Reconstructing a kiwi fruit… with SBEM (sort of)


Volumetric kiwi. Check out the dataset!

How would you explain SBEM/volume EM and 3D reconstruction to your grandparents?
With a camera, a knife, and a kiwi fruit.

We sliced and recorded a whole kiwi and uploaded the data to WEBKNOSSOS. We aligned and segmented all slices, densely annotated the boundaries and extracted 3D meshes. 
Here are the results! We might lack some resolution compared to a real EM but on the other hand you easily get the idea.


First, we set up our working area.
● We used a table as the “(moving) sample stage”, on which the fruit would stand during each recording.● A high-resolution DSLR camera, our substitution for an “electron beam scanner”, was mounted stationary on a tripod so that it could photograph the kiwi from the top along the process.● We used a super sharp knife, the “ultra-microtome”, to slice the fruit in sections as thin as possible.● And of course, the “tissu sample”: our kiwi.


Setup of our working area.

Then, we began the recording process. We cut the kiwi slice by slice, being careful not to move it from its platform. We used a remote trigger for the camera to photograph the kiwi with as little motion as possible and repeated the process again and again.


Cutting a kiwi slice...


... and repeating.

The biggest challenge was to cut the sections very thinly — for a good Z resolution!

Of course, the kiwi and the camera did not stay completely still during the acquisition of the data. Thus, we used Voxelytics to align it and get a perfect 3D dataset.
With the annotation tools of webKnossos, we segmented the data in no time. With a combination of the quick-select tool and the interpolation tool, the actual brushing was necessary only on a few sections. The whole volumetric reconstruction took us less than 5 minutes.


Segmenting the kiwi with the quick-select and the interpolation tool.


Computing meshes of the two segments.

Watch the video to see the experiment in action!

PS: No kiwi went to waste — it ended up as a delicious, super-thin snack for the team.