# NeuroExM

> **NIH NIH R42** · MICROBRIGHTFIELD, LLC · 2022 · $994,964

## Abstract

Abstract
This project describes the development of NeuroExM™, a highly innovative system for performing
comprehensive spatial distribution analysis of populations of messenger RNAs (mRNAs) and proteins in tissue
processed for expansion microscopy (ExM)). The groundbreaking technological advantage of ExM, which was
recently developed by Dr. Edward S. Boyden (Dept. Biol. Engin., Media Lab and Dept. Brain Cognit. Sci., MIT,
Cambridge, MA) and colleagues, is the ability to isotropically expand tissue and increase the size of the biological
structures. This allows nanoscale-resolution, light-microscopic imaging of small objects that are too small to be
resolved without expansion due to the diffraction limit of light. Among other benefits, ExM allows those small
structures to be imaged with a wider range of microscopy techniques. Processing tissue for ExM also allows
repeated hybridization (for investigations of mRNAs) and/or repeated antibody staining (for investigations of
proteins) of the same tissue, combined with repeated microscopic imaging rounds. Each round yields adjacent,
high-magnification, single field-of-view image stacks, consisting of at least one morphology reference channel
showing neuronal sub-cellular structures (somas, axons, dendrites, dendritic spines, synapses) as well as one
or several info channels showing mRNAs and/or proteins. Comprehensive analysis of the spatial distribution of
populations of mRNAs and proteins in neurons in situ requires assembling the image stacks of all performed
rounds into a single, seamless and aligned, three-dimensional (3D) ExM image, which is high-dimensional and
can be several terabytes in size. However, this presents a number of computational challenges with respect to
microscopy image registration, segmentation and analysis. The game-changing innovation in NeuroExM is the
ability to perform all of these tasks without the need to have a computer scientist on staff to run the existing,
individual lab-based software scripts developed for each step of this kind of complex analysis. This is made
possible by implementing a number of significant technical innovations into NeuroExM. Based on pilot work
performed in collaboration with the Boyden lab during preparation of this proposal, we are convinced that
NeuroExM will make a significant impact on the field of neuroscience research. Specifically, the combination of
ExM and NeuroExM will enable substantial advancements in research studies focusing on alterations in the
spatial transcriptome and proteome of neurons associated with neurodevelopmental, neuropsychiatric,
neurodegenerative and neurological disorders as well as in aging research and drug development. Ultimately,
this will result in an improved basis for developing novel treatment strategies for a wide spectrum of complex
brain diseases. In Phase I we will demonstrate feasibility of this novel technology by developing prototype
software; work in Phase II will focus on creating the full functio...

## Key facts

- **NIH application ID:** 10495622
- **Project number:** 4R42MH124566-02
- **Recipient organization:** MICROBRIGHTFIELD, LLC
- **Principal Investigator:** JACOB R GLASER
- **Activity code:** R42 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $994,964
- **Award type:** 4N
- **Project period:** 2021-07-02 → 2025-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10495622

## Citation

> US National Institutes of Health, RePORTER application 10495622, NeuroExM (4R42MH124566-02). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10495622. Licensed CC0.

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