Spots and tracks invisible when exporting from ilastik to MaMuT

I’m trying to export tracks from ilastik to mamut to manually check/correct them. However, both when importing the data via “open Mamut Annotation” as well as when merging the data with a new mamut project, the spots and tracks are invisible in the mamut viewer. They are present in the 3d-viewer as well as trackscheme, so I know they are (or at least something is) there. I have checked that “display spots” as well as “display tracks” are on.

so I have found the spots, but I have to zoom out a lot (to the point of the image being invisible) to find them. Adding new spots also adds them there. This issue doesn’t persist in all images. I assume that for some reason the image is shown at strange coordinates

Do I understand correctly, that the spots are not overlaid at the correct positions?
Does your original image come with some kind of scaling?

Hi @NicP,

Thanks for sharing your solution, glad it works for you now!

In the future, I’d recommend to just add a new reply with the solution and mark this post as a solution (using the icon below the post). That way, others can better follow the chronology of the discussion, and the solution will still be shown right below the first post so it can’t be missed.

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Ok, thanks. I’ll do that

For anyone else facing a similar problem: For me, the issue was with the scale. BDV took the Scale from the metadata, whilst ilastik did not. simply removing the scale in imagej before saving the bdv .xml file fixed the issue


hiya, don’t you need the scale in Ilastik? I want to track in Ilastik and have the results in MaMut too.
I am just confused as to why Ilastik doesnt take the scale…

Ilastik doesn’t use the metadata of the image, but if you have anisotropic pixels you can set the relative pixel edges along with other parameters in the automatic tracking workflow. We didn’t use the MaMut export option too much, but rather exported as csv and then converted to µm values by multiplying with the respective pixel lengths

you don’t happen to be in France by the way?? looking for an Ilastik expert here :slight_smile: