NeuroDataViz v2.0 Beta

Web visualization and analysis for neuroimaging datasets. Powered by Neuroglancer.

Features

In addition to most current Neuroglancer features, NDViz adds...

• False coloring and Min/max intensity correction controls.
• Variable blend modes (press h to bring up the help menu that lists the corresponding keyboard shortcut).
• Single-channel overlays -- overlay two different z-indices of the same channel.

Browsers

NDViz v2 is compatible with recent versions of Google Chrome and Mozilla Firefox. The Apple Safari Technology Preview seems to mostly work, but current versions of Safari do not fully support certain Javascript functionality required by NDViz.

Installation

A note about CORS: NDViz v2 loads data from remote sources into browser memory. Therefore, remote servers require CORS headers. For more information on CORS and configuring servers to allow remote loading of resources by adding the appropriate CORS headers, see https://developer.mozilla.org/en-US/docs/Web/HTTP/Access_control_CORS.

The installation intructions below will setup NDViz for development and testing purposes. For production use, we recommend placing a nginx proxy in front of the built-in nodejs web server. There are many tutorials available, and configurations may need to be adapated for specific usecases. However, this tutorial is a good starting point.

1. Install nodejs and npm.
2. Download the NeuroDataViz source (e.g. git clone https://github.com/neurodata/ndviz.git)
3. Download the Neuroglancer source. You will want to use the ndmaster branch from the Neurodata fork of Neuroglancer.
4. Enter the neuroglancer directory. Run npm install.
5. From the same directory, run npm link.
6. Switch to the ndviz directory. Run npm install.
7. Run npm link neuroglancer
8. Run npm run build. (For development, you may want to run npm run watch as a background process). This sets up the client-facing viewer code.
9. Finally, run npm start. By default, npm start will use port 80, which requires root privileges on most systems. To run on port 8000, use npm run start-dev.

Note: You will need to restart the server each time code changes while in development mode.

Deployment

We have provided a Makefile that is compatible with AWS Elastic Beanstalk. Running make will build the NDViz client JavaScript code and create a zip file containing the NodeJS application and built client facing code. The zip file can be uploaded to AWS Elastic Beanstalk in a nodejs environment, and should be compatible with other cloud platforms (PRs welcome!).

Dockerfile (BETA)

We have also provided a Dockerfile to allow you to build and deploy NDViz in a Docker container. The Dockerfile exposes the NodeJS development server on port 80.

Contributions

Contributions are always welcome! We suggest the following process:

1. Create a fork off the main NDViz master branch.
2. Add your contributions and create commits.
3. No merge commits, please! After you have added your contribution(s), rebase from the NDViz master branch:

• Checkout master.
• Run git pull to download any new commits.
• Checkout your branch.
• Run git rebase master to unwind your commits and replay them on top of the latest commits in the master branch.
• Fix any merge conflicts (this should occur during the rebase process).

4. Squash your commits into as few new commits as possible. Separating functionality into multiple commits is fine.
5. Create a pull request on GitHub.