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marksgraham / OCT-Converter

Tools for extracting the raw optical coherence tomography (OCT) and fundus data from proprietary file formats.
https://pypi.org/project/oct-converter/
MIT License
193 stars 70 forks source link

Exporting Contours (segmentation data) from E2E files #135

Closed benjaminralex closed 6 months ago

benjaminralex commented 6 months ago

Hey Mark!

Thanks always for the fantastic work!

I have an E2E file that has layer segmentations saved as contours. I can see it in the metadata (json), but can't access it.

Is there a way to actually get the contours? and overlay them on the images?

Cheers!

marksgraham commented 6 months ago

Hi,

You can view the contours overlaid on a volume by doing volume.peek(show_contours=True). The actual code for the plotting is here

benjaminralex commented 6 months ago

Thank you!