Installation

LightSuite relies on external tools and repositories. To install LightSuite and stay up-to-date, clone the LightSuite repository and add it to MATLAB's path. If you're not familiar with GitHub, the easiest starting point is using GitHub Desktop. The cleanest way to add a repository to MATLAB's path is by adding the following line to ~\Documents\MATLAB\startup.m:

addpath(genpath('~\Documents\GitHub\LightSuite'))

Follow these steps to set up your environment correctly:

1. MATLAB Requirements

You need MATLAB R2022b or newer. Ensure the following toolboxes are installed:

• Computer Vision Toolbox
• Image Processing Toolbox
• Optimization Toolbox
• Parallel Computing Toolbox
• Statistics and Machine Learning Toolbox
• Bioformats Image Toolbox
• Bioformats functions

2. Install repository dependencies

Clone the following two repositories and add them to MATLAB's path:

• matlab_elastix, updated fork based on Rob Campbell's repository
• yamlmatlab, Rob Campbell's repository
• bcpd, by Osamu Hirose

3. Install Elastix

LightSuite calls Elastix from the command line, so its executables must be globally accessible.

1. Download the version 5.1.0 executables and unzip the archive to a permanent location on your computer (e.g., C:\elastix or /opt/elastix).

2. Add Elastix to the system PATH: This is the most critical step. You must add the directory containing the elastix and transformix executables to your system's PATH environment variable.

   • Windows: Search for "Edit the system environment variables," click "Environment Variables," and add a new System variable named elastix with the path to your bin directory (e.g., C:\elastix).
   • Linux/macOS: Add export PATH="/path/to/your/elastix/bin:$PATH" to your shell configuration file.

3. Verification: To confirm that Elastix is installed correctly, open a new terminal or command prompt and type elastix --version. You should see the version information printed to the screen. If you get a "command not found" error, the PATH is not set correctly.

4. Download Atlas Data

LightSuite uses the 2020 version of the Allen Brain Atlas for brain registration. To be able to use the software you have to download all volume files along with all relevant metadata and make them available to the MATLAB path.

For spinal cord registration, LightSuite uses the Fiederling et al 2021 spinal cord atlas. Download the compressed file from here, extract its contents and make them available to the MATLAB path.

5. Check installation

Finally, run check_lightsuite_installation.m to verify whether you have installed everything correctly. If you encounter no errors, you're good to go.