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Jian Tay edited this page Jun 15, 2021 · 10 revisions

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Welcome to the Linear Assignment Tracking toolbox wiki!

The Linear Assignment Tracking Toolbox implements two MATLAB classes: LAPLinker and TrackArray for tracking and analyzing time series data.

LAPLinker tracks moving objects in a time-lapse video using the linear assignment framework described by Jaqaman et al. in Nature Methods. TrackArray is a class to data to store and analyze time series data.

The classes are designed to be used in a typical image analysis pipeline.

Example:

%Initialize the LAPLinker object
linker = LAPLinker;

for frame = 1:numFrames

    %Read in current frame
    %Segment objects of interest
    %Measure properties of each object (e.g. intensity, size)
   
    %Link objects
    linker = assignToTrack(linker, frame, data);

end

%Get the TrackArray for data analysis
trackData = linker.tracks;

Documentation

  • Getting started - Download, installation, and basic tasks
  • Contents - List of all user documentation
  • Index - List of classes, methods, and terminology

Bug report and Feature requests

Please submit any bug report or ideas for features on the Issues Board or send us an email at biof-imaging@colorado.edu.

For bug reports, please provide enough details to reproduce the error, including details of external files used. Including a minimal example that produces the error will help us identify the problem. Please also include the full error message at the end of the report.

Contributor Guide

If you are interested in contributing to the code, this section is for you.

License and acknowledging the project

We would appreciate an acknowledgement in your publications or presentations. An example acknowledgement statement is:

This project uses the Linear Assignment Tracking toolbox developed by Dr. Jian Wei Tay of the BioFrontiers Advanced Light Microscopy Core at the University of Colorado Boulder.

We also ask that you send us an email at biof-imaging@colorado.edu so we can keep track of usage stats. This helps us in reporting and securing funding for the facility.

This project is provided under the MIT License.

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