3Dscript

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.

Find more information at https://bene51.github.io/3Dscript

Requirements:

• 64-bit Operating System (Linux, Mac OS X or Windows)
• Up-to-date Fiji installation (http://www.fiji.sc)
• OpenCL 1.2-capable Graphics Card or better
• Decent graphics card, preferably from Nvidia or AMD, but newer Intel cards will work also (see below for tested hardware)

Installation:

• Start Fiji
• 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
• Installation typically takes not longer than a couple of minutes

Demo:

• Start Fiji
• Click on File>Open Samples>T1 Head
• Click on Plugins>3D script>Interactive Animation
• In the "Interactive Raycaster" window, click on "show" next to "Animation"
• Click on "Start text-based animation editor"
• In the editor window, type the following text: From frame 0 to frame 200 rotate by 360 degrees horizontally
• Click on "Run" This will render 200 frames of a movie sequence, within which the MRI data set rotates by 360 degrees.

Rendering of 200 frames of this data set will typically take less than a minute on an OpenCL-enabled Graphics Card. The resulting stack can be saved as a video file using Fiji's File>Save As>AVI... command.

To run the software on another data set, open a different image stack (instead of the T1 Head sample data) before running 3Dscript.

More information is available at https://bene51.github.io/3Dscript

Usage:

Detailed usage information is available on the wiki.

Publication:

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.

Tested hardware: