How to open .OCT file in matlab
Show older comments
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!!!
3 Comments
Image Analyst
on 11 Sep 2015
I've never heard of ocular coherence tomography. Do you really mean optical coherence tomography?
Delores Davis
on 12 Sep 2015
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.
Accepted Answer
Image Analyst
on 12 Sep 2015
0 votes
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.
7 Comments
Walter Roberson
on 13 Sep 2015
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
on 13 Sep 2015
Edited: Walter Roberson
on 13 Sep 2015
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
on 13 Sep 2015
Kevin Chng
on 17 Sep 2018
Hi any latest solution?
feng
on 3 Apr 2019
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
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.
More Answers (2)
Star Strider
on 12 Sep 2015
1 vote
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.
1 Comment
Delores Davis
on 13 Sep 2015
Tom Wright
on 14 Apr 2016
1 vote
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 .
4 Comments
feng
on 4 Apr 2019
There is already no code on github to read OCT extension files. Do you have a backup to share with me?
Walter Roberson
on 4 Apr 2019
feng
on 4 Apr 2019
Thanks!!!
Categories
Find more on Medical Physics in Help Center and File Exchange
Community Treasure Hunt
Find the treasures in MATLAB Central and discover how the community can help you!
Start Hunting!
