Team

Staff Profiles

Forrest Collman, Ph.D.

Assistant Investigator

Forrest Collman is an assistant investigator working at the Allen Institute within the Human Cell Types group with Stephen Smith. He received his undergraduate training in physics from Princeton University, where he did his senior thesis with John Hopfield on computational models of olfaction using synchrony. He then did a Ph.D., also at Princeton, but within the Molecular Biology department where he worked with David Tank, helping developing methods for two-photon microscopy in awake behaving mice, as well as the design and construction of a virtual reality behavioral environment for head-fixed mice. Before joining the Allen Institute, he was a postdoc, also with Stephen Smith, at Stanford University, where he worked on the development of conjugate IF/SEM array tomography and its application to neural plasticity. 

Research

Research Interests

I am interested in using array tomography to measure the molecular connectivity of neural circuits. At the Allen Institute, I will be working on developing better methods for the acquisition of large array tomography datasets to facilitate the high throughput screening of the distribution of different synapses on individual cells, as well as the application of this technology to imaging the molecular and structural differences between synapses of different types.  

Expertise

  • Array Tomography
  • Scanning Electron Microscopy
  • Two Photon Microscopy
  • Computational Image Analysis
  • Synaptic Diversity

Research Programs

  • Human Cell Types

Selected Publications

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

eLife
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

Cell
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

eLife
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

Common cell type nomenclature for the mammalian brain

eLife
December 29, 2020

Miller JA, Gouwens NW, Tasic B, Collman F, van Velthoven CT, Bakken TE, Hawrylycz MJ, Zeng H, Lein ES, Bernard A.

Transcriptomic evidence for dense peptidergic neuromodulation networks in mouse cortex

bioRxiv
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.

eLife
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

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