Load and plot Allen Connectivity Data (Oh et al., Nature, 2014)
See the script gettingStarted.mlx to get started. The first time the script is run, it will be slow because images need to be downloaded. In subsequent runs, these images will simply be loaded and it will be much faster.
BrainStreetView requires MATLAB>=2019a.
To begin using BrainStreetView:
- clone the repository and the dependencies.
- add BrainStreetView's and the dependancies' folders to MATLAB's path.
Dependencies:
- allenCCF, to get Allen Atlas files
- npy-matlab, to read in .npy files
- brewermap, to generate colormaps
- prettify-matlab, to make plots pretty.
- projections from visual cortices to striatum: injection sites and striatum plotted in 3D
- example injections in primary visual cortex (VISp)
- example injections in antero-lateral visual cortex (VISal)
- projections from visual cortices (VIS) to striatum (CP)
If you run into any issues or if you have any suggestions, please raise a github issue, create a pull request or email me: juliemfabre[at]gmail[dot]com.