How to open .OCT file in matlab

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.

https://www.dropbox.com/s/wu1gmfzt4o0z850/Z506_OS_V_1x1_0_0000002.OCT?dl=0

If anyone knows how to open this file type in Matlab, please help! Thanks!!!

[Image Analyst]

I've never heard of ocular coherence tomography. Do you really mean optical coherence tomography?

[Delores Davis]

You are correct.

[Walter Roberson]

When I went looking last night, all I could find was that the file might be a DICOM file.

Answer 1

[Image Analyst]

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.

[Walter Roberson]

Bioptigen has been bought by Leica as the end of May 2015. Leica has started carrying the information about the devices on their web site but it is also still on Bioptigen's site. But both web sites are terrible at making documentation available until you pay. Even then the only documentation described as being available is their user manual. By poking around a bit I was able to find a couple of places such as scribd that have the C2300 User Manual available; unfortunately it contains no information about the file format. I found further information that talked about Bioptigen having a API whose abbreviation is IVVC, but the documentation I could find about that said nothing about the file format of the OCT files.

DICOM file format seems like the best bet.

[Image Analyst]

The web site may not have the information. Best to check with your customer service representative/sales engineer. It's their job to make you a satisfied customer. You won't know unless you ask. Be assertive.

[Delores Davis]

Great advice. If they have a solution I will post it here in case someone else faces a similar dilemma.

Thanks for your response.

[Kevin Chng]

Hi any latest solution?

[Walter Roberson]

See https://www.mathworks.com/matlabcentral/answers/242474-how-to-open-oct-file-in-matlab#answer_217904

[feng]

hello, would you please share me with the reading code , it seems that the code in the github has been disappeared. Thank you!

[Image Analyst]

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.

Answer 2

[Star Strider]

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.

[Delores Davis]

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 :(

Answer 3

[Tom Wright]

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 .

[Walter Roberson]

https://github.com/tomwright01/iowa_oct_analysis

[feng]

There is already no code on github to read OCT extension files. Do you have a backup to share with me?

[Walter Roberson]

Look in https://zenodo.org/record/50230/files/iowa_oct_analysis-1.0.0.zip?download=1

[feng]

Thanks!!!