I suspect we will discover over time that any mechanism capable of analyzing a brain to the molecular level will not be able to do it without wrecking the structure in the process.

Of course, I could be wrong. I wouldn't have thought you could fit a room-sized computer onto something the size of my fingernail, either. I suppose you could come up with nanobots that could move between the cells without disturbing anything, and transmit observed structural information to larger storage facilities outside the body.

But it would be one hell of a job:

^At birth, the typical brain probably contains over one hundred billion neurons, whose number slowly diminishes with age. Each neuron has a cell body and tens of thousands of tiny branches called dendrites, which receive information from other neurons. Each neuron also has a primary axon (a projection that can travel long distances in the brain) for sending data out of the cell, and axon terminals for communication with other cells.^

^If you look at Figure 1.1, you'll notice that neurons make contacts with other neurons, at points called synapses. Each neuron makes anywhere from a thousand to ten thousand synapses with other neurons. These can be either on or off, excitatory or inhibitory. That is, some synapses turn on the juice to fire things up, whereas others release juices that calm everything down, in an ongoing dance of staggering complexity.^

^A piece of your brain the size of a grain of sand would contain one hundred thousand neurons, two million axons and one billion synapses, all "talking to" each other. Given these figures, it's been calculated that the number of possible brain states - the number of permutations and combinations of activity that are theoretically possible - exceeds the number of elementary particles in the universe.

- Phantoms in the Brain by V.S. Ramachandran and Sandra Blakeslee^