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mandorra / OCT-Reader

This repository aims to read/write RAW exported OCTs from Heidelberg Engineering machines in a Python/Numpy environment.
MIT License
6 stars 2 forks source link

Read Cube Images #1

Open gaw89 opened 6 years ago

gaw89 commented 6 years ago

This is fantastic for reading the SLO images and the headers. Do you have any idea how to extract all the slices of the cube?

mandorra commented 6 years ago

Thanks for your interest. I started this by reverse engineering the binaries of Spectralis. However, I put the project aside a while ago because I was lacking time on developing this OCT interface. That said, it shouldn't be hard to extract the A / B Scans. In the header we know how many slices we have so I guess we should try to guess the size of each slice and make a loop to extract each of them in a similar way I extracted the SLO image.

gaw89 commented 6 years ago

Thanks for the quick response! I actually found an OCT reader here that's written in Matlab. I'm trying to translate the Matlab code to Python now - though I'm not terribly familiar with Matlab. If I can figure it out, I'll submit a PR here.

mandorra commented 6 years ago

That sounds great it would save a lot of time to identify the way it's storing the B-Scans and their location on the SLO image. I use Matlab/Octave eventually, but I'm definitely more comfortable in Python that's why I started to develop this.

coin-mine commented 3 years ago

Many thanks for sharing the tool! It works very well for the overall header and the SLO image. Do you have any updates on the B-Scan extraction? @gaw89 Did you manage to translate the Matlab code?

gaw89 commented 3 years ago

@coin-mine I abandoned that project before I really went any further with the Matlab stuff. Good luck!

mandorra commented 3 years ago

I abandoned the project long ago too, but good luck hacking into the raw binaries!