Reconstructing a kiwi fruit… with SBEM (sort of)
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.
ACQUIRING THE DATA
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.
The biggest challenge was to cut the sections very thinly — for a good Z resolution!
ALIGNMENT AND PRE-PROCESSING
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.
Watch the video to see the experiment in action!