Home
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Introduction
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Tour of cellXpress
Features
Acknowledgement
Installation guide
FAQ
Documentation
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Introduction
Basic concepts
(plates, projects & markersets)
Data format requirements
Installation of cellXpress
cellXplorer and cellViewer
user interface
Quick start
Start cellXpress
Load projects
View images
Segment cells
Extract features
Count cells
Analyze intensity
Working with projects and markersets
Set root paths
Create projects
Create markersets
Manage well lists
Share projects
Quantify cellular phenotypes
Correct uneven background
Perform quick plate analysis (QC)
Segment cells
Extract features
Count cells
Plot well intensity
Export data
Use HDF5 Viewer
Load data in R
cellXplorer interface
Configure paths
Configure parallel processing
Terminate jobs
cellViewer interface
The Navigate menu
The Analysis menu
The View menu
Multivariate d-profiling
Load data in R
Compute d-profiles
Visualize d-profiles
Compare profiling methods
Generate profiles for large dataset
FAQ
FAQ
Download
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Information
System requirements
Release notes
Installation guide
End-user license agreement
Download
cellXpress pro 1.0
Sample datasets
About us
cellXpress User Guide
v1.0,
2012-13
Table of Contents
1. Introduction
1.1. Basic concepts
1.2. Data format requirements
1.3. Installation of cellXpress components
1.4. The cellXplorer and cellViewer user interface
2. Quick Start
2.1. Starting the cellXpress
2.2. Loading an existing project
2.3. Selecting wells and viewing images
2.4. Cell segmentation
2.5. Feature extraction
2.6. Cell counting
2.7. Analyze intensity
3. Working with Projects and Markersets
3.1. Set cellXpress Root directory paths
3.2. Create a new project
3.3. Create markersets
3.4. Add wells using the Well List manager
3.5. Access projects from different operating systems
4. Quantifying cellular phenotypes
4.1. Background subtraction
4.2. Quality control using Quick Plate Analysis
4.3. Cell segmentation
4.4. Object and region detection
4.5. Feature extraction
4.6. Cell counting
4.7. Analyze intensity
5. Exporting cellXpress data
5.1. Browsing cellXpress data using HDFView
5.2. Loading cellXpress data into R
6. The cellXplorer interface
6.1. Options: Set root path
6.2. Options: Parallel processing
6.3. Stop all running jobs
7. The cellViewer interface
7.1. The Navigate menu
7.2. The Analysis menu
7.3. The View menu
8. Multivariate d-profiling
8.1. Loading data into R
8.2. Computing d-profiles
8.3. Visualization
8.4. Comparison with raw features and PCA
8.5. Generating d-profiles for a large dataset
9. FAQ