What does it do?
This is a collection of MATLAB functions for handling mouse whole-brain imaging data and associated "sparse" point data such as cell locations, traced neurite trees, or traced projections from a bulk injection. This package provides functions for relating these sparse data to the Allen Reference Atlas (ARA):
- Downsampling full-resolution brain volumes to the ARA voxel size.
- Downsampling associated sparse data to the ARA voxel size and exporting of these data to a csv file.
- Registering the sample brain and sparse data to the ARA: both sample -> ARA and ARA -> sample transformations.
- Determining the ARA brain area associated with each sparse point.
- Extracting area outlines from the reference atlas that you can use for plotting.
Who is it for?
- Clone the repository in a Git client like SmartGit or SourceTree.
- You will need some or all of the dependencies listed below. Which ones you need depends on what you're doing. e.g. you won't need the registration stuff to plot cells.
- You will need a copy of the Allen Atlas and the template brain in MHD format. One is included on this page.
- Add the contents of the
codedirectory to your MATLAB path.
ARA tools depends on the following MATLAB packages and requires at least R2016b. Clone them and add to your path.
- Han 2018 MATLAB cell tracing code
- Allen API
- settings handler
- yaml matlab
- MelastiX (if you need to register brains to the ARA)
Using the toolbox
See the Wiki for documentation on using the tools.