Splitting spatially distinct segmented Arealists

splitting
trakem2
Tags: #<Tag:0x00007fd547b96a30> #<Tag:0x00007fd547b968a0>

#1

Questions about splitting AreaLists

We used Ilastik for segmentation and then identified and created individual objects in Ilastik. We then imported into TrakEM2 as AreaLists. However, after import we discovered that some of the AreaLists include >1 object, when viewing in 3D. We have tried to identify a way to split an AreaList, or to Duplicate and then delete part of an Arealist, but have not identified any solutions in our search of the manual and through the online resources and forums. Is there a way to any of the following without writing a script?

a) delete a portion of an AreaList (eg. half of the layers in which an Arealist exists)
b) split an AreaList of unconnected objects (the objects themselves are distinct in space, but share a common colour-which is probably the initial issue causing the overlap in naming when re-importing from Ilastik to TrakEM2)
c) split an Arealist into separate AreaLists (by knowing which layers contain which objects).

We have identified a solution in Blender, if we export and separate vertices by loose parts or by selection-then renaming the newly separated parts), but can we re-import to TrakEM2 and keep the new names of objects with their registration to the original images?

Thank you,
Kerri


#2

@Kerri_Ryan

Sorry for the delay in response… and sorry too I cannot help you in your specific issue here. But - perhaps @albertcardona or @axtimwalde can assist you??

eta


#3

I just wrote the function to split an AreaList instance into multiple AreaList, separating into each a spatially separated volume. It’s in the master branch, and appears in the popup menu as “Split”. Select any number of AreaList instances and run it.

Will make it into the Fiji updater soon.