Staff Profiles

Brian Long, Ph.D.

Scientist II

Brian Long joined the Allen Institute in November 2013 as a member of the computational neuroanatomy group. He is applying his extensive image and data analysis experience to extracting neuronal connectivity and cell morphology information from large imaging datasets.  In addition to image analysis, he is also working to improve electrophysiology and bioimage data acquisition through microscope automation and development of smart imaging technology. Long's previous work during his postdoc at the Vollum Institute at OHSU included 3D image processing and analysis for the systematic study of mouse thalamocortical connectivity, as well as setting up a single-molecule imaging microscope to study Protein Kinase A signaling in dendritic spines. Long's Ph. D. in Physics at the University of Oregon focused on measuring particle and polymer dynamics in nanofluidics, and computational modeling of diffusion in periodic structures. Long received his B.S. in Physics from the University of Washington.



Research Interests

Recent developments in microscopy allow neuroscientists to generate unprecedented amounts of imaging data from the scale of the entire brain down to single molecules.  As we observe and interpret the structure and function of the mammalian brain across this range of length scales, quantitative imaging data analysis is a critical bottleneck. I am interested in overcoming these challenges to address questions of long-range neuronal connectivity and cell-type identification. My previous work on thalamocortical connectivity in mouse reached the scale of the whole mouse brain, and I developed computational approaches to merge fluorescence data across many sample animals and quantify the thalamic subvolumes responsible for projections to frontal and prefrontal cortical areas.  At the micron and sub-micron scale, I have developed data analysis methods to extract biologically-relevant information from single molecule trajectories. My background on the experimental side of microscopy allows me to develop analytical methods with a clear understanding of the technical and practical aspects of bioimage acquisition.


  • Biophysics
  • fluorescence microscopy
  • computational neuroanatomy
  • image processing

Research Programs

  • MAT

Selected Publications

Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH

June 30, 2022

Fang R, Xia C, Close JL, Zhang M, He J, Huang Z, Halpern AR, Long B, Miller JA, Lein ES, Zhuang X

Spatially resolved transcriptomics in neuroscience

Nature Methods
January 18, 2021

Close JL, Long BR, Zeng H.

Conserved cell types with divergent features in human versus mouse cortex

August 21, 2019

Hodge RD, Bakken TE, Miller JA, Smith KA, Barkan ER, Graybuck LT, Close JL, Long B, Johansen N, Penn O, Yao Z, Eggermont J, Höllt T, Levi BP, Shehata SI, Aevermann B, Beller A, Bertagnolli D, Brouner K, Casper T, Cobbs C, Dalley R, Dee N, Ding SL, Ellenbogen RG, Fong O, Garren E, Goldy J, Gwinn RP, Hirschstein D, Keene CD, Keshk M, Ko AL, Lathia K, Mahfouz A, Maltzer Z, McGraw M, Nguyen TN, Nyhus J, Ojemann JG, Oldre A, Parry S, Reynolds S, Rimorin C, Shapovalova NV, Somasundaram S, Szafer A, Thomsen ER, Tieu M, Quon G, Scheuermann RH, Yuste R, Sunkin SM, Lelieveldt B, Feng D, Ng L, Bernard A, Hawrylycz M, Phillips JW, Tasic B, Zeng H, Jones AR, Koch C, Lein ES

Classification of electrophysiological and morphological neuron types in mouse visual cortex

Nature Neuroscience
June 17, 2019

Gouwens NW, Sorensen SA, Berg J, Lee C, Jarsky T, Ting J, Sunkin S, Feng D, Anastassiou C, Barkan E, Bickley K, Blesie N, Braun T, Brouner K, Budzillo A, Caldejon S, Casper T, Castelli D, Chong P, Crichton K, Cuhaciyan C, Daigle T, Dalley R, Dee N, Desta T, Dingman S, Doperalski A, Dotson N, Egdorf T, Fisher M, de Frates RA, Garren E, Garwood M, Gary A, Gaudreault N, Godfrey K, Gorham M, Gu H, Habel C, Hadley K, Harrington J, Harris J, Henry A, Hill D, Josephsen S, Kebede S, Kim L, Kroll M, Lee B, Lemon T, Liu X, Long B, Mann R, McGraw M, Mihalas S, Mukora A, Murphy GJ, Ng L, Ngo K, Nguyen TN, Nicovich PR, Oldre A, Park D, Parry S, Perkins J, Potekhina L, Reid D, Robertson M, Sandman D, Schroedter M, Slaughterbeck C, Soler-Llavina C, Sulc J, Szafer A, Tasic B, Taskin N, Teeter C, Thatra N, Tung H, Wakeman W, Williams G, Young R, Zhou Z, Farrell C, Peng H, Hawrylycz MJ, Lein E, Ng L, Arkhipov A, Bernard A, Phillips J, Zeng H, Koch C

h-Channels Contribute to Divergent Intrinsic Membrane Properties of Supragranular Pyramidal Neurons in Human versus Mouse Cerebral Cortex

November 1, 2018

Kalmbach BE, Buchin A, Long B, Close J, Nandi A, Miller JA, Bakken TE, Hodge RD, Chong P, de Frates R, Dai K, Maltzer Z, Nicovich PR, Keene CD, Silbergeld DL, Gwinn RP, Cobbs C, Ko AL, Ojemann JG, Koch C, Anastassiou CA, Lein ES, Ting JT