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:
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.
- Click on Help>Update...
- Click on Manage update sites
- Check the box in front of 3Dscript
- Click on Close
- Click on Apply changes
- Restart Fiji
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.