# Development of a 3D-VR Structural Analysis Software Ecosystem for SCI/D Research

> **NIH VA I21** · VA CONNECTICUT HEALTHCARE SYSTEM · 2023 · —

## Abstract

The goal of our proposed Small Project is: 1) to develop a more efficient, accessible, and accurate 3D
structural analysis workflow using virtual reality (VR) and the Neurodata Without Borders (NWB) data standard,
and 2) to implement this software/hardware ecosystem into our current SCI/D research program in neuropathic
pain and spasticity. By developing this 3D-VR Structural Analysis Software Ecosystem (3D-VR SASE), we will
powerfully expand our Center's experimental reach and capacity for translational studies in the future. We will
carry out experiments in two Specific Aims to address the goal of this Project.
In Specific Aim 1, we will establish a VR-based 3D structural analysis software environment (3D-VR SASE)
that will expand our ability to investigate the dynamic changes in abnormal dendritic spine plasticity associated
SCI/D. Our VA Center already operates imaging systems that have allowed us to perform a multitude of
anatomical studies of the injured CNS. However, our project trajectory has now severely outpaced the capacity
of these systems, and no commercial tools for our needs are available or in-development. Thus, to expand the
capabilities of our current hardware, we will develop a faster, more accurate reconstruction/visualization
hardware/software ecosystem with the established NWB data standard solution in our Center.
In Specific Aim 2, we will validate the 3D-VR SASE platform. We demonstrate its utility using publicly available
neuronal datasets and perform a study of dendritic spines using spinal cord tissue of transgenic reporter mice.
We will perform two experimental studies with the analysis platform. First, we will reconstruct neuronal image
stacks from the DIADEM challenge, which is a public neuroscience competition designed to encourage the
development of algorithmic methods for improved neuron morphological tracing. The DIADEM challenge
provides high-quality light-microscopy images with established specifications that allow us to score our VR
traces using metrics of accuracy against a “gold standard” trace. Second, we will perform a retrospective study
of dendritic spines in wide-dynamic range (WDR) dorsal horn neurons in post-mortem spinal tissue collected
from our previous study. WDR neurons have been of interest because they project fibers in the ascending
spinothalamic tract, a major pain pathway to the thalamic VPL nociceptive processing region. Additionally,
dendritic spine dysgenesis in WDR neurons has been associated with neuropathic pain.
In summary, this project will develop the 3D-VR SASE workflow that increases analytical speed, 3D
visualization and neuroanatomical reconstruction, and implements the NWB data standard. The flexibility and
broad utility of the 3D-VR SASE platform will facilitate our current SCI/D research program as well as the study
of neuroanatomical pathologies in other chronic diseases that are also prevalent among US Veterans, e.g.,
Alzheimer's disease, PTSD, MS, TBI. Overall, we expect t...

## Key facts

- **NIH application ID:** 10615864
- **Project number:** 5I21RX003728-02
- **Recipient organization:** VA CONNECTICUT HEALTHCARE SYSTEM
- **Principal Investigator:** Andrew Michael Tan
- **Activity code:** I21 (R01, R21, SBIR, etc.)
- **Funding institute:** VA
- **Fiscal year:** 2023
- **Award amount:** —
- **Award type:** 5
- **Project period:** 2022-07-01 → 2024-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10615864

## Citation

> US National Institutes of Health, RePORTER application 10615864, Development of a 3D-VR Structural Analysis Software Ecosystem for SCI/D Research (5I21RX003728-02). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10615864. Licensed CC0.

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