[ExI] HM

[Eugen Leitl]

On Sun, Dec 06, 2009 at 04:52:06PM +0100, Anders Sandberg wrote:

> If the brain has volume V and you slice it in thickness t slices, you will get ~V^(1/3)/t slices, with a total area of V/t. 

I don't think a single scanner stage can handle more than a cube of cm^3 or so.
Even that might be a tad on the optimistic side.
 
> In the case of doing a 50 nm slices of a 450 mm^3 mouse brain, this means 153,000 slices with a total area of 9 m^2. The same case with a 1400 cm^3 human brain gives 2 million slices and total area 28,000 m^2. 
> 
> Todd and the KESM team have a 2 Tb datasets of a mouse brain, but that is of course just optical resolution. Enough to see the neurons, but not enough to get connectivity.

Right now we can handle about a PByte dataset comfortably. 10 PBytes less
comfortably, and 100 PBytes with a lot of pain. It will be
a while until we're in easy EByte country. Obviously we cannot
hold even a mouse voxel dataset explicitly, so for tracing/segmentation
you have to work with a sliding slice (anywhere in a 1 um-100 
um depth). The result would be a lot more compact, and also quite
compressible (very little difference between adjacent slices).
 
> From a WBE perspective, the big problem is getting the scanning area up and the scanning time down. If we have N microscopes scanning an area A in time T, the total time will be V/tNAT - plus overheads due to tissue handling, presumably scaling as V^a t^-b N^c for some positive constants a, b and c (more stuff to handle, more slices to move, more destinations for slices). If A and/or T can be increased, then the total time is reduced without extra overhead. 

The problem is that a dm^3 is 1000 cm^3, so these cm^3 scanner
stages (at about ~nm resolution laterally) be better cheap. This 
is something which will make even Paul Allen's people blanch.

-- 
Eugen* Leitl <a href="http://leitl.org">leitl</a> http://leitl.org
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