How to open .OCT file in matlab

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Delores Davis
Delores Davis on 11 Sep 2015
Commented: feng on 4 Apr 2019
I am analyzing optical coherence tomography files from a Bioptigen instrument. Here is a Dropbox link to a sample file which was too large to attach here (an image, with a file extension of .OCT, but not Octave). I want to measure the thicknesses of the retinal layers, but the proprietary software is hard to use and is licensed to only one computer (in my PI's office), so I want to use Matlab.
If anyone knows how to open this file type in Matlab, please help! Thanks!!!
Walter Roberson
Walter Roberson on 12 Sep 2015
When I went looking last night, all I could find was that the file might be a DICOM file.

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Accepted Answer

Image Analyst
Image Analyst on 12 Sep 2015
Ask Bioptigen for the format. If it's dicom, see if you can use dicomread(), otherwise see if they have some way to export the image to some standard format such as PNG, or else see if they'll give you the format specification so you can write your own reader for it.
Image Analyst
Image Analyst on 3 Apr 2019
You should comment to Tom Wright (below), not Me or Walter. It's his code. You can also try to contact him via his Answers profile.

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More Answers (2)

Star Strider
Star Strider on 12 Sep 2015
This is definitely not my area of expertise, so my ability to help is limited. However a PubMed search found: Image Processing in Optical Coherence Tomography: Using Matlab, Chapter 2 ACQUISITION OF IMAGE DATA. See if that discussion (including code) does what you want.
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Delores Davis
Delores Davis on 13 Sep 2015
I downloaded that book about an hour before I asked my question. I couldn't make Matlab open my image, which is why I asked. I like their work so much that I want to emulate it in my project.
I could use the company's licensed software...I just find it boring :(

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Tom Wright
Tom Wright on 14 Apr 2016
As suggested Bioptigen will supply matlab code for reading the .OCT file format. It's not Dicom. Alternately I have re-implemented their code in python available here .

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