Retinal and Lens Analysis MATLAB Code for Zebrafish Research

Two MATLAB scripts provide semi-automated analysis methods for retinal imaging studies. The first measures retinal ganglion cell layer and whole retina thickness via user-guided ROI selection and intensity-profile landmarking. The second quantifies pixel intensity variability in the adult zebrafish lens core by calculating standard deviation and full width at half maximum.

Use Cases

• Implement semi-automated retinal ganglion cell layer thickness measurement using user-guided ROI selection and intensity-profile landmark identification.
• Analyze whole retina thickness from retinal images with a method combining anatomical verification and automated segmentation steps.
• Quantify pixel intensity variability in the core region of the adult zebrafish lens by calculating the standard deviation of pixel intensity distribution.
• Perform texture analysis on OCT-derived or grayscale lens images by measuring the full width at half maximum of the pixel intensity profile.
• Conduct anatomically informed thickness measurements for retinal imaging research where manual verification is preferred over fully automated processes.

Strengths

• Code is designed for research use in retinal imaging studies, providing a specific application context.
• Analysis methods are semi-automated, combining user guidance with algorithmic steps for consistency.
• The second script provides concrete quantitative outputs: standard deviation and full width at half maximum of pixel intensity.

Limitations

• The dataset consists of analysis code, not a pre-processed tabular or image dataset, limiting immediate use for model training.
• Sample data and expected output formats are unavailable, requiring users to supply their own compatible image data.
• The methodology relies on minimal user input for ROI placement, which may introduce variability between operators.

Provenance

Source

Harvard Dataverse, authored by Nima Tabatabaei.

Collection Method

MATLAB scripts providing semi-automated analysis workflows for retinal and lens images.

Freshness

Last updated on 2026-01-19.