github.com/cvetkovicdamjan/neurilium @main

neurilium

Simple and fast code to simulate small brains.

quick start

How to simulate fruit fly brain using this tool:
Go to CodexFlyWireDownload
You would probably need to signin to download the data
Download Neurotransmitter Type Predictions, Connections (Filtered) and Marked Neuron Coordinates
Extract those 3 csv files and they should be named neurons.csv, connections_princeton.csv and coordiantes.csv
Clone this repo and inside made a data/ folder
Place 3 csv files into data/ folder
Then just run cargo run

controls

right mouse click/hold + wasd to pan and move
q and e to go down and up

architecture

Code is really simple:

loader.rs - loads neurons and connections
renderer.rs - setups wgpu and renders neurons
shader.wgsl - shader used to display neurons
camera.rs - controls camera
simulation.rs - manages neuron data for compute shader
compute.wgsl - simulates neurons
main.rs - glues everything together

Simple, easy to thinker, that is the point.

why?

Why Izhikevich neuron model?
Izhikevich neurons are both computationally simple and they produce great neuron behavior.

Why use rust and wgpu?
Because they raplace C++, CUDA, Vulkan stack in increadibly better and unified way.

Why fruifly brian for example?
Because it is currently most complex full brain we mapped.

Why not use AI to simulate brain?
Because AI and neuromorphic computing works fundamentally different.

other brains

Try thinkering the code to simulate other brains.
Here are some ideas what other brain to simulate:
H01 - small area of human brain reconstruction
MICrONS - small area of mouse brain reconstruction
Hildebrand17 - zebrafish whole brain reconstruction
WormWiring - worm whole nervous system reconstruction
Those links don't point to datasets, but with a bit of effort you will find them.
Good luck!

acknowledgements

Thanks to the team from FlyWire and CodexFlyWire for having datasets of fruifly brain availbale to everyone. Their effort makes brain simulation possible!