Project summary, Scalable technologies for brain-wide connectomics of
transcriptomic cell types: focus on brainstem
This proposal is to develop a scalable pipeline to combine high-resolution morphology and molecular
classification of individual neurons to define morpho-molecular cell types in the br
Funded Awards
The National Institutes of Health (NIH) BRAIN Initiative funds a wide-variety of research: toolmakers, trainees, individual labs testing new hypotheses, and large, team-based efforts aiming to catalyze neuroscience inquiry forward. Explore NIH BRAIN Initiative funded awards listed below. Click on the project title to learn more about it within NIH RePORTER.
To see more NIH-funded awards and associated publications, please visit the NIH RePORTER.
Title
Investigator(s)
Institution
Fiscal Year
Funding Opportunity #
Project #
TitleScalable technologies for brain-wide connectomics of transcriptomic cell types: focus on brainstem
Investigator
Jayaram Chandrashekar, Karel Svoboda
Institute
allen institute
Fiscal Year
Funding Opportunities Number
Project Number
TitleA 3D multimodal micron-scale human brain atlas bridging single cell data, neuropathology and neuroradiology
Investigator
Partha Pratim Mitra, Jiangyang Zhang
Institute
cold spring harbor laboratory
Fiscal Year
Funding Opportunities Number
Project Number
Digitized reference brains, also referred to as Common Coordinate Frameworks (CCFs), together
with superposed atlas annotations, are of central importance to neuroscience. They bear the
same relation to neuroscience as do reference genomes and genome annotations to cellular and
molecular biology.
TitleA cellular atlas of the primate and human basal ganglia
Investigator
Jason Daniel Buenrostro, Fei Chen, Gordon J Fishell, Evan Z Macosko
Institute
broad institute, inc.
Fiscal Year
Funding Opportunities Number
Project Number
PROJECT SUMMARY
The human basal ganglia (BG) are a collection of subcortical regions whose diverse, specialized cell types
influence motor control, emotional regulation, habit formation, and higher cognition.
TitleA regulome and transcriptome atlas of fetal and adult human neurogenesis
Investigator
Long Cai, Patrick R Hof, Panagiotis Roussos, Nenad Sestan, Guo-Cheng Yuan
Institute
icahn school of medicine at mount sinai
Fiscal Year
Funding Opportunities Number
Project Number
PROJECT SUMMARY
Dynamic changes in the spatiotemporal patterning of transcription factor binding on cis-regulatory DNA
elements drives the developmental transition of cell lineages during neurogenesis.
TitleA scalable mass spectrometry platform for proteome mapping of brain tissues
Investigator
Tujin Shi
Institute
battelle pacific northwest laboratories
Fiscal Year
Funding Opportunities Number
Project Number
ABSTRACT
The brain is the most complex organ in the mammalian body. Bulk analysis obscures heterogeneity of cell
types present even in the smallest brain regions.
TitleCell type atlasing of whole human brains using HOLiS: an optimized pipeline for staining, clearing, imaging, and analysis
Investigator
Elizabeth M. C. Hillman, Pavel Osten, Zhuhao Wu
Institute
columbia university health sciences
Fiscal Year
Funding Opportunities Number
Project Number
Project Summary (Abstract)
Gaining a comprehensive understanding of brain-wide cellular organization in the human brain has long been
recognized as a critical foundation for understanding complex brain functions, including who we are as humans.
In this project we propose to take on this challenge an
TitleComprehensive and multi-resolution mapping of cell morphology and wiring through X-ray holographic nano-tomography
Investigator
Alexandra Teodora Joita Pacureanu, Wei-Chung Allen Lee
Institute
harvard medical school
Fiscal Year
Funding Opportunities Number
Project Number
Project Summary / Abstract
A fundamental goal in neuroscience is understanding how information is processed in neuronal circuits.
However, the immense complexity of most brain networks has been a significant barrier to progress.
TitleDevelopment of a high throughput system for molecular imaging of different cell types in mouse brain tissues
Investigator
Gaurav Chopra, Julia Laskin
Institute
purdue university
Fiscal Year
Funding Opportunities Number
Project Number
Development of a high throughput system for molecular imaging of different cell types in mouse brain
tissues
Mass spectrometry imaging (MSI) is a powerful tool for developing detailed molecular maps of biological
tissues with high specificity and sensitivity.
TitleHigh-content single-cell epigenetic technologies scalable to the human brain
Investigator
Andrew Adey
Institute
oregon health & science university
Fiscal Year
Funding Opportunities Number
Project Number
PROJECT ABSTRACT
To meet the goal of the BRAIN Initiative Cell Census Network to catalogue and produce molecular profiles of
every cell type in the human brain; order-of-magnitude improvements in single-cell assay throughput and
coverage are required.
TitleHighly scalable and sensitive spatial transcriptomic and epigenomic sequencing of brain tissues from human and non-human primate
Investigator
Rong Fan, Nenad Sestan
Institute
yale university
Fiscal Year
Funding Opportunities Number
Project Number
SUMMARY
The human nervous system is possibly the most complex biological tissue, organized into multiple functionally
distinct regions and comprised of over 200 billion neural and non-neural cells, requiring novel scalable tools to
profile cell types and relationships in the tissue context with high
TitleNext-generation MORF Mice for Scalable Brainwide Morphological Mapping and Genetic Perturbation of Single Neurons
Investigator
Hong-Wei Dong, Xiangdong William Yang
Institute
university of california los angeles
Fiscal Year
Funding Opportunities Number
Project Number
PROJECT SUMMARY
A major challenge in studying the mammalian brain is to characterize the integrative properties of
individual neurons, such as molecular profiles, complete morphology (dendrites, axons, synapses),
connectivity, and activity; furthermore, this must be done at a scale that is commensu
TitlePlatform technologies for scalable highly multiplexed proteomic phenotyping of the brain
Investigator
Kwanghun Chung, Hong-Wei Dong, Matthew P Frosch, Guoping Feng, Peng Yin
Institute
harvard university
Fiscal Year
Funding Opportunities Number
Project Number
The complexity of the mammalian brain is unparalleled by any other organs, and understanding its cellular
composition and their brain-wide organization is essential to understand the brain functions and dysfunctions.
Extensive efforts have been made toward mapping brain cells through various lenses,
TitleScalable 3D molecular imaging and data analysis for cell census generation
Investigator
Steve Presse, Douglas Shepherd
Institute
arizona state university-tempe campus
Fiscal Year
Funding Opportunities Number
Project Number
PROJECT SUMMARY
This project is a collaboration across two universities and multiple scientific disciplines to develop new scalable
3D molecular imaging and analysis approaches for cell type identification within human brain tissue.
TitleScalable integration of cell types and connectivity in the motor cortex of rodents and non-human primates
Investigator
Forrest Christie Collman, Nuno Macarico Da Costa, R Clay Reid
Institute
allen institute
Fiscal Year
Funding Opportunities Number
Project Number
Project Summary
The BICCN has recently completed a broad survey of the cellular components of motor cortex, including
transcriptomic profiling, patch-seq, multiplexed FISH, inter-areal connectivity, and single neuron morphology.
Missing from this view is a detailed picture of how individual neurons
TitleUltra-high Throughout Single Cell Multi-omic Analysis of Histone Modifications and Transcriptome in Mouse and Human Brains
Investigator
M Margarita Behrens, Bing Ren
Institute
university of california, san diego
Fiscal Year
Funding Opportunities Number
Project Number
Histone modification carries rich epigenetic information that constitutes a mechanism of cellular memory.
Single cell analysis of histone modification in conjunction with transcriptome could help uncover this critical
layer of cellular memory and lead to better definition of cell types and states in
TitleA high-resolution molecular and lineage atlas of the mouse brain using Slide-seq
Investigator
Fei Chen, Evan Z Macosko
Institute
broad institute, inc.
Fiscal Year
Funding Opportunities Number
Project Number
PROJECT SUMMARY
The mouse brain is composed of thousands of highly specialized cell types, distributed across hundreds of
anatomical regions.
TitleDevelopment of a scalable strategy for reconstructing cell-type determined connectome of the mammalian brain
Investigator
Dawen Cai, Meng Cui, Yan Yan, Peng Yin
Institute
university of michigan at ann arbor
Fiscal Year
Funding Opportunities Number
Project Number
Abstract
In order to fully understand the structural substrates underlying the brain function, it is central to curate
multiple attributes of the same neurons.
TitleDevelopmental cell census of human and non-human primate brain
Investigator
Nenad Sestan
Institute
yale university
Fiscal Year
Funding Opportunities Number
Project Number
ABSTRACT
The human brain is a highly complex biological tissue organized into hundreds of regions composed of a myriad
of cell types with distinct molecular, morphological, and physiological properties.
TitleEstablishing Common Coordinate Framework for Quantitative Cell Census in Developing Mouse Brains
Investigator
James C Gee, Yongsoo Kim, Lydia Lup-Ming Ng
Institute
pennsylvania state univ hershey med ctr
Fiscal Year
Funding Opportunities Number
Project Number
Abstract
Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing
complex 3D structures across time.
TitleMultiplexed Nanoscale Protein Mapping Through Expansion Microscopy and Immuno-SABER
Investigator
Edward S. Boyden, Peng Yin
Institute
massachusetts institute of technology
Fiscal Year
Funding Opportunities Number
Project Number
Tools for surveying brain cell types and circuits must be scalable, both in the number of molecular targets
visualizable at once, and in the size of the tissues that can be assessed.