cyan example

Example

This document will walk you through a full example of using the CyAn toolbox.

Prerequisites

• CyAn toolbox installed
• Download example time-lapse image

Step-by-step guide

Set up CyTracker

1. In MATLAB, create a new CyTracker object

CT = CyTracker;

2. Define settings for tracking. In this example, we will set the following:

• Segmentation algorithm: 'brightfield'
• Threshold level: 10
• MaxCellMinDepth: 5
• Channel to segment: 1

CT.ChannelToSegment = 1;
CT.SegMode = 'redSeg';
CT.ThresholdLevel = 10;
CT.MaxCellMinDepth = 5;

Processing files

Start processing

process(CT);

A dialog box will pop up allowing you to select an image file. Navigate to where you saved the example image file and double-click it to select.

A second dialog will then open allowing you to select the output directory. Choose a new directory so we can see what files are generated.

By default, the tracking code will produce three files:

• An AVI-file that shows the outline of each cell along with the cell IDs
• A MAT-file that contains the tracked data
• A settings.txt file that contains the CyTracker settings.

Data Analysis

Note: Data analysis functions are still in development

Create a DataAnalyzer object

1. In MATLAB, create a new DataAnalyzer object

   DA = DataAnalyzer;

2. Import data

   DA = importdata(DA)

   • Select the MAT-file