U01NS142100
Cooperative Agreement
Overview
Grant Description
Brain Connects: Light microscopy for cell-type specific mesoscale to nanoscale dense connectomics - Project summary
In recent years, there has been remarkable progress in mapping the connectivity of cell types in the brain.
We now have complete connectomes for insects and worms, and in mammals, we can map synapse connectivity across millimeter-scale regions.
As the Brain Connects program aims to extend this capability to entire mammalian brains across multiple scales, it is essential to link these connectivity breakthroughs with the brain's molecular architecture.
Until now, the connection between fine connectivity obtained through electron microscopy (EM) and molecular cell types has been established through indirect methods such as PATCH-SEQ.
Recent developments in light-microscopy-based connectomics (LICONN) have shown promising results for dense connectivity mapping.
LICONN has the potential to register connectomics results to molecular subclasses at the single-neuron level and at scale.
This project leverages LICONN and our expertise in creating and analyzing EM data to address three main objectives of the Brain Connects program.
The first objective is to demonstrate that LICONN can be used to create molecularly informed cell type connectivity patterns by integrating its results with large-scale EM data.
This approach can provide a powerful tool to establish a ground truth link between molecular and connectivity types across datasets planned with the Connects portfolio.
The second objective is to combine light-microscopy-based connectomics with mesoscale expansion microscopy in a multiscale fashion.
This integration allows mapping microscale connectivity in gray matter and linking it with white matter connections between brain regions.
The third objective is to test the feasibility of expanding LICONN to larger volumes and scale nanoscale expansion microscopy.
The goal is to demonstrate that regions larger than a cubic millimeter can be expanded 16 times to achieve LICONN resolution, which is about ten times greater than the current state-of-the-art.
In recent years, there has been remarkable progress in mapping the connectivity of cell types in the brain.
We now have complete connectomes for insects and worms, and in mammals, we can map synapse connectivity across millimeter-scale regions.
As the Brain Connects program aims to extend this capability to entire mammalian brains across multiple scales, it is essential to link these connectivity breakthroughs with the brain's molecular architecture.
Until now, the connection between fine connectivity obtained through electron microscopy (EM) and molecular cell types has been established through indirect methods such as PATCH-SEQ.
Recent developments in light-microscopy-based connectomics (LICONN) have shown promising results for dense connectivity mapping.
LICONN has the potential to register connectomics results to molecular subclasses at the single-neuron level and at scale.
This project leverages LICONN and our expertise in creating and analyzing EM data to address three main objectives of the Brain Connects program.
The first objective is to demonstrate that LICONN can be used to create molecularly informed cell type connectivity patterns by integrating its results with large-scale EM data.
This approach can provide a powerful tool to establish a ground truth link between molecular and connectivity types across datasets planned with the Connects portfolio.
The second objective is to combine light-microscopy-based connectomics with mesoscale expansion microscopy in a multiscale fashion.
This integration allows mapping microscale connectivity in gray matter and linking it with white matter connections between brain regions.
The third objective is to test the feasibility of expanding LICONN to larger volumes and scale nanoscale expansion microscopy.
The goal is to demonstrate that regions larger than a cubic millimeter can be expanded 16 times to achieve LICONN resolution, which is about ten times greater than the current state-of-the-art.
Awardee
Funding Goals
NOT APPLICABLE
Grant Program (CFDA)
Awarding / Funding Agency
Place of Performance
Seattle,
Washington
981094307
United States
Geographic Scope
Single Zip Code
Related Opportunity
Analysis Notes
Amendment Since initial award the total obligations have increased 130% from $1,855,816 to $4,260,011.
Allen Institute was awarded
Brain Connects: LICONN for Cell-Type Connectomics
Cooperative Agreement U01NS142100
worth $4,260,011
from the National Institute of Neurological Disorders and Stroke in August 2025 with work to be completed primarily in Seattle Washington United States.
The grant
has a duration of 2 years 9 months and
was awarded through assistance program 93.372 21st Century Cures Act - Brain Research through Advancing Innovative Neurotechnologies.
The Cooperative Agreement was awarded through grant opportunity BRAIN Initiative Connectivity across Scales (BRAIN CONNECTS): Specialized Projects for Scalable Technologies (U01 Clinical Trial Not Allowed).
Status
(Ongoing)
Last Modified 6/22/26
Period of Performance
8/11/25
Start Date
5/31/28
End Date
Funding Split
$4.3M
Federal Obligation
$0.0
Non-Federal Obligation
$4.3M
Total Obligated
Activity Timeline
Transaction History
Modifications to U01NS142100
Additional Detail
Award ID FAIN
U01NS142100
SAI Number
U01NS142100-3569055388
Award ID URI
SAI UNAVAILABLE
Awardee Classifications
Nonprofit With 501(c)(3) IRS Status (Other Than An Institution Of Higher Education)
Awarding Office
75NQ00 NIH National Institute of Neurological Disorders and Stroke
Funding Office
75NQ00 NIH National Institute of Neurological Disorders and Stroke
Awardee UEI
NFHEUCKBFMU4
Awardee CAGE
35DM7
Performance District
WA-07
Senators
Maria Cantwell
Patty Murray
Patty Murray
Modified: 6/22/26