Dave Mitchell's DigitalMicrograph™ Scripting Website

D. Mitchell and Frank Niessen
23/7/19

1. Download the Windows 64bit Fiji variant of ImageJ available from:

https://imagej.net/Fiji/Downloads

2. At the download prompt – choose Save, and save it to the Desktop. The download may take several minutes.
3. Create a folder on your desktop called Fiji.
4. Locate the downloaded Fiji program, which downloads as a compressed archive called Fiji-win64.zip. Double click on this to launch a decompression program. If you do not have one installed – Google Peazip
5. Choose the Extract option and extract the files to the empty folder called Fiji, which you just created on your desktop.
6. Move the Fiji folder to somewhere inside your User folder eg Documents. Do NOT put it into any of the Windows Program Folders. It must go to a location which you have write permission to.
7. Open the Fiji folder and locate the ImageJ-win64 application. Create a shortcut to this by click and dragging it to the taskbar at the bottom of the screen. Alternatively, right click on the icon and choose ‘Create Shortcut’. Then copy the Shortcut to somewhere convenient, like the desktop.
8. Launch the Fiji program (from the Task bar or from the Shortcut you just created) and have the program shown front-most.
9. An update may run when you launch it – click yes and let it update.
10. In the Windows desktop locate the DM stack file you want to convert to a movie (.dm4 extension) and drag and drop the stack onto the work area of Fiji (where it says ‘Command Finished – in the row below all the tool buttons).
11. A prompt will appear – choose the options ‘All Series’ and ‘Greyscale’ (see below).

12. The stack opens in Fiji. You can adjust the stack before converting it to a movie.
    • To add a scalebar choose Analyze/Tools/Scale Bar.
    • To adjust the brightness/contrast choose Image/Adjust/Brightness and Contrast. You can play the stack through my moving the slider below the stack from left to right.
13. When you are happy with the way the stack looks save it as a movie by choosing File/Save As/AVI format. A prompt appears – choose the JPEG format. Set the frame rate to suit the speed at which you want the move to play. If you want your movie clip to last say 10s and you have 80 images (slices) in your stack, then choose a display rate of 8 frames per second (fps) ie movie duration = total number of slices/Frame rate.
14. The movie file you have now saved can be played in the built-in windows movie player – just double click on the saved movie file and the player should launch and play.
15. Note this process dramatically reduces the file size. A DM stack of just 10 slices may be 30MB in size. The resulting move may be only 30KB in size.
16.  Play movies on your movie player of choice. If you want to embed movies into a Powerpoint presentation, have the Powerpoint slide open. Click on the Insert menu item to display the Insert tab commands. Click on the Video option and select Video on my PC – and choose your movie file. Embed the movie and resize and position to suit. To set how the movie starts, right click on it and choose Start. You can set the movie to start automatically as soon as you open the slide, or you can set it to start only when you click on the movie. For more sophisticated control use the controls in the Animation tab.