates
Creating Data Specific Gates
Accessing Data Specific Gates
Grouping 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 Classifier 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
Linking Quadrant Set
Markers
Creating Markers
Marker to Gate Linking
Compensation
Manual Compensation
Automatic Compensation
Automatic Compensation - Optional Steps 4
Automatic Compensation - Optional Steps 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)
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
Creating Bar Charts
Creating Pie Charts
Creating Scatter Charts
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
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
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
Spectral Unmixing
Unmixing from Single Stained Controls
Fluidigm CyTOF Data Analysis
Fluidigm 7 color (7C) kit demonstration