Staff Profiles

Dan Bumbarger, Ph.D.

Scientist III

Dan joined the Neural Coding group at the Allen Institute in 2014 under the direction of Clay Reid. He has contributed to the development and deployment of a pipeline for automated serial section collection and high throughput transmission electron microscopy. 

Prior to Joining the Allen Institute, he was a postdoctoral fellow at the Max Planck Institute for Developmental Biology under Ralf Sommer, where he headed a team that reconstructed synapse-level wiring in the anterior nervous system of the nematode Pristionchus pacificus. Their efforts led to identifying circuit architecture that act as a substrate for evolutionary differences in feeding behavior.

Dan earned his PhD at the University of California, Riverside in the lab of James Baldwin where he studied nematode anatomy and systematics of the poorly understood, but phylogenetically important Cephablobidae using a combination of molecular phylogeny, species descriptions based on light microscopy and scanning electron microscopy, and detailed anatomical studies of sensory anatomy using serial section transmission electron microscopy.


Research Interests

Dense, petascale descriptions of cortical anatomy at the ultrastructural level have the potential to lay the foundation for a new understanding of cortical circuit function and to help us translate knowledge gained in animal models to the human brain. I’ve been developing hardware and software for automated serial collection of ultrathin sections of brain tissue, working with our team on data acquisition, and developing methods for analyzing the resulting data. As we continue to scale tools for automated analysis of nervous system microanatomy, we’ll be able to rethink the kinds of questions we can ask about nervous system function and circuit level computation.


  • Serial Section Transmission Electron Microscopy 
  • Automation 
  • Synaptic connectivity analysis 
  • Evolutionary biology 

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

Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity

March 17, 2022

Turner NL, Macrina T, Bae JA, Yang R, Wilson AM, Schneider-Mizell C, Lee K, Lu R, Wu J, Bodor AL, Bleckert AA, Brittain D, Froudarakis E, Dorkenwald S, Collman F, Kemnitz N, Ih D, Silversmith WM, Zung J, Zlateski A, Tartavull I, Yu SC, Popovych S, Mu S, Wong W, Jordan CS, Castro M, Buchanan J, Bumbarger DJ, Takeno M, Torres R, Mahalingam G, Elabbady L, Li Y, Cobos E, Zhou P, Suckow S, Becker L, Paninski L, Polleux F, Reimer J, Tolias AS, Reid RC, da Costa NM, Seung HS

Structure and function of axo-axonic inhibition

December 1, 2021

Schneider-Mizell CM, Bodor AL, Collman F, Brittain D, Bleckert A, Dorkenwald S, Turner NL, Macrina T, Lee K, Lu R, Wu J, Zhuang J, Nandi A, Hu B, Buchanan J, Takeno MM, Torres R, Mahalingam G, Bumbarger DJ, Li Y, Chartrand T, Kemnitz N, Silversmith WM, Ih D, Zung J, Zlateski A, Tartavull I, Popovych S, Wong W, Castro M, Jordan CS, Froudarakis E, Becker L, Suckow S, Reimer J, Tolias AS, Anastassiou CA, Seung HS, Reid RC, da Costa NM

Capillary- and Stokes-based trapping of serial sections for scalable 3D-EM connectomics

February 24, 2020

Lee TJ, Yip MC, Kumar A, Lewallen CF, Bumbarger DJ, Reid RC, Forest CR

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

Transport and trapping of nanosheets via hydrodynamic forces and curvature-induced capillary quadrupolar interactions

July 18, 2018

Lee TJ, Lewallen CF, Bumbarger DJ, Yunker PJ, Reid RC, Forest CR

Large-scale neuroanatomy using LASSO: Loop-based Automated Serial Sectioning Operation

October 23, 2018

Lee TJ, Kumar A, Balwani AH, Brittain D, Kinn S, Tovey CA, Dyer EL, da Costa NM, Reid RC, Forest CR, Bumbarger DJ