Animate stacks of images in ImageJ

Use the free photo processing program, Fiji, to make a gif out of your stack of z-stepped images! You'll produce a nice little video clip that scrolls through all of the layered shots that you've taken of your specimen.

The images were taken on a Zeiss Stemi SV 6 microscope with an Axiocam 105 color camera. There are a total of 56 images. We don't have an automatic z-stepper for taking stacks of images, but we manually roll the focus knob to capture each of the 56 shots. 

Thanks to my labmate, Silas Bossert, for the species ID. Anthidium oblongatum is not a native bee, but is introduced, as is the flower on which I caught it, Lotus corniculatus.

Anthidium oblongatum (Megachilidae) from Ithaca, NY

make a gif using ImageJ and your stack of images:

1. download Fiji, which is a distribution of ImageJ especially for image processing
2. make a folder only containing your images (I used tifs)
3. open the Fiji executable and then go to FILE > Import > Image Sequence; you can just click on one image and click 'open' (you can't select them all, but it will tell you how many images it counts in the folder) --> from here a scrollable window with your images will open
4. to save, go to FILE > Save As > Animated GIF (scroll down)​

The 56 images stacked with Zerene Stacker

 Also note:

• Watch the animation in Fiji by going to: FILE > Image > Stacks > Animation > Start Animation.
• It's a nicer video to save as an AVI file (but not as easy for the web).
• My first gif was too large, but I reduced the size of the final file by shrinking the image. Just go to IMAGE > Adjust > Size. I reduced these shown from a width of 2560 pixels to 1500. The final gif was 71MB which is still a big file, but I didn't want the bee to look any fuzzier than it is naturally!