Trackmate, how do I know what units the speed is in?


I’ve been tracking the movement of microparticles over cilia and capturing the paths on Trackamate. I can see from the data that it has velocity, speed and distance however how do I know what units the should be in. Ideally I would want it in µm/sec. I know the particle size is 10µm but I dont know how that related to speed of them.


TrackMate will use the units of the current image. You can set these in ImageJ using Image > Properties…:


The settings will be reflected in the TrackMate dialog:

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Thanks. Is there an easy way to find out the pixel width?

“pixel width” is actually a misnomer, since pixels are just sample points in space and don’t have an extent. What’s meant here is the pixel spacing, i.e. the distance between two sample points.

That’s determined by your image acquisition. If you use a calibrated system, the acquisition software might write the correct pixel calibration into your image metadata, and ImageJ (more specifically, Bio-Formats) will be able to read them.
But I wouldn’t always trust the metadata read by ImageJ, since it can get wrong in several ways. So be sure you know the scaling at which you acquire images. If necessary, you can simply measure the image of a ruler and calibrate the image yourself, using Analyze > Set Scale….

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I’ve managed to set the scale and its changed all the settings in trackmate which is good.

Last question (hopefully):

How do i set the time to have it in µm/sec? My frame rate is 31 frames per second. I see that in the picture above your time interval is set in seconds, mine automatically sets to frames.

Enter anything else than 0 followed by sec in the Frame interval field of the properties dialog.