paros

PAROS is a method to calculate the magnification of fundus photographs.

https://github.com/mreye-lumc/paros

Science Score: 57.0%

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
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 2 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (13.2%) to scientific vocabulary

Keywords

medical-imaging ophthalmology optics physics

Last synced: 6 months ago · JSON representation ·

Repository

PAROS is a method to calculate the magnification of fundus photographs.

Basic Info

Host: GitHub
Owner: MREYE-LUMC
License: mit
Language: Python
Default Branch: main
Homepage: https://demo.mreye.nl/paros
Size: 255 KB

Statistics

Stars: 3
Watchers: 0
Forks: 0
Open Issues: 2
Releases: 2

Topics

medical-imaging ophthalmology optics physics

Created over 2 years ago · Last pushed 9 months ago

Metadata Files

Readme Contributing License Citation

PARaxial Optical fundus Scaling (PAROS)

Paros is a method to calculate the magnification of fundus images based on the optical characteristics of the patient's eye. The full method and validation are described in Pors LJ, Haasjes C, van Vught L, et al. Correction Method for Optical Scaling of Fundoscopy Images: Development, Validation, and First Implementation. Invest Ophthalmol Vis Sci. 2024;65(1):43. doi:10.1167/iovs.65.1.43

License

The code is provided as is, without any warranty, under the MIT license. This license requires that reusers give credit to the creator. It allows reusers to distribute, remix, adapt, and build upon the material in any medium or format.

Basic usage

Try it online

A basic version of PAROS can most easily be run online here: basic version

Install the library

The full package is also available on PyPI:

pip install PAROS

PAROS consists of two main functions:

fundus_camera_calibration.ipynb: a method to calibrate camera using eye phantom measurements.
calculate_ocular_magnification.ipynb: a method to calculate magnification fundus images of a subject.

Implementation

The implementation of PAROS in this repository is functional for the camera in our center, and with the specific software used at our center. Both have impact on the calculated magnification. We therefore recommend calibration of the camera and software using the method described in the article mentioned below before implementation for quantitative purposes.

Camera constants

Please find here a table of known camera calibration constants; this can be added upon by other contributors. | Camera type | CCD type | Condenser lens power (D) | First order calibration term | | --------------- | -------- | ------------------------ | ---------------------------- | | Topcon TRC-50DX | | 38.0 | -0.011 | | Topcon TRC-50IX | | 38.0 | -0.012 |

Referencing

When publishing results obtained with this package, please cite the paper that describes the full method and validation: Pors LJ, Haasjes C, van Vught L, et al. Correction Method for Optical Scaling of Fundoscopy Images: Development, Validation, and First Implementation. Invest Ophthalmol Vis Sci. 2024;65(1):43. doi:10.1167/iovs.65.1.43

Contributing

Please read our contribution guidelines prior to opening a Pull Request.

Contact

Feel free to contact us for any inquiries:

L.J. Pors (email)
J.W.M. Beenakker (email)

Owner

Name: MREYE
Login: MREYE-LUMC
Kind: organization

Repositories: 2
Profile: https://github.com/MREYE-LUMC

Citation (CITATION.cff)

cff-version: "1.2.0"
authors:
- family-names: Pors
  given-names: Lennart
  orcid: "https://orcid.org/0000-0003-0907-6637"
- family-names: Haasjes
  given-names: Corné
  orcid: "https://orcid.org/0000-0003-0187-4116"
- family-names: Beenakker
  given-names: Jan-Willem M.
  orcid: "https://orcid.org/0000-0003-0479-5587"
contact:
- family-names: Beenakker
  given-names: Jan-Willem M.
  orcid: "https://orcid.org/0000-0003-0479-5587"
message: If you use this software, please cite our article in 
  Investigative Ophthalmology & Visual Science.
preferred-citation:
  authors:
  - family-names: Pors
    given-names: Lennart
    orcid: "https://orcid.org/0000-0003-0907-6637"
  - family-names: Haasjes
    given-names: Corné
    orcid: "https://orcid.org/0000-0003-0187-4116"
  - family-names: Vught
    given-names: Luc
    name-particle: van
    orcid: "https://orcid.org/0000-0001-8290-9071"
  - family-names: Hoes
    given-names: Noor P.
    orcid: https://orcid.org/0009-0005-2024-9676
  - family-names: Luyten
    given-names: Gregorius P.M.
    orcid: https://orcid.org/0000-0003-3685-3868
  - family-names: Rijn
    given-names: Gwyneth A.
    name-particle: van
    orcid: https://orcid.org/0000-0003-3835-1087
  - family-names: Vu
    given-names: T.H. Khanh
    orcid: https://orcid.org/0000-0003-1809-4001
  - family-names: Rasch
    given-names: Coen R.N.
    orcid: https://orcid.org/0000-0001-6950-3376
  - family-names: Horeweg
    given-names: Nanda
    orcid: https://orcid.org/0000-0002-8581-4753
  - family-names: Beenakker
    given-names: Jan-Willem M.
    orcid: "https://orcid.org/0000-0003-0479-5587"
  date-published: 2024-01-25
  doi: 10.1167/iovs.65.1.43
  issn: 1552-5783
  issue: 1
  journal: Investigative Ophthalmology & Visual Science
  start: 43
  title: "Correction Method for Optical Scaling of Fundoscopy Images: Development, Validation, and First Implementation"
  type: article
  url: "https://iovs.arvojournals.org/article.aspx?articleid=2793314"
  volume: 65
title: "PARaxial Optical fundus Scaling (PAROS)"
repository-code: 'https://github.com/MREYE-LUMC/PAROS'
license: MIT

GitHub Events

Total

Issues event: 2
Delete event: 1
Issue comment event: 3
Push event: 5
Pull request review event: 3
Pull request event: 3
Create event: 1

Last Year

Issues event: 2
Delete event: 1
Issue comment event: 3
Push event: 5
Pull request review event: 3
Pull request event: 3
Create event: 1

Committers

Last synced: over 1 year ago

All Time

Total Commits: 15
Total Committers: 3
Avg Commits per committer: 5.0
Development Distribution Score (DDS): 0.4

Past Year

Commits: 15
Committers: 3
Avg Commits per committer: 5.0
Development Distribution Score (DDS): 0.4

Top Committers

Name	Email	Commits
crnh	3****h	9
chaasjes	c**s@l**l	3
Lennart Pors	1****s	3

Committer Domains (Top 20 + Academic)

lumc.nl: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 2
Total pull requests: 11
Average time to close issues: N/A
Average time to close pull requests: 23 days
Total issue authors: 1
Total pull request authors: 2
Average comments per issue: 2.5
Average comments per pull request: 0.0
Merged pull requests: 11
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 3
Average time to close issues: N/A
Average time to close pull requests: 3 months
Issue authors: 1
Pull request authors: 1
Average comments per issue: 2.5
Average comments per pull request: 0.0
Merged pull requests: 3
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

crnh (2)

Pull Request Authors

crnh (9)
ljpors (2)

Top Labels

Issue Labels

question (1)

Pull Request Labels

documentation (2)

Dependencies

.github/workflows/ci.yml actions

actions/checkout v4 composite
actions/setup-python v5 composite

.github/workflows/release.yml actions

actions/checkout v4 composite
actions/download-artifact v4 composite
actions/setup-python v5 composite
actions/upload-artifact v4 composite
pypa/gh-action-pypi-publish v1.8.11 composite
svenstaro/upload-release-action 2.7.0 composite

.github/workflows/test-release.yml actions

actions/checkout v4 composite
actions/download-artifact v4 composite
actions/setup-python v5 composite
actions/upload-artifact v4 composite
pypa/gh-action-pypi-publish v1.8.11 composite

.github/workflows/voici.yml actions

actions/checkout v4 composite
actions/deploy-pages v4 composite
actions/setup-python v5 composite
actions/upload-pages-artifact v3 composite
mamba-org/setup-micromamba v1 composite

pyproject.toml pypi

matplotlib *
numpy *
pandas *
scipy *
sympy *

voici/environment.yml conda

ipywidgets
matplotlib
numpy
pandas
pip
python 3.10.*
scipy
sympy
xeus-lite
xeus-python 0.15.9.*

paros

Science Score: 57.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

PARaxial Optical fundus Scaling (PAROS)

License

Basic usage

Try it online

Install the library

Implementation

Camera constants

Referencing

Contributing

Contact

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

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

Dependencies