Friedrich Forstner is a PhD student at the Max Planck Institute of Neurobiology, Martinsried, Germany. He studied bioinformatics at the Ludwig Maximilian Universitaet and Technische Universitaet Muenchen/Munich and is interested in mathematical and computational descriptions of biological systems and their visualization.
www.neuro.mpg.de/english/people/foerstner_f.shtml
In this talk I wanted to show how I use Blender in my PhD project to visualize, arrange and investigate neural networks from the visual system in flies.
There are about 60 connected neurons in the fly's brain that we think are mainly responsible for motion processing. These cells have been investigated for over 30 years. The aim of this project is to gather all available knowledge about these cells that has been published so far and to build a computer simulation that works like the real network.
What I have are detailed anatomical reconstructions from in vivo images, a preliminary circuit diagram and some electrical and chemical properties of these cells. A lot of open parameters are still to be fitted or guessed.
This is the recent workflow draft:
1. stimulus
Blender is used to create a virtual flight of a fly through a 3D-World. It also takes the fly's 360 degrees field of view into account and records movies.
2. model
based on published data the model is anatomically setup with Blender, electrically with the Neuron Simulation environment [1]
3. simulation
after application of special filter functions the recorded flight is given as input to the network, calculations are done using common network simulators
4. results
what we get out of the simulations are e.g. voltage values for each position in the cell in each time step of the simulation, I use Blender to map the color coded values onto the anatomical model and to access the local data interactively
This work is still in progress and estimated to be finished in 2009. Besides the gain of scientific working experience in the end I would like to present what we already know about this system, what still has to be investigated and to create an intuitive tool that enables other interested people to browse through the data.
If you are interested in this project please read the commented presentation or contact me directly.
[1] Neural Networks in the Cockpit of the fly, Borst A, Haag J, J Comp Phys, 2002
[2] NEURON: A tool for neuroscientists, Hines ML, Carnevale NT, Neuroscientists. 2001
Download here the presentation.