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Making animated SFP, MIP, and Iso Surface renderings


AVI animations


Introduction

The 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;
  • Totem;
  • MPlayer;
without installing any third-party codecs.

How-to

The 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.

FreeSFP

In the freeware SFP volume renderer FreeSFP, animation is limited to a rotation about the vertical axis. The use is very simple: set the viewpoint and render parameters and hit the Animate button.

Sample animations

Image
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 animations

Besides 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 convert tool 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 dmconvert that directly writes QuickTime movies from a tiff series. Example: to convert the series animatedSfp_t000000, ..., animatedSfp_t000360.tiff to a .mov file use:
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:
  • Bink Video is a freeware program for Windows that creates AVI movies.
  • Apple QuickTime is a commercial software package for Mac OS X and Windows that makes H.264 QuickTime movies.
  • ffmpeg for converting a series of tiff images into a movie

Contact Information

Scientific Volume Imaging B.V.

Laapersveld 63
1213 VB Hilversum
The Netherlands


Phone: +31 (0)35 64216 26
Fax: +31 (0)35 683 7971
E-mail: info at svi.nl

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