# Customized cleared tissue light-sheet fluorescence microscope for imaging large brain samples

> **NIH NIH S10** · UNIVERSITY OF CALIFORNIA-IRVINE · 2021 · $436,293

## Abstract

Project Summary/Abstract
 In response to RFA-MH-20-555, this Instrumentation grant application requests NIMH funds to
purchase a customized state-of-the-art light-sheet fluorescence microscope system from the 3i
Corporation (Intelligent Imaging Innovations, Inc.). The system has a unique custom-designed stage
for imaging large cleared brain samples from mice, rats and non-human primates. This instrumentation
will allow for high-speed, three-dimensional imaging of whole rodent brains and large non-human
primate and human brain samples at single cell resolution. Our team has the required expertise. We
have combined whole brain clearing and light sheet imaging to improve localization and quantification
of virally mapped neurons across the entire mouse brain. Available turnkey imaging systems sold by
LaVision/Miltenyi and Zeiss are not capable of large brain sample imaging. Our proposed 3i system
has large sample imaging capability, superior automated performance and superior analysis capability
based on hardware and software improvements developed by the 3i Corporation. Quantitative
comparisons of connection patterns will be achieved with our analysis pipeline using automated
quantification of brain wide fluorescent labeling, which allows for rapid quantification and analysis. We
foresee that this enhanced microscope will allow us to effectively perform 3-D large scale neural circuit
mapping in mouse, rat and monkey brain samples to better achieve the goals of our research projects
funded by 9 active NIMH grant awards and 14 other NIH grant awards at UCI. This proposed instrument
will be located at and managed by the core facility of the newly established UCI Center for Neural
Circuit Mapping. We request funds to purchase the customized light-sheet microscope system. The
UCI Center for Neural Circuit Mapping will ensure that the instrument is covered under full service
contract through the estimated 5 years of instrument lifetime. Institutional commitment of the UCI
School of Medicine will cover maintenance and software upgrade needs throughout the instrument
lifetime. This new imaging system will significantly enhance data acquisition for our ongoing NIH-
funded basic and translational research programs, which address the areas of high priority to NIMH.

## Key facts

- **NIH application ID:** 10103951
- **Project number:** 1S10MH124715-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA-IRVINE
- **Principal Investigator:** XIANGMIN XU
- **Activity code:** S10 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $436,293
- **Award type:** 1
- **Project period:** 2021-09-08 → 2022-09-07

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10103951

## Citation

> US National Institutes of Health, RePORTER application 10103951, Customized cleared tissue light-sheet fluorescence microscope for imaging large brain samples (1S10MH124715-01). Retrieved via AI Analytics 2026-05-28 from https://api.ai-analytics.org/grant/nih/10103951. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*