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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:

Graphics card Operating system
NVIDIA Quadro P2000 Windows 10
NVIDIA Quadro M4000 Windows 10
NVIDIA Quadro M2000 Windows 10
NVIDIA Quadro K620 Windows 10
NVIDIA Quadro K600 Windows 10
NVIDIA Quadro K420 Windows 7
NVIDIA GeForce GTX760 Windows 7
AMD FirePro W5100 Windows 7
Intel HD Graphics 4600 Windows 7
Intel HD Graphics 4000 Mac OS X
Intel HD Graphics 5000 Mac OS X
Intel HD Graphics 530 Windows 10

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Create 3D/4D animations using a natural language-based syntax

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