eyepy
Use Python to import, analyse and visualize retinal imaging data.
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 (fundus) 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 Data (Heyex-E2E, Heyex-VOL, Heyex-XML, Topcon-FDA, B-Scan collections, RETOUCH Challenge, AMD Dataset from Duke University)
- Analyze OCT volumes (compute and quantify drusen)
- Visualize OCT volumes with annotations and quantifications
- Save and load EyeVolume objects
Getting Started
Installation
Attention: If you want to use a version prior to 0.12.0 you have to install from the eyepie name instead. This is because we used eyepie as a package name on PyPI until the previous owner of the eyepy name on PyPI was so kind to transfer it to us.
To install the latest version of eyepy run pip install -U eyepy. (It is eyepie for versions < 0.12.0)
Getting Started
When you don't hava a supported OCT volume at hand you can check out our sample dataset to get familiar with eyepy.
from eyepy.data import load
ev = load("drusen_patient")If you have data at hand use one of eyepys import functions.
# Import HEYEX E2E export
ev = ep.import_heyex_e2e("path/to/file.e2e")
# Import HEYEX XML export
ev = ep.import_heyex_xml("path/to/folder")
# Import HEYEX VOL export
ev = ep.import_heyex_vol("path/to/file.vol")
# Import Topcon FDA export
ev = ep.import_topcon_fda("path/to/file.fda")
# Import volume from Duke public dataset
ev = ep.import_duke_mat("path/to/file.mat")
# Import volume form RETOUCH challenge
ev = ep.import_retouch("path/to/volume_folder")Related Projects:
- eyeseg: A python package for segmentation of retinal layers and drusen in OCT data.
- 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
