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scalableminds / webknossos

Visualize, share and annotate your large 3D images online
https://webknossos.org
GNU Affero General Public License v3.0
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3D Brush Tool #7634

Open thorstenwagner opened 9 months ago

thorstenwagner commented 9 months ago

In other tools like Amira or DragonFly you can use 3D brush. We use this a lot in combination with otsu thresholding (https://github.com/scalableminds/webknossos/issues/7626). As far as I can see this is not available in Webknossos.

Would be great to have this implemented :-)

normanrz commented 9 months ago

Hi @thorstenwagner, could you please explain your use case for 3D brushes in more detail? Is it just useful for quickly annotating spherical objects? Thanks!

GavinR1 commented 9 months ago

Hi @normanrz I can comment here. Our main data type is cryo-electron tomograms where we segment individual macromolecules, larger protein complexes and organelles in their native cellular environment. Due to the high resolution of our data (voxel sizes range from 1-10 angstoms) a large macromolecular complex like a ribosome or an actin filament will persist through several Z-slices. Rather than annotating the density for each slice independently, 3D brushes with otsu thresholding allow us to navigate to the slice where a filament or particle is centered, adjust the size of the spherical brush appropriately, and then make one annotation which then fills the corresponding voxels in the above and below slices.

In practice this makes accurately segmenting these data significantly faster and easier than with a full brush or having to annotate each slice independently.

normanrz commented 9 months ago

I was wondering how a 3D brush would compare to the volume interpolation feature for your use case?