The Python package for working with ophthalmological data.
Project description
eyepy
The eyepy python package provides a simple interface to import and process OCT volumes. Everything you import with one of our import functions becomes an EyeVolume object which provides a unified interface to the data. The EyeVolume object provides methods to plot the localizer image and B-scans as well as to compute and plot quantifications of voxel annotations such as drusen. Check out the documentation, especially the Cookbook chapter, for more information.
Features
- Import HEYEY E2E, VOL and XML exports
- Import B-Scans from a folder
- Import public AMD Dataset from Duke University
- Import data of the RETOUCH Challenge.
- Compute Drusen voxel annotation from BM and RPE layer segmentations
- Quantify voxel annotations on a customizable circular grid
- Plot annotated localizer
- Plot annotated B-scans
- Save and load EyeVolume objects
Getting Started
Installation
To install the latest version of eyepy run pip install -U eyepie. It is eyepie and not eyepy for installation with pip.
When you don't hava a supported OCT volume at hand you can check out our sample dataset to get familiar with eyepy.
import eyepy as ep
# Import HEYEX XML export
ev = ep.data.load("drusen_patient")
Related Projects:
- OCT-Converter: Extract raw optical coherence tomography (OCT) and fundus data from proprietary file formats. (.fds/.fda/.e2e/.img/.oct/.dcm)
- eyelab: A GUI for annotation of OCT data based on eyepy
- Projects by the Translational Neuroimaging Laboratory
- UOCTE Unofficial continuation of https://bitbucket.org/uocte/uocte
- OCTAnnotate
- heyexReader
- OCTExplorer Iowa Reference Algorithm
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