Open Science

We embrace the Open Science movement to make research more transparent and share data as much as possible. This means our projects are reviewed and validated by our peers and our output, whether it is software, methods or data, are made accessible to the benefit of other scientists, healthcare professionals and patients.

Software

  • ZOSPy is our open source platform to perform optical simulations in Optic Studio and to share with other scientists through Jupyter notebooks

  • PAROS is a tool to calculate the magnification of fundus photographs based on the optical characteristics of the patient’s eye, as described in Correction Method for Optical Scaling of Fundoscopy Images

  • Visisipy is a Python library for optical simulations of the eye. It provides an easy-to-use interface to define and build eye models, and to perform common ophthalmic analyses on these models.

  • VFPy a python package for automated digitalization of ophthalmic visual field data

Methods

Quantitative MRI

  • EPG-based fit to obtain the T2water from multi-echo spin-echo MRI-scans of muscles, as described in T2 relaxation-time mapping in healthy and diseased skeletal muscle using extended phase graph algorithms

  • Decomposition of water and fat images from multi-echo (Dixon) MRI scans, which uses an iterative fitting method, wherein B0 field and relaxation time R2* included

Ray tracing

  • Determine the peripheral retinal illumination in models of the (pseudophakic) eye, as described in Effect of anatomical differences and intraocular lens design on Negative Dysphotopsia

MRI protocols

  • MRI protocol for intra-ocular pathology, our standard MRI protocol to visualize the eye and internal structures. It contains high-resolution anatomical sequences to assess the lesions extent and origin, as well as functional sequences that can aid in the differential diagnosis.
  • Other protocols will be added soon

Other methods

  • An overview of our publications of which the methods/scripts are freely available.

Publications

Currently 98% of our publications are available free of charge:
84% as Open Access paper through the publisher's website and 14% through online repositories

List of publications by year List of publications by topic

Data

  • As many of our data, such as MRI-scans, contain potentially identifying information, they cannot be made publicly available. These data can, however, be shared with scientists who meet the criteria for access to these data and after signing of a data transfer agreement to ensure the subject’s privacy. Requests can be send to wetenschapscommissieOOG@lumc.nl.
  • Optical eye models of pseudophakic eyes with and without Negative Dysphotopsia, as described in Effect of anatomical differences and intraocular lens design on Negative Dysphotopsia
  • Radiological characteristics of 26 uveal melanoma patients before and after treatment as described in MR-based follow-up after brachytherapy and proton beam therapy in uveal melanoma
  • A complete list of our publications of which the underlying data can be downloaded for reuse.