Export TrackMate overlay to many individual ROIs

TrackMate is really good at finding my particles, and the preview function is a godsend (it takes hopelessly long to adjust the built-in particle analyser), however I can’t seem to figure out how, if possible, to export all the TrackMate overlays to individual ROIs, that I can analyse with other plugins.

Any hints?

Hi @komodovaran

So far there is only one action that exports spots as ImageJ1 multi-points, and for reasons I cannot derive now, it is disabled.

Are you looking for something like this?

I don’t know. I think I might be…? Elaborate please :grin:

There is an option to save the points from TrackMate to an xml file, but I don’t have the required knowledge to reformat this data automatically for other plugins.

Ok so the ROI exporter is in a separate package called TrackMate-extras. You can find it here:

You have to compile it, make it a jar and drop it in your Fiji/plugins folder. An action called “Export current spots to IJ rois” will appear in the menu of the action panel (the very last one in the GUI).

Hope it works for you!

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Okay, so I’ve tried compiling it with Maven, using

and I get the error

I’ve never compiled anything before, so I’m completely at a loss here. Help please.

Ok I will have to come back to you when I have a real computer. Right now I am away from the lab.

For me, the following worked after cloning the TrackMate-extras repository and cd the repository folder:

mvn clean

@komodovaran Why did you provide a path, and what path did you use?

Turns out Maven had insufficient permissions to meddle with the folder contents. I fixed the permissions and now it works fine by cd’ing to the directory, and doing above commands.

However, new problems: the ROIs are not centered. In fact, they don’t even turn into circles (is that supposed to happen? Would be much more helpful if they kept the same dimensions as the purple overlay).

Grmlmlml it seems like there is a +1 shift in the ROI positions.

Right now this tool only returns the spot positions as a multi point IJ1 ROI. Anything more will have to be coded.


I am looking for the ROI exporter described in this thread; however, I do not have any knowledge of using Maven or any other software management tools that would allow me to compile the ‘Trackmate extras’ as suggested. Can I request if possible for the compiled version (.jar) file of ‘Trackmate extras’ which I can use?

Thank you.

Best regards,

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I filed a PR (tinevez/TrackMate-extras#2) to let Travis CI build the TrackMate-extras component. If @tinevez merges it and turns it on, then builds will start appearing in the ImageJ Maven repository, so that users do not have to build it by hand.


Will do. I need to allocate the time to do it. Please stand by.

Thanks. It should be that enabling Travis takes you less than 3 minutes of your time. If not, let me know how else I can help.

Again thank you @ctrueden.

I fleshed out the TrackMate webpage with the links to downloadable jars:

@komodovaran I hope you find it useful.

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Many thanks for the downloadable .jar files @tinevez, @ctrueden.


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sorry to put back this thread after years,
since I am having some troubles with Trackmate-extras track analysis:

I was trying to download again and test it.
I think the .jar links is not working anymore.
could it be possible or is it a problem of my connection?