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Here you can find download links and installation instructions for the MATLAB sources and binaries for several platforms.

Contents

System Requirements

Operating System

You can run TLM-Tracker on Windows and Linux platforms.


Matlab

You can either run TLM-Tracker as executable binary file or without any Matlab installation.

Alternatively, you can use your Matlab installation, download the TLM-Tracker source code and execute TLM-Tracker in your MATLAB version.

TLM-Tracker was developed and tested in Matlab Version 7.9 (R2009b), so it is not guaranteed to work with former MATLAB versions. The Image-Processing Toolbox is widely used, so TLM-Tracker won't work without it. The Statistics-Toolbox is used to calculate growth- and product formation rates, so by avoiding these functions, TLM-Tracker can be used without this toolbox.


GraphViz

GraphViz is an open source tool for the visualization of graphs and networks (http://graphviz.org/). Some functions of TLM-Tracker require GraphViz as an external tool. Thus, you will need to download GraphViz from this link and install it before using TLM-Tracker. Ubuntu users can install Graphviz with the Synaptic package manager (System > Administration > Synaptic Package Manager; search for Graphviz; select for installation; apply; see details in German here).

Afterwards you should check if the installation path was successfully added to the search path.

Check the path variable

1. Open a console.

Windows: Start > All Programs > Accessories > Command Prompt
Linux: Applications > Accessories > Terminal

2. Type 'dot -V' and press enter. If something like 'dot - graphviz version 2.26.3 (20100126.1600)' appears the path has been set correctly and you can skip the following section. If a message is displayed, saying the command might be misspelled or could not be found, the path has not been set correctly yet and has to be set manually.

Set the path variable

  • Windows
  1. type into the commandline prompt ('cmd'): 'set PATH=<graphvizPath>\bin;%PATH%' (where <graphvizPath> is the folder which Graphviz has been installed to; e.g. C:\Program Files (x86)\Graphviz2.26.3)
OR
  1. Right click on the 'My Computer'-Icon on the desktop and select 'Properties'.
  2. In the system properties window select the 'Advanced'-Tab and click on the 'Environment variables'-Button.
  3. In the environment variables window click on the path variable in the system variables section and click the 'Edit'-Button.
  4. Add the directory of your GraphViz-Installation (i.e. 'C:\Program Files (x86)\Graphviz2.26.3\bin') to the end of the line in the value field. This entry has to be separated from the former ones by a semicolon.
  • Linux
  1. determine the path to the installation directory: Type 'whereis dot'
  2. Set a symbolic link that points to that path: Type 'sudo ln -s /path/to/your/dot /usr/bin/dot'


Download

Binaries including the MATLAB Compiler Runtime

Use these versions to work without a local MATLAB installation.

Windows

Windows 32 bit

Windows 64 bit

Linux

Linux 32 bit

Linux 64 bit


TLM-Tracker source code

Use this version to integrate TLM-Tracker in your local MATLAB installation independently of your operating system.

TLMTracker source code

Installation

TLM-Tracker binary

Windows

  1. First install GraphViz as described here.
  2. Download the TLM-Tracker binary from here.
  3. Unpack the contents of the downloaded zip archive to a folder of your choice.
  4. Install the MCR (Matlab Component Runtime) by executing MCRInstaller.exe and follow the instructions.
    1. make sure the <MCR installation path> is added to the environmental PATH variable (should be done automatically) as described for Graphviz here
    2. can be set by 'set PATH=<MCRPath>\v713\runtime\win32;%PATH%' for Windows 32-bit or by 'set PATH=<MCRPath>\v713\runtime\win64;%PATH%' for Windows 64-bit in the commandline prompt
  5. for Windows 64-bit platforms it might be necessary to install Microsoft Visual C++ 2010 Redistributable Package (x64) (e.g. from here)
  6. Start TLM-Tracker by executing TLMTracker.exe

Linux

  1. First install GraphViz as described here.
  2. Download the TLM-Tracker binary from here.
  3. Unpack the contents of the downloaded zip archive to a folder of your choice.
  4. Open a console and change to this directory.
  5. Install the MCR (Matlab Component Runtime) by executing in a command line terminal: 'sudo ./MCRInstaller.bin'. Follow the instructions and select an installation path of your choice, e.g., /usr/local/tlmtracker. Be sure to keep in mind the installation path.
  6. Now start TLM-Tracker by typing './run_TLMTracker.sh <MCR_Installation_Path>/v711/'. The MCR installation path could be: '/opt/MATLAB/MATLAB_Compiler_Runtime'.


TLM-Tracker MatLab source code

  1. A MatLab Version 7.9 (R2009b) environment or higher is needed
  2. MatLab image processing toolbox must be installed
  3. First install GraphViz as described here.
  4. Download the TLM-Tracker source code from here.
  5. Create a directory in your Matlab Working Directory and unpack the content of the zip file to it.
  6. Start MATLAB.
  7. In MATLAB change to the TLM-Tracker program directory.
  8. Type 'TLMTracker' to the MATLAB console and press enter to start the program.

Example images

Here an image sequence is provided to quickly test the capabilities of the program. This is an image sequence of Bacillus megaterium expressing GFP from an inducable promoter, which has been induced at the begin of the movie. In addition, a project file (bmeg_project.mat) is provided in the image folder that represents a complete segmentation and tracking analysis.

Example Bacillus megaterium

Information about the accuracy of TLM-Tracker with regard to this examplary dataset can be found here.

Segmentation of phase contrast images/videos

Here a preliminary MAT-file is provided that allows the segmentation (watersheds methods) of phase contrast images/videos. Therefore the phase contrast image sequence/video has to be assigned to the brightfield slot in TLM-Tracker. In the segmentation step of the TLM-Tracker workflow the provided MAT-file (download) can be loaded using the Load button in the Segmentation process panel.


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