Modeling the brain
Studies of brain anatomy and cellular morphology were once confined to single-subject studies wherein in vitro slices were compared to develop a complete model of the brain. With dyes, researchers could compare recordings to the reconstructed location of a given recording device. Through clever experimental design, researchers could further associate highly localized regions to their task-dependent function. Advances in 3D modeling have permitted parallel advances in multi-subject averaged anatomical models. An atlas serves as a shared reference frame for a given species. The Allen Institute has been a leader in the development of mouse atlases since 2007[^1], with regular updates[^2] that provide researchers with a shared reference frame in the study of functional neuroanatomy.
In coordination with both the Mesoscale Activity Project and the International Brain Lab, DataJoint developed mechanisms for pairing recording coordinates with the published atlases in project-specific cases that have since been generalized.
The Element's table architecture was generalized from existing project-specific pipelines to load standardized Kilosort
channel_locations.json files as well as the Allen Institute's atlas files, and pair these data sets.
The Element is separated into two schemas.
coordinate_frameworkingests standard atlases and retains voxel-based lookup tables, including references to brain region information, acronyms and standardized color codes.
electrode_localizationpairs the above reference tables with Neuropixels probe location data in a
probeschema, optionally from Element Array Ephys
One notable consession was made in development: acronyms in DataJoint do not perfectly map on to the Allen Institute's published standard. By default, DataJoint databases are not case sensitive. Instead, acronyms are convered to snake case to avoid naming collisions. While we depart from the standard, preliminary interviews with users indicate no bias toward the official standard. Visit our localization notebook for a demonstration of converting between the case sensitive and snake case standards.
[^1]: Lein, E. S., Hawrylycz, M. J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., ... & Jones, A. R. (2007). Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445(7124), 168-176. [^2]: Wang, Q., Ding, S. L., Li, Y., Royall, J., Feng, D., Lesnar, P., ... & Ng, L. (2020). The Allen mouse brain common coordinate framework: a 3D reference atlas. Cell, 181(4), 936-953.