Computational Path Visualization

The Connectivity Atlas API's mouse_connectivity_target_spatial service retrieves all of the experiments with signal density above .001 in a specific set of target coordinates. The return contains a computationally derived path through the signal between the experiment's injection site and the target voxel. This example demonstrates how that query can be used on a single experiment to reconstruct the paths from the injection site to all voxels with within a given range of signal densities that are outside annotated fiber tracts. This is similar to the code used to visualize connectivity atlas experiments in the Brain Explorer©.

The data download script also retrieves the reference atlas voxels that have been marked as belonging to the experiment's injection site. These are displayed as small yellow spheres.

The paths are displayed in 3D in the browser using the three.js JavaScript library. This experiment has a primary injection site in the primary motor area. You can see a similar visualization of this experiment in the Brain Explorer© application.

Note: your browser must support WebGL to view this demo.

Documentation and Resources A python script that downloads spatial search lines and injection site coordinates for an experiment. A python script containing API query methods.
lines.js Three.js visualization documentation.
lines.tar.gz Archived source code.