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Member-led open science activities

A number of individuals and groups at WIN have engaged in data sharing, code sharing, open educational and community standard activities. These efforts are included to highlight the contributions of WIN to the wider international open science narrative, noting where we excel and areas we could strengthen. The following is a non-exhaustive list of examples of WIN contributions: 

Open Data

Open Software

Open Education

Community Standards and Tools

OPEN DATA

 

UK Biobank 

 

UK BioBank - a national and international health resource that follows the health and well-being of 500,000 volunteer participants and provides their anonymised health information to approved researchers in the UK and overseas, from academia and industry. More than 3000 imaging derived phenotypes (IDPs) are derived and shared with the scientific community based on pipelines developed at WIN.

 Human Connectome Project

Human Connectome Project – a consortium led by Washington University, University of Minnesota, and Oxford University which is undertaking a systematic effort to map macroscopic human brain circuits and their relationship to behaviour in a large population of healthy adults.

 

The Developing Human Connectome

 

Developing Human Connectome - led by King’s College London, Imperial College London and Oxford University, aims to make major scientific progress by creating the first 4-dimensional connectome of early life. WIN PI Stephen Smith leads the Oxford team and the project is supported by various WIN members.

Dementias Platfrom UK logo

Dementias Platform UK - brings together cohort data from over 40 health studies, including records of over 3 million people. WIN collaborator include Clare Mackay, Ludovica Griffanti, Jemma Pitt, Mathew South, and Duncan Smith.

MRS hub logo

MRS Hub - a repository for open source code and data shared by the technical magnetic Resonance spectroscopy (MRS) community. Established and administered by WIN member William Clarke.

Primate Data Exchange logo

PRIMate Data Exchange - a consortium to share openly MRI data from non-human primates. WIN PI Rogier Mars and Matthew Rushworth, with WIN member Jerome Sallet have contributed anatomical, diffusion, and fMRI data from 20 monkeys, the largest single contribution to the dataset.

Digital Brain Bank logo

Digital Brain Bank - comprised of the Digital Anatomist, Digital Brain Zoo and soon the Digital Pathologist. These resources will distribute a range of datasets with MRI of post-mortem brains from human and non-human primates, many including microscopy in the same brains. Website coming soon.

Brain-CODE - a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders and non-human animal models of disorders. WIN PI Jason Lerch has released data from 31 high throughput mouse models.
Big40 logo BIG 40 - an open data server containing results from Genome-Wide Association Studies (GWAS) of almost 4,000 imaging-derived phenotypes from the multimodal brain imaging in UK Biobank. WIN PI Steve Smith leads this project, with contributions from various WIN members.

 

Open Software

                FSL logo

FMRIB Software Library - a set of image analysis tools, licensed for free use by non-commercial entities. FSL is a staple tool in image analysis across the globe and is developed by the FMRIB Analysis Group (lead by WIN PI Stephen Smith), and is supported by WIN Core staff members.

 

Quantiphyse

Quantiphyse - a visualisation and analysis tool for medical imaging data, particularly supporting quantitive and physiological imaging methods. The aim is to bring advanced analysis methods to users in biomedical research via an easy-to-use interface, that also permits the creation of analysis pipelines to be used in research studies. 

Logo of OHBA

OHBA software library - A set of Matlab tools and scripts for running M/EEG analyses on CTF and Elekta Neuromag data. Lead by WIN PI Mark Woolrich, with WIN members Giles Colclough, Andrew Quinn, Jonathan Hadida, Diego Vidaurre, Ryan Timms, Cameron Higgins and Tom Rhys Marshall.

Hippofit project logo

Hippofit - An automated platform to calculate hippocampal volume percentile against data from over 20000 people of varying ages. Created by WIN PI Sanjay Manohar and Masud Husain, with WIN member Lisa Nobis.

MR Linear Encoding Operators

MR Linear Encoding Operators, GRAPPA Reconstruction Tools, Sparse and Regularised MR Image Reconstruction Tools, Dynamic k-t MR Image Reconstruction Tools - A MATLAB-based set of classes for image reconstruction techniques for magnetic resonance imaging. Developed by WIN PI Mark Chew 

 

OPEN EDUCATION MATERIALS

FSL Course - The FSL course has over 20 hours of self paced learning material and practical analysis exercises online

Introduction to Online Experiments - created by WIN members Melvin Kallmayer, Leila Zacharias, Amy Gillespie, Paula Kaanders, and Dejan Draschkow 

GitHub for Collaborative Documentation - developed by WIN Core Staff member Cassandra Gould van Praag. The materials are released under a CC-BY 3.0 License. 

Fitting computational models of learning - Repository for Computational Modelling Course, taught as part of the WIN Graduate Programme. Tutorials developed as part of the WIN graduate programme, by WIN PIs Laurence Hunt and Miriam Klein-Flugge, with WIN members Nils Kolling, and Jacqueline Scholl. 

Contribution to Community Standards and Tools

BIDS Extension Proposals – Several WIN members are contributing to standards including Arterial Spin Labelling (BEP005; Tom Okell), Multiple Contrasts (BEP001; Alberto Lazari) and Medical Imaging Data Structure (BEP025; Alberto Lazari)