3Dscript: animating 3D/4D microscopy data using a naturallanguage- based syntax.

Palmisano R, Tripal P, Schmid B, Fraaß T (2020)

Publication Type: Conference contribution, Conference Contribution

Publication year: 2020

Conference Proceedings Title: https://www.quantitativebioimaging.com/qbi2020/conference-and-program-booklet/

Event location: Mathematical Institute, University of Oxfoerd

DOI: 10.1038/s41592-019-0359-1

Abstract

We introduce a software framework that
assembles 3D animations of imaging data
using a textual description with a syntax
based on natural English language. In
contrast to the established key frame
based approach, smooth and complex
motion sequences are intuitively
implemented by concatenating multiple
instructions. [1] The syntax is extensible
and we demonstrate its integration into
existing 3D visualization software. The
user typically stores different rendering
settings and scene transformations in a
number of key frames along a timeline,
and the rendering engine creates a
smooth animation by interpolating
between them. Key frames save the
spatial transformation of an object as a
state, e.g. three angles for a rotation, and
not as a transition. This at least 4 key
frames are required to define a 360-
degree rotation with constant speed
unambiguously. Even more are required if the motion is non-linear, which is essential for achieving
smooth and pleasant motions. Software packages therefore typically provide a shortcut to insert key
frames for rotations around common axes. More complex motions such as combined rotations around
multiple axes, however, are difficult to achieve.
The syntax based on natural English language maximizes experience and provides easy access for
users of distinct fields. Each instruction is an English sentence. Complex motion sequences are
implemented by combining multiple instructions which are applied in the order they appear in the text.
The syntax comprises phrases for standard non-linear accelerations, resulting in smooth and natural
animations. Self-defined macro functions can be used to define motion and other parameters as
functions over time. We provide 3DScript as a Fiji/ImageJ plugin including an hardware-accelerated 3D
renderer and a dedicated editor featuring auto-completion and recording. Although tailored to the
included rendering engine, both the syntax and our animation framework can be easily adapted by other
rendering software.

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How to cite

APA:

Palmisano, R., Tripal, P., Schmid, B., & Fraaß, T. (2020). 3Dscript: animating 3D/4D microscopy data using a naturallanguage- based syntax. In https://www.quantitativebioimaging.com/qbi2020/conference-and-program-booklet/. Mathematical Institute, University of Oxfoerd, GB.

MLA:

Palmisano, Ralf, et al. "3Dscript: animating 3D/4D microscopy data using a naturallanguage- based syntax." Proceedings of the Quantitative BioImaging, Mathematical Institute, University of Oxfoerd 2020.

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