Source and Compiling Instructions on GitHub
Prebuilt Binaries for Windows and Mac OS X
Version 0.2 provides improved support for larger images and longer tracks by employing spatial decomposition, faster snake correspondence solver, and command-line exectuable batch_tsoax (David Rutkowski, 2022-2024)
TSOAX (v0.2.0) for Windows.
TSOAX (v0.2.0) with batch_tsoax.exe (v0.2.1) for Windows.
TSOAX (v0.2.0) for Mac OS X.
Older versionsTSOAX (v0.1.8) for Windows.
TSOAX (v0.1.8) for Mac OS X.
TSOAX (v0.1.7) for Windows.
TSOAX (v0.1.7) for Mac OS X.
Docker Image
TSOAX and batch_tsoax can be run on Windows, Mac OS X, and Linux within a docker container, using docker image: vavylonis/tsoax_v0.2.1
This version includes both the GUI and command line TSOAX (batch_tsoax) in /usr/local/bin of a Ubuntu 22.04 image. Note that on Windows and Mac OS X you may need to install an X server such as Xming (Windows) to run the GUI version.
The provided docker image contains the libraries and source code needed to compile TSOAX. These may be deleted in the docker container, if not needed, to reduce its size.
Brief instructions:
• Install docker desktop
• Open a native terminal or command prompt in Windows and pull the docker image by typing:
docker pull vavylonis/tsoax_v0.2.1
You should be able to see this image in the docker Images tab of the docker GUI.
• Make a folder for your data on your local machine. For example, in Windows it can be D:\TSOAX_docker. We call this path path_to_my_data in the next step.
• In your native terminal or command prompt type:
docker run --volume=path_to_my_data:/home/working --name TSOAX -dit vavylonis/tsoax_v0.2.1
That creates and runs a docker container from the image pulled from dockerhub. You only need to run this once, to create the container. You should be able to see the TSOAX container in the Containers tab of the docker GUI.
• From your native terminal, or windows command prompt, start the container by typing: docker exec -it TSOAX /bin/bash
Alternatively, you can start a terminal from within the docker GUI desktop by selecting "open external terminal". Type bash in this terminal to use the bash shell.
This will give you a terminal in which /home/working maps to path_to_my_data. The executables are in /usr/local/bin/TSOAX and /usr/local/bin/batch_tsoax
• If you have an X server on Windows, the GUI version of TSOAX may start after using:
export DISPLAY=host.docker.internal:0.0
Examples of Image Data, Parameters and Results
We provide examples of time lapse movies and parameter files (with or without extracted snake tracks) from the data in the paper T. Xu, C. Langouras, M. Adeli Koudehi, B. Vos, N. Wang, G. H. Koenderink, D. Vavylonis, and X. Huang, "Automated Tracking of Biopolymer Growth and Network Deformation with TSOAX".
Simulated 2D image of elongating actin filaments imaged by TIRFM (Fig. 3).
Elongating actin filaments imaged in 2D by TIRFM (Fig. 4) from Fujiwara et al. (2007).
3D image of dividing mid1Δ fission yeast cell expressing Rlc1-GFP (Fig. 5).
Simulated 3D image of network undergoing uniform shear (Fig. 7).