3D neuroimaging data in online journal articles

About the 3D neuroimaging viewer

Authors of relevant articles are invited to enrich their online articles by providing neuroimaging data in NIfTI format. This will be visualized for the readers using the interactive viewer embedded within the article, and will enable them to: browse through available neuroimaging datasets; zoom, rotate and pan the 3D brain reconstruction; cut through the volume; change opacity and color mapping; switch between 3D and 2D projected views; and download the data. It will also be possible to open the viewer in a detached full-screen mode.

neuroimaging 

                      Representation of the 3D neuroimaging viewer on ScienceDirect.

The viewer has been developed in collaboration with Kitware SAS and supports all major browsers and mobile devices.

Articles featuring the 3D neuroimaging viewer:
http://www.sciencedirect.com/science/article/pii/S0028393214000086
http://www.sciencedirect.com/science/article/pii/S1053811914002419 
http://www.sciencedirect.com/science/article/pii/S0306452213005903
http://www.sciencedirect.com/science/article/pii/S1053811913002188
http://www.sciencedirect.com/science/article/pii/S1053811911006926

Benefits for authors and readers

The 3D neuroimaging viewer enables authors to enrich and extend their articles by adding a possibility to optimally express the results of research through improved visualization. This provides a way to highlight their findings in a visual and easily accessible manner, helping readers to quickly understand the relevance of a research paper, to visualize research data for deeper insights, and to access the underlying data. The enriched article may contribute to a better understanding of experiments described in the article and help encourage re-use of the neuroimaging data.

As an experiment, 3D visualizations were automatically synthesized based on keywords and data extracted from the following published articles:
http://www.sciencedirect.com/science/article/pii/S105381191301029X;
http://www.sciencedirect.com/science/article/pii/S1053811913011117;
http://www.sciencedirect.com/science/article/pii/S2213158213001472

Supported data formats

The Elsevier's 3D neuroimaging viewer supports NIfTI data format. NIfTI format (Neuroimaging Informatics Technology Initiative), a standard data format used in neuroimaging to capture volumetric (f)MRI data.

The viewer supports single (.nii) and dual (.hdr and .img) NIfTI file formats.

More information about this data format can be found here.

NEW: You can also upload three-dimensional renderings as OBJ, PLY or U3D models.

Submission & publication

Please submit your neuroimaging data in NIfTI format with the manuscript. We support single (.nii) and dual (.hdr and .img) NIfTI file formats.Multiple datasets can be submitted with a single article. Each dataset will have to be zipped and uploaded to online submission system via the "3D neuroimaging data" submission category. Recommended size of a single uncompressed dataset is ≤100 MB.  Please provide a short informative description for each data file by filling in the "Description" field when uploading your data. 

The 3D neuroimaging viewer also integrates a specific visualization mapper which automatically combines a master volume of the brain with functional magnetic resonance images (fMRI). The brain template file has to be zipped and uploaded to the online submission system separately.

NEW: You can also upload three-dimensional renderings as OBJ, PLY or U3D models.

Note: all datasets will be available for download from the online article on ScienceDirect. If you have concerns about your data being downloadable, please provide a video instead.

3D neuroimaging viewer will appear in the online version of the article. The PDF/printed version of the article will feature static figures only (if those figures are included in the article manuscript).

If you wish to provide feedback on the 3D neuroimaging viewer or have a suggestion for another innovation that would further enhance the online article please get in touch