Project to infer 3D structure from Open Connectome data
Requirements:
- Minka's Lightspeed MATLAB toolbox
- vlfeat
- PGF and TikZ
Files:
- latex/ -- see submission.tex.
- src/ -- code for this project. cd to this directory and run
startup
to prepare the environment. In particular,- experiment/ -- main functions; entry point for running code
- neal3_iter.m, neal8_iter.m -- Implementations of MCMC sampling based on Radford Neal's papers (details in comments)
- MDP.m, MDPLight.m, NormalWishart.m, GammaGamma.m, etc. -- Class implementations of conjugate distributions supporting online inference.
- GraphDist.m, GraphDistDistribution.m -- Support for Geodesic distances (details in paper)
- src/scrape - scripts (mostly curl) to download data from openconnecto.me and compatible servers. Some scripts placeholders for secret keys. Please email the repository collaborators for details.
- ddpcode/ - Dependence Dirichlet Process tracking module due to Willie Neiswanger.
- data/ - Code expects data to live here. Scraping code puts it here.