Maybrain update

It's time for an update on the brain  simulation project, Maybrain. The aim is to combine a few Python modules to be able to map and manipulate the connectome of a brain (i.e. neuronal nodes and their connections) and show in conjunction with isosurfaces of the skull and other data.

There's been a few important changes over the past couple of weeks. We implemented algorithms for degeneration, either by node spatial proximity or along edges connecting nodes. There's also a whole host of analysis and input/output functions that will no doubt continue to expand over time.

On a programming level, you can now call Maybrain as a Python module and there are maybrain.write and maybrain.analysis functions to neatly separate out the writing and analytical functions from those that actually change the connectome, which are still in maybrain.brainObj. All this is explained on the wiki quickstart guide, although other wiki changes are lagging behind the development a little at the moment!

Here's a taster of the degeneration functions on a 10 by 10 grid where each node is connected to its four nearest neighbours.

Maybrain

This will be brief, more details to follow! I've just established a project on googlecode called MayBrain. Ok, so the name is a bit lame, but it is trying to get at the project being the application of Mayavi, a powerful 3D visualisation program in Python, to look at brain data.

Very little of the plotting code is original, it's just patching together modules for loading, analysing and visualising the data. The hope is that it will be useful for those working in neurology to quickly visualise data, overlay several different kinds of data and create videos to share.

If you want to get involved, please do! I'm indebted to my brother, Tim, for kicking off the project and writing a lot of the code before I became involved.

Over the next few days and weeks, the plan is to add a few extra features, finish off the GUI and write  a wiki so that it can actually be useful to someone some day.