Open Science and Data
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, is made accessible to the benefit of other scientists, healthcare professionals and patients.
Software
See the software overview page for a complete list of our software, including main contributors, requirements and related publications.
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. A simple version of Visisipy can even run from your browser.
pyROT is a Python library that complements RayOcular, the eye-specific module of RayStation. For example, it provides methods to build patient-specific eye models for radiotherapy planning.
ZOSPy is our open-source platform to perform optical simulations in OpticStudio and share them 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.
OPT Tumour Models generates polynomial tumor models for ocular proton therapy planning from 3D tumor delineations.
We are also active users of, and contributors to, third-party open-source tools, such as Optiland, the open-source ray-tracing engine used by Visisipy.
Methods
Quantitative MRI
EPG-based fit to obtain the water T2 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, using an iterative fitting method that includes the B0 field and R2* relaxation
Ray tracing
Patient-specific simulations to correlate camera angles to retinal locations to improve the accuracy of ocular radiotherapy planning, as described in Patient-specific mapping of fundus photographs to three-dimensional ocular imaging
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 intraocular pathology, our standard MRI protocol to visualize the eye and internal structures. It contains high-resolution anatomical sequences to assess the lesion’s extent and origin, as well as functional sequences that can aid in the differential diagnosis.
- Other protocols will be added at a later stage
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:
88% as Open Access paper through the publisher's website and
10% through online repositories
Data
- As most 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 a data transfer agreement to ensure the subjects’ privacy. Requests can be sent 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.