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ImageJ-Fiji Quick Tip #2: Easily annotating videos

Updated: Jun 16, 2020

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"...