SOAX

Standalone Executables for Windows

SOAX (v3.7.0) is a standalone executable for Windows.

Batch SOAX (v3.7.0) is a command-line SOAX in batch mode that can be executed with options to set the image or directory names and to set different combinations of parameters.

Best SOACs (v3.7.0) is a command-line utility that generates candidate extractions from a large set of 3D extraction results (usually obtained by batch extraction using Batch SOAX).

Batch Length (v3.7.0) is a command-line utility that generates SOAC lengths from multiple SOAC files.

Batch Resample (v3.7.0) is a command-line utility that resamples TIFF images to have isotropic voxel size.

Older and 32-bit versions of Windows SOAX versions and its related applications are available in the archive.

Standalone Executables for Mac OS X (High Sierra)

SOAX (v3.7.0) as a Mac OS X Application.

Batch SOAX (v3.7.0) is a command-line SOAX in batch mode that can be executed with options to set the image or directory names and to set different combinations of parameters.

Best SOACs (v3.7.0) is a command-line utility that generates candidate extractions from a large set of 3D extraction results (usually obtained by batch extraction using Batch SOAX).

Batch Length (v3.7.0) is a command-line utility that generates SOAC lengths from multiple SOAC files.

Batch Resample (v3.7.0) is a command-line utility that resamples TIFF images to have isotropic voxel size.

Docker Image

SOAX GUI and SOAX batch command lines can be run on Windows, Mac OS X, and Linux within a docker container, using docker image: vavylonis/soax_v.3.8.0_tsoax_v0.2.2 that contains both SOAX v3.8.0 and TSOAX v0.2.2

This version includes the executables 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 also contains the libraries and source code needed to compile SOAX. 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/soax_v.3.8.0_tsoax_v0.2.2

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:\SOAX_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 SOAX -dit vavylonis/soax_v.3.8.0_tsoax_v0.2.2

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 SOAX 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 SOAX /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 /usr/local/bin/SOAX, /usr/local/bin/batch_soax, etc.

• If you have an X server on Windows, the GUI version of SOAX may start after using:

export DISPLAY=host.docker.internal:0.0

Image Data for Validation

We provide a synthetic image of actin cable network and its ground truth centerlines. The ground truth can be loaded via Load JFilament Snakes in SOAX's File menu.