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
- 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)
| 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 |
- 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
- 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