Import masks into TrakEM2

imagej
trakem2

#1

I would like to import a confidence map / mask into TrakEM2 as an annotation layer which can be used for segmentation. I have looked in the forum for threads about this but could only find import info of raw images/stacks.

Background for why I want to do this: I am running a deep learning model to create a confidence map for dendrites. I would like to bring a representation of it, as masks which would behave as annotations made in TrakEM2 so that I can trace the dendrite segments and their branching.

Any help would be greatly appreciated!
Thanks!

Luciano


#2

Hi @LucianoLucas,

Short answer:
After right click you can Import > Import labels as arealists..
which seem closest to what you want.

I’m not completely clear on what you would like to do after importing the confidence map though - do you want to use it to guide tracing/manual painting? (i.e., prevent you from looking where there is low confidence?).

If you only want to look at them, then it would seem that importing them as images should be fine. If you want to mask some other image, then you’ll have to threshold your map at some level, in which case you could do that outside trakem2 and then import it as an arealist as above.

I may also just be totally misunderstanding, hope this helps anyway,
John


#3

Hi @bogovicj,

Thanks! Your replied helped us move in the right direction.

To reply to your question:
We wanted to import the confidence maps and automatic segmentation masks we generate from them into TrakEM2 because our collaborator currently uses it to manually trace/manual painting.

See data in TrakEM2 below!

Thanks!
Luciano