Python scripts to load swc files from neuromorpho.org into Blender. The part of the script that actually does the heavy lifting of loading swc files into Blender uses code from Martin Pyka's SWC2Blender package, which needed some modification to be working in Blender 2.8.
This Jupyter notebook and accompanying Python script allow users to programmatically access neuronal reconstructions from the NeuroMorpho.org database. For example, one can play neuro-roulette by finding random neurons:
Once you find one you like, find it's unique ID : i.e for this example neuron
NeuroMorpho.Org ID : NMO_56794 Only the number "56794" is needed to download it's swc into Blender.
In addition to the files in this repo, additional summary data files must be downloaded from: https://drive.google.com/drive/folders/1PMbQZ6UIU8ZXup8qidgtzbtOh_nNald8?usp=sharing
I am providing this summary so that the NeuroMorpho server doesn't get overloaded
Images and 3D models of the neurons can be previewed in the notebook. An animation of the neuron can also be rendered in Blender 2.8 using a headless instance of Blender.
If Blender 2.8 is already installed, the trickiest part of the process is making sure that the relevant packages are installed in the Blender Python installation (not the same as the Python environment used with Jupyter)
To do this, open a command prompt and navigate to where blender is installed, i.e.
cd path_to_blender\2.80\python\bin
The ensure pip is there:
python.exe -m ensurepip
Then install the missing dependencies, (Pandas, neuromirpholib):
python.exe -m pip install pandas --user
python.exe -m pip install neuromorpholib --user