Matplotlib surface plotting

Project info

Title: Matplotlib Brain Surface Plotting

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 dependencies 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:

Settings for visualising flattened surfaces
Adding arrows to the surface
Labelling colorbars
User-suggested features

Good first issues:

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

Type of project: coding_methods, #documentation, #visualization
Project development status: 0_concept_no_content, #1_basic structure, 2_releases_existing
Topic of the projet:

data_visualisation,
Tools used in the project:

Jupyter
Tools skill level required to enter the project (more than one possible):

comfortable, #familiar,
Programming language used in the project:

documentation, #Python,
Modalities involved in the project (if any):

fMRI,
Git skills reuired to enter the project (more than one possible):

0_no_git_skills, #1_commit_push, #2_branches_PRs,
[x] I added all of the labels I want an associate to my project

Project Submission

Submission checklist

Once the issue is submitted, please check items in this list as you add under ‘Additional project info’

[x] Link to your project: could be a code repository, a shared document, etc.
[x] Goals for Brainhack Global 2020: describe what you want to achieve during this brainhack.
[x] Flesh out at least 2 “good first issues”: those are tasks that do not require any prior knowledge about your project, could be defined as issues in a GitHub repository, or in a shared document.
[x] Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill. Use the issue labels for this purpose.
[x] Chat channel: A link to a chat channel that will be used during the Brainhack Global 2020 event. This can be an existing channel or a new one. We recommend using the Brainhack space on Mattermost.

Optionally, you can also include information about:

[ ] Number of participants required.
[ ] Twitter-sized summary of your project pitch.
[ ] Provide an image of your project for the Brainhack Global 2020 website.

We would like to think about how you will credit and onboard new members to your project. If you’d like to share your thoughts with future project participants, you can include information about:

[ ] Specify how you will acknowledge contributions (e.g. listing members on a contributing page).
[ ] Provide links to onboarding documents if you have some:

brainhackorg / global2020