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Installation

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marwan-abdellah edited this page Oct 24, 2022 · 10 revisions

Table of Contents

Prerequisites

To run the installation script, the following tools must be installed on your system:

Installation Procedure using Command Line (for Linux and macOSX)

VessMorphoVis can be installed on Linux and macOSX as follows:

  1. Download the setup.py script.

From the browser, this script can be downloaded by clicking on the link and then Save link as...

On Linux, this script can be downloaded from the terminal as follows

wget https://raw.githubusercontent.com/BlueBrain/VessMorphoVis/master/setup.py

On macOSX, this script can be downloaded from the terminal as follows

curl https://raw.githubusercontent.com/BlueBrain/VessMorphoVis/master/setup.py >setup.py .
  1. Change access permissions of the setup.py script to be able to execute it as follows
chmod +x setup.py
  1. Run the setup.py script and provide a valida or existing directory where the artifacts will be downloaded and installed.
./setup.py --prefix=VALID_DIRECTORY  --verbose

Users can select the version of Blender using the --blender-version option.

--blender-version BLENDER_VERSION
                    Blender version. 2.79, 2.80, or 2.81. By default it is 2.80.
  1. Once done, change directory to this VALID_DIRECTORY as follows
cd VALID_DIRECTORY/blender-bluebrain
  1. Run Blender from the terminal
./blender
  1. From the Edit panel, open Preferences.

  1. Go to the Add-ons panel and load VessMorphoVis from the list by checking the box: System: VessMorphoVis.

  1. Once loaded without errors, close the Blender Pereferences window.

  2. If you click N, VessMorphoVis panel will appear on the right side of Blender (in Blender 2.8). In Blender 2.79 or earlier, this panel will appear on the left side of Blender.

Installation Procedure on Windows

To install VessMorphoVis on Windows, you need to download a portable version of Blender and a clone of the VessMorphoVis code.

Blender

You can download Blender from any of the following links, depending on the version:

Then you should extract this .zip archive.

VessMorphoVis

Then, you need to download a clone of the latest release of VessMorphoVis from this link.

Then, you should extract this .zip archive.

Adding VessMorphoVis to the addons Directory

After unarchiving, copy the folder that contains the VessMorphoVis addon (must hasve an init.py file) into the addons directory. This addon directory is found under BLENDER_VERSION/scripts/addons, where BLENDER_VERSION should be replaced by the version of the downloaded blender (3.0, 3.1, 3.2, or 3.3).

Once added, you can execute Blender, and follow the following instructions to load the addon in Blender.

  1. From the Edit panel, open Preferences.

  1. Go to the Add-ons panel and load VessMorphoVis from the list by checking the box: System: VessMorphoVis. Note that this step might takes a while to download and install all the dependencies (2-5 minutes) in case they are not installed.

  1. Once loaded without errors, close the Blender Pereferences window.

  2. If you click N, VessMorphoVis panel will appear on the right side of Blender (in Blender 2.8). In Blender 2.79 or earlier, this panel will appear on the left side of Blender.

Sample Morphologies

To test the package, a set of sample morphology files (in VMV , SWCand H5 formats) are available upon request from the Blue Brain Project. SWC morphologies are available from the brain vasculature (BraVA) database.

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