FCS Express 6 Manual

Index

FCS Express 6 Manual

Contents | Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

- 1 -

1D Plot Preferences

- 2 -

2D Plot Preferences

2D Plot Statistics

- A -

About the Manual

Accuri CFlow Files

Tips for Importing

	Working with Picture Plots
	Well Gates

Adding a Text Box to a Plot

Adding Custom Data

Adding Signatures

Advanced Publishing

Advanced Publishing Preferences

Aligning Objects

Analysis of FCS Data

Application Button

Applying Compensation Definitions

Applying Gates to Plots

Auto Recovery Files

- B -

Save As Picture

Save to PowerPoint

Batch Process

Batch Processes

batch processing

	Batch Processing
	Batch Processing Snapshots

Adding Items to Reports

Adding Pictures to Reports

Creating Templates for Reports

Report Item Specific Properties

Working with Reports

Batch Processing Actions

Batch Processing Reports

Reordering and Copying Items

Batch Processing Tokens

- C -

Calculating a Single Concentration

Calculating Compensation

Cell Number Gates

Changing FCS Files

Changing Parameters on Plot Axes

Channel Calibration

Channel Calibration Tool

Channel Calibration Window

Closing Layouts

Compensation Definitions

Adjusting from a 2D Plot

Compensation Files

Compensation Tokens

Compensation Tool

Concentration Calculator

Single Concentration

Statistics Page

Creating a New Channel Calibration

Creating a New Layout

Creating a User

Creating Custom Tokens

Creating Gates from Quadrants

Creating Markers

Creating Security Groups

	Creating a Permission Rule
	Creating a User Security Group

Current FCS File

Adding/Defining

Custom Token Formulas

Inserting Functions

	Inserting Functions into Formulas
	Inserting Functions into Formulas

	Using Boolean Values in Custom Tokens
	Using Boolean Values in 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
	More Complex Custom Token Examples
	Custom Token Example 3: Appending Text
	Custom Token Example 4: Conditional Statements
	More Complex Custom Token Examples

Formula Reference

Using Array Formulas

Customizing Default Preferences

Customizing the Ribbon

- D -

Parameters to Display

Data List

Adding Data Sets

Change File Button

Changing Data Sets

Cell Profiler Options

IsoCyte Options

Default Files/Directories

Default Preferences

Defining Custom Data

Deleting a User

Deleting Custom Data

Deleting Custom Tokens

Deleting Markers

Deleting Security Groups

	Deleting a Permission Rule
	Deleting a Security Group

Deleting Signatures

Dialog Preferences

Displaying Plots

DNA Histograms

DNA Position Markers

DNA Preferences

Position Markers

DNA-Specific Tokens

Dockable Windows

Docking a Window

Duplicating Security Groups

- E -

Editing a Compensation Definition

Editing Keyword Tokens

Editing Layout Tokens

Editing Security Groups

	Editing a Permission Rule
	Editing a Security Group

Editing Statistic Tokens

Electronic Signatures

Exporting FCS File Data

Exporting Layouts

Extra Hosting Plans

- F -

Tips for Importing

FCS Data

FCS Express Reader

Upgrading to FCS Express

FCS File Data

Exporting Single Files

FCS File Headers

Viewing and Changing

FCS File Options

FCS Files

Formatting

2D Plot Overlays

2D Plot Specific Options

3D Display Options

Border and Size

Histogram Markers

Histogram Overlays

Histogram Specific Options

Options Shared by All Objects

Options Shared by All Plots

Resolution Options

Formatting DNA Histograms

Background Options

General Options

Formatting Objects

	Formatting Objects
	Overview

Formatting Pictures

Formatting Proliferation Histograms

Position Markers

Formatting Statistics

Formatting Tables

Formatting Text

Formatting Text Boxes

- G -

Gate Preferences

Gate View Object

Gates

Applying to Plots

General Preferences

Getting Started

Graphing Custom Data

Grouping Items on a Page

- H -

Setting Parameters

Help

Integrated Help System

Hiding Quadrants

Hierarchical Gating

Histogram Statistics

Histogram Subtraction Tool

- I -

Importing External Documents

Inserting Items on a Page

Inserting Pictures

Inserting Plots

Inserting Tables

Inserting Tokens

Introduction to the Layout

- K -

Keyword Dialog Preferences

Kinetics Analysis

Kinetics Histograms

Kinetics Statistics

Kinetics-Specific Tokens

- L -

Layout Navigator

Layout Security Groups

Layout-based Security

Layouts

Exporting a Page to PowerPoint

Exporting as a PDF

Exporting Page as a Picture

Inserting and Deleting Pages

Learning FCS Express

Linking Markers to Gates

Linking Quadrants to Gates

Linking Quadrants to Quadrants

Loading Compensation Definitions

- M -

Maintaining Signatures

Managing Password Configurations

Managing the Databases

Markers

Master Page

Changing Background

Modifying Signatures

Moving Quadrants

Multicycle Functions

- N -

Navigating through a Layout

Data Loading and Saving

- O -

Objects

	Formatting Objects
	Overview

Obtaining and Installing Multicycle

Obtaining the Proliferation Add-on

Ordering Objects

- P -

Pages

Inserting Items

Selecting Items

Panels

Parameter Label Sets

Creating a Calculation

Creating a Sequence

Pictures

	Inserting Pictures
	Inserting Text Boxes onto a Page

Pinning a Window

Plot Preferences

Plot Statistic Preferences

Plots

Preferences

DNA Cycle Statistics

DNA Experiment Statistics

DNA Model Statistics

Files/Directories

Plot Statistics

Poliferation Population Statistics

Proliferation Fit Statistics

Proliferation Analysis

Proliferation Fit Parameters

Proliferation Fit Statistic Preferences

Proliferation Histograms

Proliferation Population Statistic Preferences

Proliferation Postion Markers

Proliferation Statistics

Proliferation-Specific Tokens

Publishing

De Novo Software Site

Default Options

Maintaining Layouts

- Q -

Quadrants

Creating Gates from

Linking Gates to

Quick Access Toolbar

Quick Tour of FCS Express

- R -

Regression Analysis

Renaming Custom Data

Resizing Markers

Resizing Objects

Resizing Text Boxes

Ribbon

Ribbon Interface

Application Button

Quick Access Toolbar

- S -

Save Preferences

Saving a Layout

Saving Compensation Definitions

	User-Based Security
	Working with User-Based Security

Security Groups

	Creating a Permission Rule
	Creating a User Security Group

	Deleting a Permission Rule
	Deleting a Security Group

	Editing a Permission Rule
	Editing a Security Group

Security Preferences

Selecting Items on a Page

Selecting the Default Compensation

Setting DNA Preferences

Setting Proliferation Preferences

Setting Up Compensation Definitions

Sharing Published Layouts

Showing Quadrants

Signatures

Signing Layouts

Software Compensation Caveats

Stacked Overlay Data

Startup Preferences

Statistic Preferences

Statistic Tokens

2D Plot Options

Histogram Options

Support

System Requirements

- T -

Tables

Text Box Preferences

Formatting Text

Token Properties

Batch Processing

Inserting a Page Layout Token

Tutorial

Aligning Objects

Always Display Selection Dialog

Analysis of 3-Cycle Data

Analyzing Data in Heat Maps

Apply Regression to an FCS File

Applying Gating and Statistics

Autofit Selection (1-Cycle Analysis)

Automatic Compensation

Bar and Scatter Plots

Batch Processing

Cell Concentration

CellProfiler Export

Changing Histogram Overlays

Channel Calibration

Channel Calibration Defaults

Channel Calibration Demonstration

Channel Calibration Tool Setup

Complete a Custom Data Grid

Concentration Calculator (Time/Flow Rate)

Concentration Calculator Using Beads

Copying Objects

Create 1D Gate on 2D Plot

Create a Gate from a Marker

Create a Linear Regression Token

Create Custom Tokens

Create Token Classifiers

Creating a Custom Data Table

Creating a Custom Token

Creating a Gate from a Quadrant

Creating Combination Gates

Creating Custom Data

Creating the Layout

Data Navigator Features

Deleting an Object

Docking Features (Multiple Windows)

Duplicating Objects

Excel Report (Cell Mode)

Excel Report (Column Mode)

Expanded Analysis with Autofit

Export an IsoCyte Experiment

Export IsoCyte Data in Numeric Form

Exporting 96 Well Format Images

Exporting from IsoCyte

Exporting Numeric Data (96 Well)

Exporting Plots to PowerPoint

Exporting Single Image Numeric Data

Exporting Single Images

Features of a Docked Window

Fitting Proliferating T-cells

Format to Change Resolution

Formatting 3D Options

Formatting a DNA Histogram

Formatting a Proliferation Histogram

Formatting Legend

Formatting Multiple Plots

Formatting Plot Axes

Formatting Plot Background

Formatting Plot Titles

Formatting Plots

Formatting Text Box Properties

Formatting Text in a Text Box

Formatting using the Pop-up Menu

Gate Navigator Features

Gating with Picture Plots

Grouping Objects

High Content Flow

Import and Analyze 96 Well Images

Import IsoCyte Numeric Form Data

Import Single Image Data

Import Single Image Numeric Data

Importing Numeric Data (96 Well)

Insert a Scatter Plot

Insert and Format Picture Plots

Insert Plots from Windows Explorer

Inserting a 2D Plot

Inserting a Data Grid

Inserting a Histogram

Inserting an Object

Inserting and Modifying a Table

Inserting and Modifying a Token

Inserting Plots

Inserting Text Boxes

Layout Navigator

Layout Navigator Features

Load Layout for Custom Data

Load, Insert, and Format Heat Maps

Manual Compensation

Marker to Gate Linking

Moving an Object

Open/Dock Data Navigator

Open/Dock Gate Navigator

Open/Dock Layout Navigator

Ordering Objects

Overlay and Format Kinetics Plots

Pasting Objects

Percentile Quadrants

Plotting Values

Quadrant to Gate Linking

Quadrant/Marker to Gate Linking

Rectangular and Floating Quadrants

Resizing an Object

Save a Regression

Saving and Loading Panels

Saving/Loading Channel Calibrations

Selecting and Deselecting Objects

Selecting Multiple Objects

Setting Bead Gates and Markers

Setting Up a Panel

Setting up Bead Gates

Showing Concentration (Statistics Window)

Showing the Concentration as a Token

Text Boxes and Tokens

Undocking a Window

Undoing Changes

Using Batch Analysis

Using Data Grids for Analysis

	Using Objects
	Immunophenotyping

Using Parameter Math

Using the Panel

Using the Z-Prime Function

- U -

Undoing Changes

Unsigning Layouts

Upgrading from Version 3

User

User Information

User-based Security

Using Quadrants

Using Templates

Using the Master Page

- V -

Viewing the Raw Data

- W -

Working with Custom Data

Working with Heat Maps

Working with Layouts

Working with Multiple Layouts

Working with Panels

Working with Pictures

Working with Text Boxes

Working with the Data List

- Z -

Zooming a Layout