YouTube Tutorial Video
You can use this YouTube Video for visualized instructions on how to download, setup and run VesselExpress on example data:
- Docker Setup & Download Guide: https://youtu.be/h0Lwtcje-Jo
- Starting VesselExpress CMD prompt:
docker run -p 5000:5000 philippasp/vesselexpress - Browser-Based User-Interface:
localhost:5000 - Download Example data: https://github.com/RUB-Bioinf/VesselExpress/wiki/Example-Data
Hi everyone and welcome to this tutorial on how to run VesselExpress.
VesselExpress runs on any operating system and only requires Docker to be installed on your system. We have linked another tutorial in the descriptions below on how to install Docker on Windows. So if you’ve already installed Docker you’re good to go and can follow along this tutorial to run VesselExpress via the web interface.
First of all, you need to start Docker desktop and then open the command line. You can search for the applications in windows explorer. Then type this command in the terminal to start a Docker container. You can copy the command from the descriptions below. If you do this the first time it might take a few minutes because the Docker image is downloaded from DockerHub. As soon as you see the prompt with “running” the process is finished and you can start using the web interface.
For this demonstration we will be using Microsoft Edge but you can use any other modern browser like Firefox or Google Chrome as well.
In your web browser navigate to localhost:5000. We have also provided this address in the description below so you can copy it.
Now you can see the main interface of VesselExpress. On the left you see several parameters which can be adjusted. Normally the default settings should work fine. You just may want to adjust the general parameters at the top. Here you can select if you want to process 2D or 3D images. As you can see you can always hover over the parameters to get a description. Here you can also enable the preview feature. This will generate previews of the rendered skeletonized and binarized vasculature. In this case we will enable this to show you all features of the software, but you should be aware that this will require more processing time. So if you’re only interested in the numerical data it makes sense to disable this. Then you should set the pixel dimensions in microns. For more information on parameter settings click “More information”. One other parameter we will be adjusting here is the gamma parameter of the Frangi filter which is used for segmentation. 500 is a good default parameter. If your data isn’t noisy you can even set a lower value or otherwise set a higher value if you’re image is very noisy. After you’ve made your changes click on apply configurations.
Then you can simply drag and drop your files which you want to process into the browser. You can upload multiple images. They will then be processed in parallel. VesselExpress supports most image file formats as you can see in the description box at the top. You only need to make sure that the files are single-channel grayscale images. Here we are uploading an image of our example data from the mouse brain which we have linked here on our website as well as other useful links like the GitHub repository.
After you’ve uploaded your data, you can click “run pipeline” to start the analysis. Now VesselExpress will process all data fully automatically. You can view the process in the right panel or just grab a coffee in the meantime.
As soon as you see the prompt “100% done” in the right panel, VesselExpress is done with processing all your files. If you’ve enabled the previews feature you will also see the processed files in the lower panel. Click on the file names to view the previews. The previews will be shown in a new tab in your browser. You can use the mouse and drag and pan to view the model from different angles. You can also use the mouse wheel to zoom in and out.
After running VesselExpress you have the option to download all results including model and image files of the skeletonized and binarized vasculature or you can just download the quantitative data which includes key measures such as vessel length and volume. Here we will download all results. This might take some time.
In your download folder you’ll find the results in a zip folder. First unzip the data. You’ll find a folder for each image containing the binarized and skeletonized vasculature in several file formats and a folder containing the key measures. For each key measure a csv file is generated which can be opened in Microsoft Excel. Here we’ll open the segment lengths file as an example. As you you can see the file contains a row for each segment including the length and the image coordinates of the segments. Now you can use this for further analysis.
Thanks for watching this tutorial. We hope this video is helpful for you and you’ll benefit from VesselExpress as an analysis tool for your microscopic images. If you have any questions or comments, please feel free to reach out to us via mail or leave a comment below.
