Staff Profiles

Gayathri Mahalingam, Ph.D.

Scientist II

​Gayathri Mahalingam joined the Allen Institute in 2017 as a Scientist in the Neural Coding department. She works with the Network Anatomy group in its efforts to generate peta scale datasets with a goal of mapping the wiring diagram of the mouse neocortex and its functional connectivity. Gayathri graduated with a Ph.D. in Computer Science from the University of Delaware with specializations in the field of Computer Vision and Machine Learning, and Biometrics.  She worked as a Post-Doctoral fellow at the Institute of Interdisciplinary Sciences in Identity Sciences at the University of North Carolina, Wilmington before joining the Institute.  


Research Interests

As a member of the Network Anatomy group, Gayathri has worked in the stitching and alignment of Peta-scale datasets comprising the cubic mm of the mouse neocortex. She has developed tools for linear and elastic registration and 3D alignment optimized for large scale datasets. She has also developed machine learning based tools to handle anomalies in these datasets. She is also interested in developing tools that aid data analysis that helps in some interesting biological findings on the functionality of the mouse brain.


  • Computer Vision

  • Machine Learning

Research Programs

  • Neural Coding

Selected Publications

A petascale automated imaging pipeline for mapping neuronal circuits with high-throughput transmission electron microscopy

Nature Communications
October 2, 2020

Yin W, Brittain D, Borseth J, Scott ME, Williams D, Perkins J, Own CS, Murfitt M, Torres RM, Kapner D, Mahalingam G, Bleckert A, Castelli D, Reid D, Lee WA, Graham BJ, Takeno M, Bumbarger DJ, Farrell C, Reid RC, da Costa NM