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Welcome to CyAn, a MATLAB toolbox for segmenting and tracking cyanobacteria cells!
CyAn is designed to be easy to configure and used for batch processing of time-lapse images:
%Create a new CyTracker object
CT = CyTracker;
%Adjust settings
CT.ChannelToSegment = 'Red';
%Process your files!
process(CT);The CyTo toolbox defines two main classes:
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CyTracker- Process, segment, and track cyanobacteria cells in time-laspe images -
DataAnalyzer- Analyze resulting data
The DataAnalyzer class is a subclass of TrackArray from the Linear
Assignment Tracking toolbox and can be used as a
starting template for writing your own data analysis functions.
- Getting started - Installation and basic usage
- User guide - List of user documentation
- Code reference - List of classes and data structure
If you encounter any issues or have ideas for new features, please post on the Issues Board or send an email to [email protected].
For bug reports, please provide enough details to reproduce the error, including details of external files used. If possible, please include a minimal example that produces the error and post that. Please also include the full error message at the end of the report.
If you are interested in contributing to the toolbox, this section is for you.
We would appreciate an acknowledgment in your publications or presentations. An example acknowledgment statement could be:
This project uses the CyAn toolbox developed by the BioFrontiers Advanced Light Microscopy Core and the Cameron Lab at the University of Colorado Boulder.
We also ask that you send us an email at [email protected] so we can keep track of usage stats. This helps us in reporting and securing funding for the facility.