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Making movies with ImageJ

ImageJ can read in a number of image formats and has a graphical user interface (for those who don't like mpeg2enc). However in saving a movie it can only build .AVI files (unless you're using a plugin).

To make a movie using ImageJ:

  1. save your images in a folder:

    • if your script saves file names without space-filling 0's (e.g. Image1.jpg, Image2.jpg ...., Image10.jpg, ...., Image112.jpg) you can simply rename them using the 'rename' command.

    • the following will convert them all to 3-digit numbers:

      > rename Image Image0 Image?.jpg
      > rename Image Image0 Image??.jpg
  2. open ImageJ:

    • if you don't have it, download from
    • the linux version is quite big (25mb) because it contains Java runtime stuff.
    • in other OS's, the binary files are typically below (<2mb) (no I'm not lobbying for Windows!)
  3. open the images in ImageJ:

    • click on File>Import>Image Sequence...
    • just click on any of the file names that appear in a list
    • in the dialogue that appears, fill in the box for "File Name Contains" if your directory contains more than just the images
    • The image size can be arbitrary but it doesn't like compressed Tiff files (requires a separate plugin to do this).
  4. to make sure everything's ok, check the opened stack by pressing

    • real time animation through the stack should start. you can stop this by pressing esc or again. you can also move backwards and forwards by , (<) and . (>) keys.
  5. save the AVI file by clicking File>Save as...>AVI

    • enjoy