Staff Profiles

Nikhil Bhagwat, Ph.D.

Scientist I

Nikhil joined the Neuroanatomy group at the Allen Institute in July 2019. He works on developing machine-learning techniques for analyzing neuroimaging data from Alzheimer’s disease mouse models. Particularly, he is interested in characterizing neuronal connectivity patterns using 2-photon microscopy images for predicting disease progression. Nikhil received B.S. and M.S. degrees in Electrical Engineering from George Mason University and a Ph.D. in Biomedical Engineering from the University of Toronto.


Research Interests

Nikhil is interested in understanding the mapping and mechanisms of neuronal circuitry and its role in brain function. The high-resolution microscopy images offer a wealth of information that can help further our understanding of neuronal networks, especially in the context of degenerative diseases. In this regard, my work involves developing computational algorithms and machine-learning models to extract phenotypic patterns associated with healthy and pathological connectivity. This would help us identify vulnerable neuronal networks to predict disease progression. Moreover, this will potentially help towards development of clinical applications for prevention and prognosis of the neurodegenerative diseases.


  • Computational neuroscience
  • Machine-learning
  • Alzheimer’s disease
  • MR image segmentation

Research Programs

  • ​​Connectivity in mouse models of Alzheimer’s disease​​