Scale Bar for Microscope Video

I’ve learned how to use Fiji ImageJ to bar scale microscope still images in microns. When I try to bar scale microscope videos I get nowhere. I can’t find any info online or in the manual. Feel free to jump in right here. Thanks, Mike

Is the metadata present in the video file, so that FIJI knows what the pixel to micron scale is? If not, you can manually enter the scale by going to Analyze>Set Scale. Not sure if that is your issue, the scale not being correct?

Fiji won’t open the video so going to Analyze won’t work since there’s nothing to analyze.

When I try to open the video, I get a box with a bunch of check-offs. Since I haven’t a clue as to what to do, I simply hit OK. Then I get an error message as follows. Have you had this kind of experience yourself?


What is the file format of your video? I’ve had trouble opening .mov and .mp4 files, my videos are usually either kept in the microscope file format (nd2, oib, etc), TIF stacks, or avi. The window you are seeing is Bio-Formats, which is how ImageJ opens microscope file formats. I usually have View Stack With set to Hyperstack, not Standard ImageJ. Try that?

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Thanks for the information Sara. Found a way to open a video file. There’s an excellent video on YouTube by Lipke Lab which involves downloading a plugin called FFMPEG. ImageJ does this automatically for you, all you have to do is check off some boxes. Lipke shows you how to do it with a silent video. If you watch it, go to full screen and half speed, which makes it a lot easier to understand. Now that my videos open (all mov and mp4), I still have to figure out how to fill in the Distance in Pixels blank in the Set Scale Dialogue box, which has to be done before going on to the Scale Bar dialogue box. This number is usually provided by ImageJ when opening a photo, but it is missing when opening videos. I can probably work around it by taking a still of one of the frames of the video in question and opening that. Can’t believe no one else seems to be having this problem. Here’s the link: Best, Mike

One final comment. I missed up. The Distance in Pixels number that Fiji provides comes from the line drawn on the image of the stage micrometer, not the video image. The final result looked like this (the scale bar disappeared as soon as the video started running):

If your scale is incorrect, you can go to Analyze, Set Scale, and type in the correct value. If your image stills are correct, you can look at what the scale is for those at Set Scale, and then change it in your video files.

When you go to Analyze, Tools, Scale Bar to create a bar for your video, if you have Label All Slices selected, it should label all frames of your video. If Overlay is checked, it will maintain it as an overlay, if unchecked, it will burn it into the image and it will be permanently there and not modifiable.

I wasn’t sure what overlay meant, thanks for explaining it. Don’t recall having Label All Slices as a choice in Scale Bar. Will check again. Thanks again for your help, Sara. Best, Mike