Making animated SFP, MIP, and Iso Surface renderings
IntroductionThe Movie Maker, present in the Huygens Software since version 3.4, is a tool that allows you to easily create sophisticated animations of your multi-channel 3D images using all Huygens Visualization renderers. This tool assists you in creating the key frames that define the main scenes, and the smooth transtitions between them. Interactive manipulation of the scenes is possible using the renderers interfaces or the timeline plot with the variable parameters.
Besides the Movie Maker, the Huygens Sfp Renderer, MIP Renderer, and Surface Renderer are capable of making simple AVI movies that are insightful and attractive. Not only the viewpoint, time frame, and zoom can be animated, but also render parameters like the threshold can be varied over time.
The AVI movie is compressed using the MJPEG codec, which can be played with e.g.
- Windows Media Player;
- Apple QuickTime;
How-toThe Movie Maker Tutorial explains how to use the Huygens Movie Maker to combine frames from all 3D renderers into a smooth and sophisticated movie.
To generate a simple movie without using the Movie Maker, select the SFP volume renderer, MIP renderer, or Surface renderer from the Visualization menu in Huygens Professional or Huygens Essential.
To define the initial position and visualization parameters, set the desired configuration and click Set > Home. Now select the settings for the final frame and click Set > End. Finally, press the Animate button, and
select a directory to save the AVI movie. The frame count and frame rate can be changed in the renderer's Visualization menu.
Get AVI file.
Dataset: Macrophage, fluorescently stained for tubulin (green), actin (red), and the nucleus (DAPI, blue). Recorded by Dr. James Evans, White-head Institute, MIT, Boston MA, USA' using widefield microscopy.
Tiff animationsBesides AVI, the Movie Maker and the SFP, MIP and Surface renderers can save the animation frame as a TIFF series. Third-party software like Image Magick can be used to merge these TIFF frames into a single movie file. Many video formats are platform dependent, but here we include some widespread alternatives:
- Image Magick is freeware and available for all platforms. It's powerful
converttool can convert to e.g. animated GIF and MPEG. Animated GIF uses palette compression (256 colors) and can be shown in any internet browser. MPEG is a strong compression technique which results in small file sizes.
- Irix has a tool called
dmconvertthat directly writes QuickTime movies from a tiff series. Example: to convert the series
animatedSfp_t000000, ..., animatedSfp_t000360.tiffto a
dmconvert -v -f qt -p video,comp=qt_video,rate=15 -n animatedSfp_t000###.tiff,start=0,end=360,step=1 animatedSfp_t000###.tiff out.mov
Other alternatives are: