VesselVio

An open-source application for
the analysis and visualization
of segemented vasculature datasets.

View the Project on GitHub
JacobBumgarner/VesselVio


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Overview

If you are unable to run the bundled VesselVio app or prefer to create the app locally, this page is for you. Below you’ll find detailed instructions explaining how to download the necessary files and then run the application from your command prompt/terminal.

We’ve tried to make this process as streamlined as possible! By the end, you should be able to run the app with a single line of code. Please contact us if you need help or have questions.

If you’re using a PC, follow the Windows Build Instructions guide.

If you’re using a Mac, follow the MacOS Build Instructions guide.


Windows Build Instructions

First, you’ll need to install python 3.8.8. This can be messy if you’ve got python installed elsewhere or if you don’t have an environment manager.

To avoid this mess, we use the popular python environment manager: pyenv. If you’ve already got a python environment setup, skip to step 4.

  1. Install Git as directed by the developers.

  2. Install pyenv-windows as directed by the developers or by following the instructions below.
    • Paste the following command into your command prompt
      git clone https://github.com/pyenv-win/pyenv-win.git "%USERPROFILE%\.pyenv"
      
    • Paste the following commands one-by-one into a powershell.
      [System.Environment]::SetEnvironmentVariable('PYENV',$env:USERPROFILE + "\.pyenv\pyenv-win\","User")
      [System.Environment]::SetEnvironmentVariable('PYENV_HOME',$env:USERPROFILE + "\.pyenv\pyenv-win\","User")
      [System.Environment]::SetEnvironmentVariable('path', $env:USERPROFILE + "\.pyenv\pyenv-win\bin;" + $env:USERPROFILE + "\.pyenv\pyenv-win\shims;" + [System.Environment]::GetEnvironmentVariable('path', "User"),"User")
      
    • Restart your command prompt, and then paste the command below to ensure pyenv was installed correctly. A version # will show if the installation worked.
      pyenv --version
      
    • Restart your terminal
  3. Install python version 3.8.8.
    • First, paste the following command into your command prompt.
      pyenv install 3.8.8 
      
    • Following successful installation, paste the following into the command prompt to complete the installation, and restart the prompt.
      pyenv rehash
      
    • Then, activate python version 3.8.8 using the following command.
      pyenv local 3.8.8
      
    • Lastly, update your pip installer the command below.
      pip install -U pip
      
  4. Download the VesselVio source code from our GitHub page.
    • On the GitHub page, click the green Code dropdown button, then Download ZIP.
    • Unzip the package, and place it somewhere accessible to you (e.g., your desktop).
  5. Navigate to the vesselVio file directory to install the required python packages.
    • For example, if the directory is located on your desktop, navigate to it by typing the following into your command prompt:
      cd desktop\VesselVio
      
    • Make sure python 3.8.8 is activated (step 3.1)
    • Install the necessary VesselVio dependency packages
      pip install -r requirements.txt
      
  6. You should now be able to execute the VesselVio.py file to run the application!
    • First make sure you’ve activated python 3.8.8 in your command prompt.
      python local 3.8.8
      
    • Then make sure you’ve navigated to the VesselVio source code folder (example below).
      cd desktop\VesselVio
      
    • Finally, run the application by typing the following command into your command prompt.
      python VesselVio.py
      

Windows App Bundling

If you want to build a local standalone VesselVio application, follow these instructions.

You should now be able to successfuly use VesselVio on your PC either from the command prompt or as a local standalone application!


MacOS Build Instructions

First, you’ll need to install python 3.8.8. This can be messy if you’ve got python installed elsewhere or if you don’t have an environment manager.

To avoid this mess, we use the popular python environment manager: pyenv. If you’ve already got a python environment setup, skip to step 5.

  1. Install Homebrew as instructed by the developers (a simple copy and paste).

  2. Install pyenv and pyenv-virtualenv.
    • First, install the packages by pasting the following commands into your terminal.
      brew install pyenv
      brew install pyenv-virtualenv
      
    • Then, configure your shell’s environment for pyenv and virtualenv (we use Zsh, see here if you use Bash or Fish). To do this, paste the following commands into your terminal to modify the .zprofile and .zshrc
      echo 'eval "$(pyenv init --path)"' >> ~/.zprofile
      echo 'eval "$(pyenv init -)"' >> ~/.zshrc
      echo 'eval "$(pyenv virtualenv-init -)"' >> ~/.zshrc
      
    • Restart your terminal.
    • Lastly, ensure pyenv is set up by typing pyenv into a new terminal window. If set up correctly, you should see a list of commands.
  3. Install the python version 3.8.8.
    • Paste the following into the terminal
      pyenv install 3.8.8
      
    • Make sure pip is up to date by typing in.
      pip install -U pip
      
  4. Create a new virtual environment called ‘VV’ (or whatever name you prefer), and activate this environment.
    • Create the environment by pasting the following command into your terminal. Replace ‘VV’ if you prefer a different name.
      pyenv virtualenv 3.8.8 VV
      
    • Activate the environment by typing the following into your terminal
      pyenv activate VV
      
  5. Download the VesselVio source code from our GitHub page.
    • On the GitHub page, click the green Code dropdown button, then Download ZIP.
    • Unzip the package, and place it somewhere accessible to you (e.g., your desktop).
  6. Then navigate to the VesselVio file directory to install the required python packages.
    • For example, if the directory is located on your desktop, navigate to your directory by typing the following into your terminal:
      cd desktop/VesselVio
      
    • Make sure your virtual environment is activated (step 4.2, example below)
      pyenv activate VV
      
    • Install the necessary VesselVio dependency packages using the following command.
      pip install -r requirements.txt
      
  7. You should now be able to execute the VesselVio.py file to run the application!
    • First make sure you’ve activated your python environment (example below)
      pyenv activate VV
      
    • Then, navigate to the VesselVio directory (example below)
      cd desktop/VesselVio
      
    • Finally, run the application by typing the following command into your terminal.
      python VesselVio.py
      

MacOS App Bundling

To build a local version of the application, you’ll first have to reinstall python 3.8.8 with an updated framework configuration.

sudo env PYTHON_CONFIGURE_OPTS="--enable-framework" pyenv install 3.8.8

You should now be able to successfuly use VesselVio on your Mac either from the terminal or as a local standalone application!