An open-source application for
the analysis and visualization
of segemented vasculature datasets.
View the Project on GitHub
JacobBumgarner/VesselVio
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.
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.
Install Git as directed by the developers.
git clone https://github.com/pyenv-win/pyenv-win.git "%USERPROFILE%\.pyenv"
[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;" + $env:USERPROFILE + "\.pyenv\pyenv-win\shims;" + [System.Environment]::GetEnvironmentVariable('path', "User"),"User")
pyenv --version
pyenv install 3.8.8
pyenv rehash
pyenv local 3.8.8
pip install -U pip
cd desktop\VesselVio
pip install -r requirements.txt
python local 3.8.8
cd desktop\VesselVio
python VesselVio.py
If you want to build a local standalone VesselVio application, follow these instructions.
.pyenv>pyenv-win>versions>3.8.8>Scripts>pyinstaller.exe
pyinstaller --add-data=Library;Library --additional-hooks-dir=Hooks --icon library\icons\icon.ico --windowed VesselVio.py
You should now be able to successfuly use VesselVio on your PC either from the command prompt or as a local standalone application!
First, you’ll need to install python 3.8.8. This can be messy if you’ve got python installed elsewhere or if you don’t have an environment manager.
To avoid this mess, we use the popular python environment manager: pyenv. If you’ve already got a python environment setup, skip to step 5.
Install Homebrew as instructed by the developers (a simple copy and paste).
brew install pyenv
brew install pyenv-virtualenv
echo 'eval "$(pyenv init --path)"' >> ~/.zprofile
echo 'eval "$(pyenv init -)"' >> ~/.zshrc
echo 'eval "$(pyenv virtualenv-init -)"' >> ~/.zshrc
pyenv
into a new terminal window. If set up correctly, you should see a list of commands.pyenv install 3.8.8
pip install -U pip
pyenv virtualenv 3.8.8 VV
pyenv activate VV
cd desktop/VesselVio
pyenv activate VV
pip install -r requirements.txt
pyenv activate VV
cd desktop/VesselVio
python VesselVio.py
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
pyinstaller \
--add-data=./Library:Library \
--additional-hooks-dir=./Hooks \
--icon Icons/icon.icns
--windowed \
VesselVio.py
You should now be able to successfuly use VesselVio on your Mac either from the terminal or as a local standalone application!