eyepie

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

To install the latest version of eyepy run pip install -U eyepie. It is eyepie and not eyepy for installation with pip.

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:

• 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
  • LibOctData
  • LibE2E
  • OCT-Marker
• UOCTE Unofficial continuation of https://bitbucket.org/uocte/uocte
• OCTAnnotate
• heyexReader
• OCTExplorer Iowa Reference Algorithm