Automated Cell Counting of OCT Scans

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?

[Image Analyst]

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]

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).

Answer 1

[Pratyush]

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.

[Mohammad Mehdi]

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