Title: Development of the SLAM -Surface anaLysis And Modeling- python package
Project lead: Guillaume Auzias will be the main project manager and will be helped by Alexandre Pron during this brainhack.
Project collaborators: Main developers are the members of the MeCA team (http://meca-brain.org/), but we are welcoming warmly external collaborators, contributors and users.
Registered Brainhack Global 2020 Event: Brainhack Marseille
Project Description: Slam (https://gauzias.github.io/slam/) is an open source python package dedicated to the representation of neuroanatomical surfaces stemming from MRI data in the form of triangular meshes and to their processing and analysis.
Main features include read/write gifti (and nifti) file format, geodesic distance computation, several implementations of graph Laplacian and Gradient, mesh surgery (boundary identification, large hole closing), several types of mapping between the mesh and a sphere, a disc… Have a look at the examples on the documentation website: https://gauzias.github.io/slam/auto_examples/index.html
Data to use:
Link to project repository/sources: https://github.com/gauzias
Goals for Brainhack Global 2020: During this brainhack, our objectives are:
to add as a new feature the algorithms for computing surface profiling as described in Li, K., Guo, L., Li, G., Nie, J., Faraco, C., Cui, G., Zhao, Q., Miller, L.S. and Liu, T., 2010. Gyral folding pattern analysis via surface profiling. NeuroImage, 52(4), pp.1202-1214. https://doi.org/10.1016/j.neuroimage.2010.04.263
to improve the documentation with new examples to enrich the gallery (https://gauzias.github.io/slam/auto_examples/index.html), which helps a lot potential new users
to further improve code quality with new unitest and potential speed-up of specific pieces of code such as for instance the computation of the curvature
to help potential users to get familiar with this python package
we are of course also open if new features are proposed from the contributors
Good first issues:
Skills: python 50%, mesh processing 20%, will to share ideas and good time 100% Minimal skills in python coding and github are required, but various levels of expertise are welcome since some of our objectives can be addressed with limited coding effort such as augmenting the documentation.
Tools/Software/Methods to Use:
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