eyepy

A python package to read, analyse and visualize OCT and fundus data from various sources.

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
Links to: zenodo.org
○
Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.1%) to scientific vocabulary

Keywords

amd drusen e2e enface etdrs filereader fundus heidelberg heyex localizer nir oct python reader retouch spectralis visualization vol

Keywords from Contributors

spacy-extension climate-science dimensionality-reduction eof-analysis pattern-recognition pca electronic-healthcare-data irregular-time-series covariate-shift data-distributions

Last synced: 4 months ago · JSON representation ·

Repository

A python package to read, analyse and visualize OCT and fundus data from various sources.

Basic Info

Host: GitHub
Owner: MedVisBonn
License: mit
Language: Python
Default Branch: master
Homepage: https://medvisbonn.github.io/eyepy/
Size: 13.5 MB

Statistics

Stars: 71
Watchers: 6
Forks: 12
Open Issues: 8
Releases: 39

Topics

amd drusen e2e enface etdrs filereader fundus heidelberg heyex localizer nir oct python reader retouch spectralis visualization vol

Created over 5 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Citation

eyepy

A powerful Python package for importing, analyzing, and visualizing retinal imaging data, including OCT and OCT Angiography.

header_gif

eyepy provides a unified and user-friendly interface for working with retinal imaging data. With support for a wide range of file formats, it enables researchers and clinicians to import, process, and visualize OCT volumes and angiography data with ease. The core EyeVolume object offers intuitive methods for plotting fundus images, B-scans, and quantitative analyses such as drusen and retinal layer thickness. Comprehensive documentation and example workflows are available to help you get started quickly.

Features

Import Structural Data (HEYEX-E2E, HEYEX-VOL, HEYEX-XML, Topcon-FDA, B-Scan collections, RETOUCH Challenge, AMD Dataset from Duke University)
Import Angiographic OCT Data (HEYEX-VOL)
Analyze OCT volumes (compute and quantify drusen)
Visualize OCT volumes with annotations and quantifications
Compute and visualize retinal layer thickness
Compute and visualize OCTA enface projections.
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 have a supported OCT volume at hand you can check out our sample datasets to get familiar with eyepy.

python from eyepy.data import load struc_ev = load("drusen_patient") struc_ev = load("healthy_OD") angio_ev = load("healthy_OD_Angio")

If you have data at hand use one of eyepy's import functions.

```python

Import HEYEX E2E export

ev = ep.importheyexe2e("path/to/file.e2e")

Import HEYEX XML export

ev = ep.importheyexxml("path/to/folder")

Import HEYEX VOL export

ev = ep.importheyexvol("path/to/file.vol")

Import Topcon FDA export

ev = ep.importtopconfda("path/to/file.fda")

Import volume from Duke public dataset

ev = ep.importdukemat("path/to/file.mat")

Import volume from RETOUCH challenge

ev = ep.importretouch("path/to/volumefolder")

Import HEYEX OCTA VOL export

evangio = ep.importheyexangiovol("path/to/volume_folder") ```

Spectralis OCTA (OCT Angiography) Support

eyepy is capable of reading and visualizing OCT Angiography (OCTA) data from Heidelberg Spectralis devices. You can explore and analyze both structural and angiography volumes using the same unified interface.

Example: Load and Visualize Spectralis OCTA Sample Data

The following example demonstrates how to load OCTA sample data, and plot the enface projections.

```python import eyepy as ep import matplotlib.pyplot as plt

Load sample data

angioOD = ep.data.load("healthyODAngio") angioOS = ep.data.load("healthyOSAngio")

fig, axes = plt.subplots(1, 2, figsize=(14, 7)) for i, (angio, title) in enumerate(zip([angioOD, angioOS], ["Right Eye (OD)", "Left Eye (OS)"])): # Show localizer with Angiography overlay for the complete retina angio.plot(ax=axes[i], slabs=["RET"]) axes[i].set_title(title) axes[i].axis("off")

plt.tight_layout() ``` Example OCTA

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

Citation

If you use eyepy in your research, please cite it. You can find citation information and export BibTeX entries via the Zenodo record:

Contributing

For details on contributing and setting up a development environment, see the Contributing Guide.

Owner

Name: MedVisBonn
Login: MedVisBonn
Kind: organization

Repositories: 6
Profile: https://github.com/MedVisBonn

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: eyepy
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Olivier
    family-names: Morelle
    email: oli4morelle@gmail.com
    orcid: 'https://orcid.org/0000-0001-6404-2726'
    affiliation: >-
      University of Bonn - Bonn-Aachen International
      Center for Information Technology (b-it) /
      University Hospital Bonn - Department of
      Ophthalmology
identifiers:
  - type: url
    value: 'https://github.com/MedVisBonn/eyepy/tree/v0.12.2'
repository-code: 'https://github.com/MedVisBonn/eyepy/tree/v0.12.2'
abstract: >-
  Eye imaging data from different device vendors
  often come in different file formats. Additionally,
  public datasets often have their own way of storing
  data for distribution. The lack of documentation
  for many device-specific formats is a problem
  already when working with a single data source
  while the pure amount of different formats slows
  down everyone trying to use data from multiple
  sources.

  This Python package aims at providing a unified
  interface to a wide variety of eye imaging formats
  and the execution of standard tasks such as data
  visualization and quantification on ETDRS grids.
  Thereby, it enables the development of
  device-independent software and algorithms.
keywords:
  - OCT
  - Drusen
  - Heidelberg
  - HEYEX
  - ETDRS
license: MIT
version: v0.12.2
date-released: '2023-11-15'

GitHub Events

Total

Create event: 4
Release event: 4
Issues event: 5
Watch event: 25
Delete event: 2
Issue comment event: 24
Push event: 13
Pull request review comment event: 1
Pull request review event: 2
Pull request event: 2
Fork event: 6

Last Year

Create event: 4
Release event: 4
Issues event: 5
Watch event: 25
Delete event: 2
Issue comment event: 24
Push event: 13
Pull request review comment event: 1
Pull request review event: 2
Pull request event: 2
Fork event: 6

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 196
Total Committers: 5
Avg Commits per committer: 39.2
Development Distribution Score (DDS): 0.179

Top Committers

Name	Email	Commits
Olivier Morelle	o**e@g**m	161
semantic-release	s****e	17
github-actions	a**n@g**m	11
github-actions	g**s@g**m	6
Olivier Morelle	O**4@u**m	1

Committer Domains (Top 20 + Academic)

github.com: 2

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 17
Total pull requests: 2
Average time to close issues: 4 months
Average time to close pull requests: 6 days
Total issue authors: 14
Total pull request authors: 2
Average comments per issue: 5.59
Average comments per pull request: 9.0
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 6
Pull requests: 1
Average time to close issues: 15 days
Average time to close pull requests: 2 days
Issue authors: 6
Pull request authors: 1
Average comments per issue: 4.17
Average comments per pull request: 7.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

drombas (2)
yiqian-wang (2)
SaeedShurrab (2)
Oli4 (2)
Naveedkhan283 (1)
mattmagic149 (1)
big97kai (1)
Borja21091 (1)
paulschmeida (1)
ly1998117 (1)
charsooghi (1)
AlanZhang1995 (1)
EndingCredits (1)
msseibel (1)

Pull Request Authors

Borja21091 (2)
drombas (1)

Top Labels

Issue Labels

enhancement (2)

Pull Request Labels

Packages

Total packages: 2
Total downloads:
- pypi 551 last-month

Total dependent packages: 1
(may contain duplicates)
Total dependent repositories: 2
(may contain duplicates)
Total versions: 44
Total maintainers: 1

pypi.org: eyepie

A python package to read, analyse and visualize OCT and fundus data form various sources.

Homepage: https://github.com/MedVisBonn/eyepy
Documentation: https://eyepie.readthedocs.io/
License: MIT
Latest release: 0.11.3
published over 2 years ago

Versions: 38
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 136 Last month

Rankings

Dependent packages count: 4.7%

Stargazers count: 12.3%

Downloads: 13.2%

Average: 13.2%

Forks count: 14.2%

Dependent repos count: 21.8%

Maintainers (1)

Oli4

Last synced: 4 months ago

pypi.org: eyepy

A python package to read, analyse and visualize OCT and fundus data form various sources.

Documentation: https://eyepy.readthedocs.io/
License: MIT
Latest release: 0.14.0
published 6 months ago

Versions: 6
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 415 Last month

Rankings

Dependent packages count: 10.0%

Stargazers count: 12.3%

Forks count: 14.2%

Average: 16.5%

Dependent repos count: 21.8%

Downloads: 24.4%

Maintainers (1)

Oli4

Last synced: 4 months ago

Dependencies

poetry.lock pypi

argcomplete 1.12.3 develop
atomicwrites 1.4.0 develop
attrs 21.4.0 develop
cfgv 3.3.1 develop
colorama 0.4.4 develop
commitizen 2.23.0 develop
coverage 6.4.1 develop
decli 0.5.2 develop
distlib 0.3.4 develop
filelock 3.6.0 develop
identify 2.4.12 develop
importlib-metadata 4.11.3 develop
iniconfig 1.1.1 develop
jinja2 3.1.1 develop
markupsafe 2.1.1 develop
nodeenv 1.6.0 develop
platformdirs 2.5.1 develop
pluggy 1.0.0 develop
pre-commit 2.17.0 develop
prompt-toolkit 3.0.28 develop
py 1.11.0 develop
pytest 6.2.5 develop
pytest-cov 3.0.0 develop
pyyaml 6.0 develop
questionary 1.10.0 develop
termcolor 1.1.0 develop
toml 0.10.2 develop
tomlkit 0.10.1 develop
virtualenv 20.14.0 develop
wcwidth 0.2.5 develop
zipp 3.7.0 develop
cycler 0.11.0
fonttools 4.31.2
imagecodecs 2021.11.20
imageio 2.16.1
itk 5.2.1.post1
itk-core 5.2.1.post1
itk-filtering 5.2.1.post1
itk-io 5.2.1.post1
itk-numerics 5.2.1.post1
itk-registration 5.2.1.post1
itk-segmentation 5.2.1.post1
kiwisolver 1.4.2
matplotlib 3.5.1
networkx 2.6.3
numpy 1.21.5
packaging 21.3
pillow 9.0.1
pyparsing 3.0.7
python-dateutil 2.8.2
pywavelets 1.3.0
scikit-image 0.19.2
scipy 1.7.3
setuptools-scm 6.4.2
six 1.16.0
tifffile 2021.11.2
tomli 2.0.1
typing-extensions 4.1.1

pyproject.toml pypi

commitizen ^2.20.4 develop
pre-commit ^2.16.0 develop
pytest ^6.2.5 develop
pytest-cov ^3.0.0 develop
imagecodecs ^2021.11.20
itk ^5.2.1
matplotlib ^3.5.1
python >=3.7,<3.11
scikit-image ^0.19.1

.github/workflows/_quality.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/setup-python v2 composite
snok/install-poetry v1.3 composite

.github/workflows/ci.yaml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite

eyepy

Science Score: 54.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

eyepy

Features

Getting Started

Installation

Getting Started

Import HEYEX E2E export

Import HEYEX XML export

Import HEYEX VOL export

Import Topcon FDA export

Import volume from Duke public dataset

Import volume from RETOUCH challenge

Import HEYEX OCTA VOL export

Spectralis OCTA (OCT Angiography) Support

Example: Load and Visualize Spectralis OCTA Sample Data

Load sample data

Related Projects:

Citation

Contributing

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: eyepie

Rankings

Maintainers (1)

pypi.org: eyepy

Rankings

Maintainers (1)

Dependencies