Linear Assignment Cell Tracker

Cell tracking based on the linear assignment framework

Linear Assignment Tracking

The Linear Assignment Tracking toolbox implements MATLAB classes to track moving cells in microscope images and analyze resulting data.

Downloading and using the toolbox

The latest releases can be found here.

Full instructions on how to download, install, and use the toolbox is on the Project Wiki.

Downloading the source code

⚠️ You do not need the source code unless you are planning to contribute to this project.

The master branch contains the latest stable code, while the dev branch contains daily builds. You should only use the dev branch if you know what you are doing.

Using the Gitlab interface

To download the source code using Gitlab:

1. Click on the Repository tab above.
2. Click on the Download icon and select the desired format. It is recommended that you download the "master" branch as it contains the latest stable code.

Cloning using Git

If this is your first time using the biof-git repository, you must add an SSH key to your profile.

To clone the repository using Git:

1. Click on the Project tab above.
2. Look for the SSH box (you might need to maximize your browser window if the box is missing). Copy the SSH URL to the clipboard. The URL should look like: [e-mail]:<groupname>/<projectname>.git
3. Windows: Start the Git bash application and navigate to a folder of your choice. Linux/Mac: Start the Terminal application and navigate to a folder of your choice.
4. Enter the following command:

  git clone <SSH URL>

If you have any issues, please email the developer or [e-mail] for help.

Developer's Guide

Directory structure

The directory of the Git repository is arranged according to the best practices described in this MathWorks blog post. The following table describes the folders in this repository:

Folder name	Description
tbx\lap-tracker	Main toolbox code
tbx\docs	Examples and MATLAB user documentation
build	Files for building the toolbox (typically a MATLAB project (.prj) file and an icon)
tests	Unit tests

Contributing to the code

Reporting bugs and issues

Please report bugs and issues using the Issues Tracker.

Merge/Pull requests

To contribute code directly, please submit a Pull Request.

Note: In general, your code will have to pass the unit tests listed in the tests folder. You can check that they do by using the runtests function in MATLAB.

References

K. Jaqaman, et al. "Robust single particle tracking in live cell time-lapse sequences" Nature Methods 5, 695-702 (2008)