Printing neurons in 3D from WEBKNOSSOS
For the Connectomics conference, we wanted to create neuron sculptures to showcase the beauty and complexity of the brain through art. As many of you know, the shape and architecture of neurons are extremely challenging to reproduce. Instead of building a full neuron in 3D, we focused on synapses, allowing us to zoom in on this particularly interesting region.
We based our sculptures on data published in “Connectomic Comparison of Mouse and Human Cortex” by Loomba et al. (Science, 2022) that was reconstructed with Voxelytics, our AI neuron reconstruction pipeline. We selected different types of synapses from various species:
- Mouse spinehead synapse: Reconstruction of an excitatory axon forming a synapse at the spine of a layer 2 pyramidal cell dendrite in the anterior cingulate cortex of a 56-day-old mouse. Data from Karimi et al., 2020, eLife. See on WEBKNOSSOS.
- Human shaft: Reconstruction of an axon forming a synapse at the shaft of a layer 2 pyramidal cell dendrite in the inferior frontal gyrus of a 69-year-old female. Data from Loomba et al., 2022, Science. See on WEBKNOSSOS.
- Macaque soma synapse: Reconstruction of an axon forming synapses with the cell body of a layer 2 pyramidal cell in the superior temporal gyrus of a 15.6-year-old male rhesus macaque (Macaca mulatta). Data from Loomba et al., 2022, Science. See on WEBKNOSSOS.
Let us show you our process and what we learned along the way!
Step 1: Exploring synapses in WEBKNOSSOS and downloading the meshes
First, we opened the connectome files on WEBKNOSSOS and explored the data. Clicking on a neuron revealed its synaptic partners, making it easy to select a synapse, locate it in the EM data, and load the corresponding meshes to ensure it was a good candidate for the sculpture. Then, we downloaded the meshes as STL files, ready to edit them in other 3D programs for printing.
Step 2: Preparing the meshes for 3D printing
We imported the meshes into Rhino (though any other 3D software like Blender or even the slicer program from the 3D printer should work), trimmed and scaled them to fit our vision, and oriented them to minimize support during printing while ensuring stability. For complex dendrites, we even cut them in half lengthwise to glue together later. We also decided to smooth some meshes using the “Smooth” and “Subsurface Division” modifiers in Blender.
Once everything was ready, we printed the presynaptic partners (axons) in black and postsynaptic partners in blue. We made the sculptures out of PLA filament, a material known for its easy printability on our desktop FDM 3D printer.
Step 3: Assembling the 3D puzzle!
Now for the fun part. Once the neuron pieces were printed, we needed to assemble them. We thought it would be challenging, constantly comparing with the 3D file on the computer to align the synaptic partners correctly. However, we soon realized how biology was going to help us out: the neurons’ shapes had natural marks where they touched other neurons. Like a 3D puzzle, the pieces fit together remarkably well. Some didn’t even need glue and are simply held by the tight fit caused by the morphology of the neurons.
Step 4: Building the presentation boxes
Lastly, we built transparent boxes to display the sculptures and keep them in place. We used a wooden plate for the base, laser-engraved with our logo, and assembled the acrylic walls — carefully avoiding excess glue. We then placed the neurons inside, added a bit of glue for security, and finally, placed the transparent lid.
This project was incredibly fun and fascinating. Observing the cells in real life and holding them in our hands, we could truly appreciate how they fit together — something hard to see on a screen!
