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Brian Long

Scientist III

teams /
Allenite

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 focus

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.

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featured publications

publication / 2024
Integrated multimodal cell atlas of Alzheimer's disease
Nature Neuroscience
publication / 2024
SEA-AD is a multimodal cellular atlas and resource for Alzheimer's disease
Nature Aging
publication / 2023
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
Nature
publication / 2023
Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex
Science (New York, N.Y.)
publication / 2023
Comparative transcriptomics reveals human-specific cortical features
Science (New York, N.Y.)
publication / 2023
Transcriptomic cytoarchitecture reveals principles of human neocortex organization
Science (New York, N.Y.)
publication / 2023
Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex
Science (New York, N.Y.)
publication / 2023
Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain
Scientific Reports
publication / 2023
Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex
eLife
publication / 2022
Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH
Science (New York, N.Y.)
publication / 2021
Comprehensive in situ mapping of human cortical transcriptomic cell types
Communications Biology
publication / 2021
Cell segmentation-free inference of cell types from in situ transcriptomics data
Nature Communications
publication / 2019
Conserved cell types with divergent features in human versus mouse cortex
Nature
publication / 2019
Classification of electrophysiological and morphological neuron types in the mouse visual cortex
Nature Neuroscience
publication / 2018
h-Channels Contribute to Divergent Intrinsic Membrane Properties of Supragranular Pyramidal Neurons in Human versus Mouse Cerebral Cortex
Neuron
publication / 2017
SmartScope2: Simultaneous Imaging and Reconstruction of Neuronal Morphology
Scientific Reports
publication / 2016
Bioimage Informatics for Big Data
Advances in Anatomy, Embryology, and Cell Biology
publication / 2016
TReMAP: Automatic 3D Neuron Reconstruction Based on Tracing, Reverse Mapping and Assembling of 2D Projections
Neuroinformatics
publication / 2015
3D Image-Guided Automatic Pipette Positioning for Single Cell Experiments in vivo
Scientific Reports
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