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Graph-based segmentation of retinal layers in oct images

version 1.1.0.0 (3.07 KB) by pangyuteng
Demonstration of graph-based segmentation of retinal layers in an optical coherence tomography image

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Updated 16 Mar 2017

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This script demonstrates how graph theory can be used to segment retinal layers in optical coherence tomography images.
USAGE:
run the script by pressing F5.
I am working on a more comprehensive open source software package for computer-aided segmentation of retinal layers in optical coherence tomography images, which currently includes 1. automated segmentation of 6 reitnal layers and 2. GUI for examination and manual correction of the automated segmentation. It can be downloaded at my github page. http://pangyuteng.github.io/caserel
CITE AS:
Chiu, Stephanie J., et al. "Automatic segmentation of seven retinal layers in SDOCT images congruent with expert manual segmentation." Optics express 18.18 (2010): 19413-19428.
Teng, Pang-yu. (2013). Caserel - An Open Source Software for Computer-aided Segmentation of Retinal Layers in Optical Coherence Tomography Images. Zenodo. 10.5281/zenodo.17893
http://dx.doi.org/10.5281/zenodo.17893

Cite As

pangyuteng (2019). Graph-based segmentation of retinal layers in oct images (https://www.mathworks.com/matlabcentral/fileexchange/43518-graph-based-segmentation-of-retinal-layers-in-oct-images), MATLAB Central File Exchange. Retrieved .

Comments and Ratings (7)

How can we segment the rest of the layers?Like choroid, it's five layer, retina, it's 10 layers and Chorioscleral interface the CSI.

Neha Gour

I am applying the code given at http://pangyuteng.github.io/caserel for my own image but finding this error. kindly tell me why.

**Attempt to reference field of non-structure array.

Error in getRetinalLayersCore (line 114)
indPathX = find(rPaths(strcmp('ilm',{rPaths.name})).pathY==k);

Error in getRetinalLayers (line 129)
[retinalLayers, ~] = getRetinalLayersCore(retinalLayerSegmentationOrder{layerInd},imgNew,params,retinalLayers);

Error in getRetinalLayersExample (line 107)
[retinalLayers, params] = getRetinalLayers(img);**

wang wang

rong

pangyuteng

@Bashir Isa Dodo, this code does not support opening of zip files, try unzipping the zip file and using the files within the zip file.

Hello, I tried running the code, by entering the folder path of the images, but I always get this error
>> updatedGTherorySimplified
Error using load
Unable to read file 'D:\Matlab TrialsCMF_v1.0.zip'. No such file or directory.

Error in updatedGTherorySimplified (line 35)
load([folderPath imageDir(1).name]);
and I am sure the images are in the directory, I tried copying the images to separate directory, and still no change
Hope to get a feedback thanks

Updates

1.1.0.0

updated summary

1.1.0.0

edit grammer.

1.1.0.0

added citation

1.1.0.0

+minor revision in the description section.
+added requirement: curve fitting toolbox.

MATLAB Release Compatibility
Created with R2012b
Compatible with any release
Platform Compatibility
Windows macOS Linux