Cortico-thalamic Projection

The ProjectionStructureUnionize model in the connectivity atlas API summarizes projection signal for each experiment at a structural level. Computed parameters include: projection density (sum of detected pixels / sum of all pixels in a structure), projection energy (sum of detected pixel intensity / sum of all pixels in a structure), and projection volume (sum of detected pixels normalized to mm3). Refer to the informatics whitepaper for a more detailed description of the informatics processing pipeline.

This example demonstrates how to download projection volume values for a specific set of structures and experiments and visualizes them as a heatmap. The experiments chosen for this example have primary injections in seven different cortical regions (y axis). The target structures span the thalamus (x axis). Notice how the projection signal volume patterns differ significantly based on injection site.

The heatmap on this page was generated by the D3 JavaScript library. Mouse over cells in the heatmap to see full structure names and numeric projection volume values. You can also see how to generate this heatmap in R in the documentation section below.

Documentation and Resources

thalamus.R R code that generates a heatmap similar to the one shown on this page.
download_data.js Javascript code that downloads ProjectionStructureUnionize values.
thalamus.js D3 code for laying out the heatmap.
thalamus.tar.gz Archived source code.