Running the Pipeline

Running the Pipeline

This page will give you a detailed guide on how to download and run the pipeline.

Testing the Pipeline on Example Data

Regardless of the method you choose on running the Pipeline, you may want to download example data. You can read up on downloading example data in this wiki page: https://github.com/RUB-Bioinf/LightSheetBrainVesselSkeletonization/wiki/Example-Data

Instructions

This section includes instructions on how to run VesselExpress locally on your device.

Using Docker

VesselExpress is provided insie a Docker container. That means, it comes in a pre-configured environment that you can get running in only a few instructions and no setup required. You can learn more about the docker version here.

Running without Docker

If you prefer to run VesselExpress without Docker and provide all dependencies yourself, you can learn more here

Needed libraries and software:

To run the pipeline without Docker please follow the instructions below:

• install Miniconda following the installation instructions
• install Snakemake following the installation instructions or use the runtime environment from the Envs folder which has Snakemake installed.

Input Data Structure

If you are running VesselExpress as a Command-Line Interface, you should place all images to be processed in a single directory. Let's assume that location is called /path/to/images. Make sure you grand read/write permission to the Docker to this directory. As such, your docker command would be: docker run -v /path/to/images:/home/user/VesselExpress/data vesselexpress_cli You must include a config.json file in the same directory as your files. You can learn more about the config here.

As an Example, the directory containing 4 example images in .tiff format, should look like this:

/path/to/images/
             /config.json
             /example_image1.tiff
             /example_image2.tiff
             /example_image3.tiff
             /example_image4.tiff

The images can be named in any pattern, but the config file must be named exactly config.json. When VesselExpress has finished, you will find the results for every image in a newly created sub-directory.

This structure does not apply, when you are using the Web-Interface version. There you can just drag and drop any files you would like to process into the UI.