cellXpress User Guide

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

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