3Dscript is a plugin for Fiji/ImageJ for creating 3D and 4D animations of microscope data. In contrast to existing 3D visualization packages, animations are not keyframe-based, but are described by a natural language-based syntax. Some illustrative examples are shown below:


Schmid, B.; Tripal, P. & Fraaß, T. et al. (2019), "3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax", Nature methods 16(4): 278-280, PMID 30886414.


To install the 3Dscript plugin, use the Fiji updater and add the 3Dscript update site (see also Following an update site from the Fiji wiki.

In short:

The source code for 3Dscript can be found on GitHub.


Detailed instructions are found in the wiki. Also, there is a detailed manual available in PDF format here. Additionally, there are a number of illustrative videos in the Gallery


Please visit the Gallery for a number of illustrative videos.

Simultaneous rotation around multiple axes. 3D animation of mouse colon tumors using blood vessel staining (CD31; red), ECi-based tissue clearing and a LaVision BioTec lightsheet UltraMicroscope II (see also Figure 1). The image volume is rotated around its y-axis (with a higher speed) and around the x-axis of the view (with a lower speed). Only a couple of text lines are required to describe an animation which is hard to achieve with key frame-based animation.