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README.md

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)

Tested hardware:

Graphics card Operating system
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

Installation:

  • Start Fiji
  • Click on Help>Update...
  • Click on "Manage update sites"
  • Click on "Add update site"
  • Enter Name: 3Dscript
  • Enter URL: https://romulus.oice.uni-erlangen.de/updatesite/
  • 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