Abstract
We provide software tools for displaying and publishing interactive 3-dimensional (3D) and 4-dimensional (4D) figures to html webpages, with examples of high-resolution brain imaging. Our framework is based in the R statistical software using the rgl package, a 3D graphics library. We build on this package to allow manipulation of figures including rotation and translation, zooming, coloring of brain substructures, adjusting transparency levels, and addition/or removal of brain structures. The need for better visualization tools of ultra high dimensional data is ever present; we are providing a clean, simple, web-based option. We also provide a package (brainR) for users to readily implement these tools.
Highlights
We provide a set of software tools that produce interactive 3-dimensional (3D) and 4-dimensional (4D) figures using currently available open-source software
We have found that web-based rendering performs much faster than those within Portable Document Format (PDF) for the dimensionality of points we are plotting
Interactive 3D figures can be created quickly. They are reproducible and can be exported to standalone webpages. This framework allows for these figures to supplement 2D figures to present results from analysis and image processing in neuroimaging research
Summary
We provide a set of software tools that produce interactive 3-dimensional (3D) and 4-dimensional (4D) figures using currently available open-source software. These images can be embedded into webpages (http://bit.ly/1kEJH6q), creating an environment where users can interact with the images without additional software or expertise. For example, the current standard is to present spatial results as a set of 2D figures, or slices. Other types of presentations can be employed, such as lightbox views where all slices of the brain are presented in series, single plane views, 3D surface images, or maximum intensity projections onto transparent cross-sectional views (known as “glass brains”, Figure 1B). We wish to improve on these data representations by using truly 3D figures
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