Tools for assisted correction of 3D segmentations?

segmentation
#1

Hello everyone,

I have a project where I do an automated 3D segmentation to create a binary mask of (a single) 3D object. The segmentation works reasonably nice but the shape is not quite ok and some parts of the volume were not detected. The raw data quality varies, so full automation of the segmentation is unlikely and I need the user to correct the mask manually.

In ImageJ one solution would be to display every single slice of the mask as a ROI region and then correct it with the brush tool. This does not sound very efficient though and there are probably smarter ways (like interpolating regions, etc).

Does anyone know of existing tools which assist in correcting a 3D segmentation/mask? For example by doing automatic interpolations or suggestions, or by providing an efficient GUI, or other?
Thanks already for any hint!

1 Like
#2

I know that @haesleinhuepf developed a tool that kind of did somthing like this…
Maybe it is available via this update site: https://sites.imagej.net/SCF-MPI-CBG/
It was a 3D ROI Manager with interpolation.

If it is not available via the update site you might want to ask @haesleinhuepf nicely =)

1 Like
#3

Hi @noreenw,
try MIB (http://mib.helsinki.fi) for that at least interpolation is there…

Ilya

#4

Hi @noreenw,

I usually use the simple yet powerful SegmentationEditor .

Best,

Thomas

1 Like
#5

Hi @ThomasBoudier,

this looks like an interesting tool! I didn’t know about it. Do you happen to know if it is possible to import a pre-segmentation (like a label image), I couldn’t find something in that direction?

#6

Hi @noreenw,

You can use this tool with an already labelled image, you can then add new objects. If you want to modify existing labelling you may want to use the drawing tool (like pencil, brush) directly in the labelled image. Maybe other software may handle label data in a better way.

Best,

Thomas