# Quantitative image analysis to determine the function of selected microglia-expressed genes in retinal development and regeneration

> **NIH NIH P20** · UNIVERSITY OF IDAHO · 2021 · $153,125

## Abstract

PROJECT SUMMARY
This Idaho INBRE Administrative Supplement will establish a collaboration between an INBRE-Developmental
Research Program Investigator, S Long, and an IDeA co-funded R01 principle investigator, D Mitchell. Dr.
Long is a computer scientist with expertise in machine learning and computer-assisted image analyses. Dr.
Mitchell is a cell biologist/immunologist with expertise in retinal development/regeneration. The project is titled,
‘Quantitative image analysis to determine the function of selected microglia-expressed genes in retinal
development and regeneration’. There are three Specific Aims:
 Specific Aim 1. Develop a collaboration between the two investigators to enhance both projects and
 increase undergraduate student research opportunities.
 Specific Aim 2: Determine the requirement for selected microglia-expressed genes in retinal
 development and regeneration.
 Specific Aim 3: Develop an image analysis pipeline to support zebrafish retinal analyses.
Microglia are the resident phagocytes in the central nervous system and engulf and degrade pathogens,
apoptotic cells, and debris. In addition, these cells may be involved in retinal degenerative disease, injury,
homeostasis, development, regeneration, and/or crosstalk with Müller glia. The Mitchell laboratory did
transcriptome analysis of microglia/macrophage populations isolated from regenerating zebrafish retinas. From
this, a shortlist of five microglia-expressed genes of interest are identified. Zebrafish mutant lines are, or will
be, established for each gene. Real-time live confocal imaging will be done on wild-type, heterozygous, and
homozygous zebrafish lines to record microglial dynamics in developing or regenerating retinas. The Long
laboratory will develop an image analysis pipeline to automate the interpretation of the large datasets from
these experiments. The analyses will quantify microglia numbers and morphology, cell death, Müller glial
proliferation, hypertrophy, migration of daughter cells, and expression of neural progenitor markers. The
machine learning techniques developed by the Long laboratory will relieve the bottleneck and potential biases
in analysis of large image datasets from the Mitchell laboratory and allow rapid testing of microglia gene
function. Strong preliminary data and investigator expertise indicate that this team will complete the proposed
work. The Long-Mitchell collaboration will provide a continuum of research opportunities for students by
delivering broadened student research experiences. Dr. Long has the expertise and the environment to propel
students into Data Science, a needed complement for modern biological research. Undergraduate students will
be supported in both the Long laboratory at the primarily undergraduate institution, Lewis-Clark State College,
and the Mitchell laboratory at the research-intensive, University of Idaho.

## Key facts

- **NIH application ID:** 10392268
- **Project number:** 3P20GM103408-21S3
- **Recipient organization:** UNIVERSITY OF IDAHO
- **Principal Investigator:** Carolyn Hovde Bohach
- **Activity code:** P20 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $153,125
- **Award type:** 3
- **Project period:** 2001-09-30 → 2024-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10392268

## Citation

> US National Institutes of Health, RePORTER application 10392268, Quantitative image analysis to determine the function of selected microglia-expressed genes in retinal development and regeneration (3P20GM103408-21S3). Retrieved via AI Analytics 2026-06-11 from https://api.ai-analytics.org/grant/nih/10392268. Licensed CC0.

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