Automated Cell Counting of OCT Scans

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Mohammad Mehdi 2023-11-16

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编辑： Mohammad Mehdi 2023-11-17

Greetings eveyone,

I want to measure the cell count on eye scans obtained via OCT scan, below is my own eye scan and you can see the retinal cells as a white trianglur particles in periphery.

Can somebody please help me and tell me wether it is possible to have a code so I can measure and extract these cells from retinal scan or not?

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Image Analyst 2023-11-17

I don't see any white triangles in the periphery of the image or anywhere else. I see snake-like white streaks and smaller irregularly-shaped white blobs. Please outline in red the triangles that you want to segment out.

Mohammad Mehdi 2023-11-17

You are right, I want to measute those snake like and irregular shaped white particles.I have outlines cells in square and circle (1 in square and 2 in circle). my aim is to extract those cells from background and then count them (red cells in figure 2).

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Answer 1

Pratyush 2023-11-17

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Hi Mohammad,

I understand that you want to measure the cell count on eye scans.

It is possible to write a MATLAB code to measure and extract these cells from an OCT retinal scan. The MATLAB Image Processing Toolbox provides a comprehensive set of reference-standard algorithms and workflow apps for image processing.

Here is a general idea of how you might approach this:

Use the "imread" function to read the image into MATLAB.
Preprocess the image which may involve converting the image to grayscale using the "rgd2gray" function, or applying a median filter to reduce noise.
You can use edge detection functions such as "edge" or "imbinarize" to segment the image. This will help to isolate the cells.
After segmentation, you can use the "bwconncomp" function to find connected components (which should correspond to cells). The "regionprops" function can provide useful measurements for these components.
If the cells are all roughly the same size, you can filter out noise by only counting components of a certain size.

Hope this helps.

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Mohammad Mehdi 2023-11-17

编辑：Mohammad Mehdi 2023-11-17

Thank you very much for prompt responce, I am pretty new with MATLAB, can I ask you for your help if I faced any problem during counting process? Also I now the range of cell size, but when I want to use thresholding, the process does not include all the cells included in the picture and some of them excluded in the process.

Thanks,

Mohammad

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