Staff Profiles

Sharmishtaa Seshamani, Ph.D.

Scientist III

At the Allen Institute for Brain Science, Sharmishtaa Seshamani is working in the Human Cell Types group. Her current research focuses on building a data processing pipeline to facilitate the imaging of neurons in the brains of mouse and human brain samples in order to reveal important details about the morphology and connectivity of neural circuits. She received her Ph.D. in Computer Science from Johns Hopkins University where she focused on developing meta registration and mosaicking techniques for endoscopic imaging. Prior to joining the Allen Institute for Brain Science, she was a Senior Fellow at the Biomedical Image Computing Group in the University of Washington. There, she was working on a pipeline for fetal fMRI analysis which included algorithms for MRI artifact correction (bias and spin history), motion estimation and reconstruction.


Research Interests

As a member of the synapse biology team, one of my primary research goals is to develop a framework for automated large scale processing of array tomography data. In particular, I am interested in developing tools for linear and elastic registration and 3D reconstruction optimized for large datasets. I am also interested in applications of machine learning techniques for automatic parameter selection and connectivity data analysis.


  • Computer vision
  • Pattern recognition
  • Medical image analysis

Research Programs

  • Human Cell Types

Selected Publications

A scalable and modular automated pipeline for stitching of large electron microscopy datasets

July 26, 2022

Mahalingam G, Torres R, Kapner D, Trautman ET, Fliss T, Seshamani S, Perlman E, Young R, Kinn S, Buchanan J, Takeno MM, Yin W, Bumbarger DJ, Gwinn RP, Nyhus J, Lein E, Smith SJ, Reid RC, Khairy KA, Saalfeld S, Collman F, Macarico da Costa N

Transcriptomic evidence for dense peptidergic neuromodulation networks in mouse cortex

January 13, 2019

Smith SJ, Sumbul U, Graybuck LT, Collman F, Sharmishtaa S, Gala R, Gliko O, Elabbady L, Miller J, Bakken T, Yao Z, Lein ES, Zeng H, Tasic B, Hawrylycz M

Single-cell transcriptomic evidence for dense intracortical neuropeptide networks.

November 11, 2019

Smith SJ, Sümbül U, Graybuck LT, Collman F, Seshamani S, Gala R, Gliko O, Elabbady L, Miller JA, Bakken TE, Rossier J, Yao Z, Lein E, Zeng H, Tasic B, Hawrylycz M

Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy.

Nature Methods
September 17, 2018

Ounkomol C, Seshamani S, Maleckar MM, Collman F, Johnson GR