# Project 1:  Atlas

> **NIH NIH U19** · HARVARD UNIVERSITY · 2021 · $723,061

## Abstract

Project 1 - A comprehensive atlas of the larval zebrafish brain - Abstract
Anatomical information about the brain, such as the identity of brain regions, the molecular and morphological makeup of
individual neurons and their connectivity arrangements, are all critical information for formulating hypotheses of neural
circuit function. While much anatomical data concerning the zebrafish brain are being generated by the community, the
field lacks a central repository which is capable of ingesting, integrating and quantitatively describing these data. To meet
this need, we propose to generate a multilayered, multimodal, and multiscale atlas of the larval zebrafish brain. This
project will provide the necessary infrastructure to import data from all the team members as well as the international
community, integrate these data into a common reference brain, and make it publicly available and easily accessible
online. This Atlas will exist at 3 levels of resolution: 1) The macro-scale, where we will define and describe the known
anatomical regions of the brain, and provide new tools for regional annotation and 3D visualization. 2) The micro-scale
will aggregate diverse datasets describing individual neurons in the brain. These will include: molecular makeup (through
transgenic and antigenic stains - neurotransmitter, neuropeptide, neuromodulator, gene expression, etc), functional
properties (through calcium and perhaps voltage imaging), morphology (through single cell imaging/tracing, and EM
reconstructions) and connectivity (through functional connectivity, viral tracing, patch clamp recordings and nano-scale
EM data). Finally, 3) The nano-scale, which will aggregate whole-brain serial EM volumes from multiple individual
larvae. It will provide the infrastructure for collaborative nano-scale annotations, such as identified synaptic connections
and high-resolution morphology.
Collectively, this Atlas will be a foundational resource for zebrafish neuroscientists, and will be an invaluable tool for
creating and constraining biologically plausible neural circuit models, including the Multiscale Virtual Fish.

## Key facts

- **NIH application ID:** 10241482
- **Project number:** 5U19NS104653-05
- **Recipient organization:** HARVARD UNIVERSITY
- **Principal Investigator:** Jeff W Lichtman
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $723,061
- **Award type:** 5
- **Project period:** 2017-09-25 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10241482

## Citation

> US National Institutes of Health, RePORTER application 10241482, Project 1:  Atlas (5U19NS104653-05). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10241482. Licensed CC0.

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