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Updated: Aug 8, 2025

Using Optical Coherence Tomography and Optokinetic Response As Structural and Functional Visual System Readouts in Mice and Rats

Using Optical Coherence Tomography and Optokinetic Response As Structural and Functional Visual System Readouts in Mice and Rats

Published on: January 10, 2019

Open-source statistical and data processing tools for wide-field optical imaging data in mice.

Lindsey M Brier¹, Joseph P Culver^1,2,3,4

¹Washington University School of Medicine, Department of Radiology, St. Louis, Missouri, United States.

|March 6, 2023

Summary

This summary is machine-generated.

Researchers developed an open-source MATLAB toolbox for processing wide-field optical imaging (WOI) data. This tool enables analysis of hemodynamic and calcium recordings in animal models, aiding disease research.

Keywords:

calcium imaging data processing optical imaging wide-field imaging

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Area of Science:

Neuroscience
Optical Imaging
Data Analysis

Background:

Wide-field optical imaging (WOI) provides concurrent hemodynamic and cell-specific calcium recordings across the entire cerebral cortex in animal models.
WOI is valuable for studying various diseases in mouse models, complementing human functional magnetic resonance imaging (fMRI).
A lack of open-source, user-friendly processing and statistical analysis toolboxes for WOI data limits its broader application.

Purpose of the Study:

To develop a MATLAB toolbox for processing WOI data.
To integrate techniques from multiple WOI research groups and fMRI analysis methods.
To provide an open-source, user-friendly platform for WOI data analysis.

Main Methods:

Assembled a MATLAB toolbox available on GitHub with data analysis packages.
Adapted a statistical approach commonly used in fMRI for WOI data.
Demonstrated the toolbox's utility by analyzing a mouse model of stroke and mapping sensory stimulus responses.

Main Results:

The processing toolbox and statistical methods identified a somatosensory deficit 3 days post-photothrombotic stroke.
The framework successfully localized sensory stimulus-evoked brain activity.
The study showcases the ability to detect established deficits and map neural activations.

Conclusions:

The developed MATLAB toolbox offers an open-source, user-friendly solution for processing WOI data.
It provides essential statistical methods applicable to diverse biological questions investigated using WOI.
This resource facilitates more accessible and robust analysis of WOI data in neuroscience research.