brainhackorg / global2020

Brainhack Global 2020
https://brainhack.org/global2020/
MIT License
13 stars 14 forks source link

Matplotlib surface plotting #114

Closed kwagstyl closed 3 years ago

kwagstyl commented 3 years ago

Project info

Title: Matplotlib Brain Surface Plotting image

Project lead: Konrad Wagstyl Twitter: @KonradWagstyl Mattermost: @konrad

Project collaborators:

Registered Brainhack Global 2020 Event: Brainhack Micro2Macro 2021

Project Description: There are lots of nice tools to plot brain meshes in python, but many come with depencies that can be tricky to install. This project aims to improve a basic tool to plot brain meshes purely using matplotlib.

Ideal for people who want a simple, easy to use tool to visual cortical surface data on meshes in notebooks or generate brain images through python scripts.

All you need is a mesh file (containing vertices and faces) and a set of values you want to display. For example, cortical thickness values across the mesh or a surface-based parcellation.

Here is the github: https://github.com/kwagstyl/matplotlib_surface_plotting

Data to use: All data is currently included in the github repo. You can use your own mesh files if you prefer.

Link to project repository/sources: https://github.com/kwagstyl/matplotlib_surface_plotting

Goals for Brainhack Global 2020: The aim for the brainhack is to add some extra visualisation options:

Good first issues:

  1. Notebook to plot a brain - download the repo and create a notebook from the example .py script
  2. Suggest a new plotting feature
  3. Implement a new feature

Skills:

Python Jupyter notebook Data visualisation

Tools/Software/Methods to Use:

Python Jupyter notebook

Communication channels:

https://mattermost.brainhack.org/brainhack/channels/matplotlib_surface_plotting

https://zoom.us/ (link will be posted in mattermost channel) **Project labels**

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