ImageJ-Fiji Quick Tip #2: Easily annotating videos

Updated: Jun 16

Showing a video with annotations is really efficient for lab meetings, conference talks. Here is a note to show you how you can quickly and easily annotate a video / time-lapse acquisition with ImageJ - Fiji software…

Give Me the Protocol

  1. Open ImageJ - Fiji and open your time-lapse video

  2. Choose a tool to make your annotation (e.g. the oval tool)

  3. Create one annotation and then press “t” on your keyboard

  4. Move to the next image and move/modify your annotation and press again “t”

  5. Once you have finished, click on "More > Options" in the ROI Manager window and tick the option "Associate Show All ROIs with slices" if not active

  6. Then Image > Overlay > From ROI Manager

  7. You can then save your video as .avi (File > Save As...)



Note: not satisfied with the result? Delete all annotations with "Image > Overlay > Remove Overlay"...


Some explanations...

Let's explain a bit what's happening here...


  • Setting the option "Associate Show All ROIs with slices" to be active ensures the ROI manager remembers where you annotated your image. It remembers the channel, the z plane and the timepoint!

  • We picked the oval tool as an example but all other shapes and text are also compatible!! See the final example below...

  • "t" is the default shortcut to add a new ROI in the ROI manager (as seen on the button itself) Important note: for text annotations, use “CTRL + t” to save each label in the ROI manager, to avoid writing a t character...

  • If you start exploring the "Overlay" menu, you'll see that you can also "Add Selection" without storing it in the ROI manager. The latter is just so much more convenient as you can come back to any selection...


Additional Thoughts

One very important note is that annotations are pixel based, so they can appear very pixelated on small images. To circumvent this, just use the "Image > Scale..." tool to enlarge your image before creating annotations.


Also, the ROI manager is a fantastic tool including a lot of options. Some interesting ones, related to this annotation topic, are:

  • "Update" button if you want to adjust only one shape, adjust the angle of one arrow, etc.

  • "More > Save..." is almost mandatory, as it allows you to come back to it later on. Let's imagine that your boss says: "Nice video! Could you just remove the arrows on the two last frames..."

  • "Properties..." to change the color of the shape.

  • Check the documentation for other functions...


Also, remember that the ROI manager can apply the shapes to any image that has compatible dimensions. This means you could have the exact same annotations on two different images... for comparison purpose for instance!


Be creative, but not too much :)