A short decription on how to create movies from OMERO.

Creating a movie from OMERO

OMERO provides a script to make Mpeg or Quicktime movies from any image in the server. These movies are created by a script called, this script has a number of options: these include: selecting a range of Z,T planes, the channels to display. The movie can also show information overlayed over the image: z-section, scale bar and timing.

The resulting movie will then be uploaded to the server by the script and become a file attachment to the source image.

Viewing the movie

The make movie script allows you to save the movie in two different formats, a DivX-encoded AVI and QuickTime movie. To view the AVI you may need to install a DivX codec from DivX. It should be noted that the DivX AVI is normally 1/3 to 1/10 the size of the QuickTime movie.

Installing the make movie script

The make movie script currently uses the mencoder utility to encode the movies, this command should be in the path of the computer (icegrid node) running the script.

We have Mac OSX installs for mencoder which were originally provided here. Unzip and put the mencoder in the PATH available to the server, e.g. /usr/local/bin/. You may need to restart the server for this to take effect.

There are also macports, rpms and debs for mencoder.

Make movie also uses Pillow and numpy.

Make movie command arguments

A detailed list of the commands accepted by the script are:

  • imageId: This id of the image to create the movie from

  • output: The name of the output file, sans the extension

  • zStart: The starting z-section to create the movie from

  • zEnd: The final z-section

  • tStart: The starting timepoint to create the movie

  • tEnd: The final timepoint.

  • channels: The list of channels to use in the movie (index, from 0)

  • splitView: Should we show the split view in the movie (not available yet)

  • showTime: Show the average time of the aquisition of the channels in the frame.

  • showPlaneInfo: Show the time and z-section of the current frame.

  • fps: The number of frames per second of the movie

  • scalebar: The scalebar size in microns, if <=0 will not show scale bar.

  • format: The format of the movie to be created currently supports ‘video/mpeg’, ‘video/quicktime’

  • overlayColour: The colour of the overlays, scalebar, time, as int(RGB)

  • fileAnnotation: The fileAnnotation id of the uploaded movie. (return value from script)