As part of my ongoing PhD in computational biology I've needed to look at methods of visualising simulated multi-cellular structures (tissue) in 3D. CompuCell3D (the modelling environment on which I develop) has the facility to render opaque surfaces of clusters of cells of the same type, which can allow you to see broad structural detail, but generally not the behaviour of individual cells. I developed a visualisation that shows individual cell surfaces, each coloured according to a chosen cell variable (for me, the level of protrusive activity), as seen in this rotation of a model 'engineered epithelial tubule':
Of course you might be interested in a certain region or cell, so I use the VTK cursor widget to allow selection of a point or cell around which cells are displayed, opacity decreasing with distance. I'm also interested in cell paths, so I incorporated these as well. This image is of the same tubule showing the region around one cell of interest, along with some other cell paths:
I recently wrote an article with this title, shamelessly exploiting the popularity of a certain famous Cell paper, and it's available to read or download on Scribd. It's a light-hearted discussion of the merits of computational modelling in biology, some of it serious, some of it less so, but all very pertinent.
Apparently there are lots of people called Dan Lea using the internet, but of course most of them aren't me.
People like Dr Daniel Lea, who is also a British physicist, and whose field of research is not dissimilar to that in which I undertook my MSci project. I do enjoy photography, but I'm not a professional like the man running danleaphotography.com, and although I played bass for redbluegreen I'm not offering bass guitar tuition in Halifax, like danlea.net. I may have done some science outreach events for children in London, but I'm not an award-winning teacher. Don't think that just because I'm a musician that I write music for film, or that I lecture in comtemporary literature at Oxford Brookes University just because I'm typing away here. To keep the list to a palatable length, I'll finish with a link that's unlikely to cause confusion: living in Ealing, I don't have a farm on which I breed the finest in AKC Registered Show or Pet Great Danes and Irish Wolfhounds.
