What is the best software platform for annotating microscopy movies?

Does anyone know of any software platform that is good at adding annotations to microscopy movies? For example - what if you want to highlight some moving cells midway through your stack - following them with arrows or so? What tools/workarounds have people come up with for such things?

Many thanks!

This question was also posted on the image.sc forum:

I do this in ImageJ/Fiji. You can add/manipulate an arrow on your image in Edit>Options>Arrow Tool until you get it where and when you want. Then “stamp” it on the image with Edit>Draw. I think there’s a way to draw on all time frames, but I typically only want it for a subset and/or I want it to move in different frames so I navigate to the correct time frame(s) and draw that way.


Agreed, Fiji is of course a winner. There are a couple of different options for timestamp overlay too which makes it really useful. https://forum.image.sc/t/how-to-apply-time-stamp-as-an-overlay-in-fiji-imagej/3304

Another option that gets into the area of a video editor would be to use the VSE section of Blender https://www.blender.org/ This has a stepper learning curve, but you can so much more once into the details.

It can also be done in Photoshop. You can add an arrow in a new layer, get the animation view from the view menu, and then the position of the arrow layer can be ‘tweened’ between different frames. I don’t recall the exact specifics, but it’s very doable and looks nice. You’ll then need to export and render the animation to save the output.

If I find time, I’ll make a YouTube and post back here.


Just saw the video in this post, which looks like it might be useful if you can figure out what created it…

I have no access to the supplemental videos at the moment, though.