Matlab_Code_Retinalayer_Analysis

The first MATLAB script provides a semi-automated method for measuring **retinal ganglion cell (RGC) layer thickness** and **whole retina thickness** from retinal images. The workflow combines user-guided region-of-interest (ROI) selection with intensity-profile–based landmark identification to enable anatomically informed thickness measurements. The script is intended for research use in retinal imaging studies where manual anatomical verification is preferred over fully automated segmentation. The second MATLAB code performs intensity-based texture analysis of the **core region of the adult zebrafish lens** from OCT-derived or grayscale image data. The primary purpose of the script is to **quantify pixel intensity variability** within the lens core by measuring the **standard deviation (SD)** and the **full width at half maximum (FWHM)** of the pixel intensity distribution. The analysis is semi-automated and relies on minimal user input to ensure consistent anatomical placement of the region of interest (ROI) across samples. If you use this code in your research, please cite the following paper: “Pannexin 1a Regulates Visual System Development and Ocular Integrity in Zebrafish” Shiva Sabour, Sarah Houshangi-Tabrizi, Georg S. O. Zoidl, Georg R. Zoidl, Nima Tabatabaei “iScience( Cell Press) Journal”首个MATLAB脚本提供了一种半自动方法，可从视网膜图像中测量**视网膜神经节细胞（retinal ganglion cell, RGC）层厚度**与**全视网膜厚度**。该工作流程将用户引导的感兴趣区域（region-of-interest, ROI）选取与基于强度剖面的地标识别相结合，以此实现具备解剖学参考依据的厚度测量。本脚本适用于更倾向于手动解剖验证而非全自动分割的视网膜成像研究场景。 第二款MATLAB代码可针对光学相干断层扫描（optical coherence tomography, OCT）衍生图像或灰度图像，对**成年斑马鱼晶状体核心区域**开展基于强度的纹理分析。该脚本的核心功能为：通过测量像素强度分布的**标准差（standard deviation, SD）**与**半高全宽（full width at half maximum, FWHM）**，量化晶状体核心区域内的像素强度变异性。本分析流程为半自动模式，仅需少量用户输入，即可确保不同样本间感兴趣区域（ROI）的解剖学定位一致性。 若您在研究中使用本代码，请引用以下论文：《泛连接蛋白1a调控斑马鱼视觉系统发育与眼部完整性》，作者：Shiva Sabour、Sarah Houshangi-Tabrizi、Georg S. O. Zoidl、Georg R. Zoidl、Nima Tabatabaei，发表于《iScience（Cell Press旗下期刊）》。