3Dscript

Introduction

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:

Publication

Installation

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.

Usage

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

Gallery

Please visit the Gallery for a number of illustrative videos.

At frame 0: - change front clipping to 0 At frame 0: - rotate by 20 degrees around (0, 0, 1) From frame 0 to frame 400: - rotate by 360 degrees horizontally - rotate by 60 degrees vertically - change front clipping to 200 From frame 400 to frame 600: - change front clipping to 600

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.