Редактирование: Whole brain emulation (раздел)

=== Optical Procedures ===

Optical microscopy methods are limited by the need for staining tissues to make relevant 
details stand out and the diffraction limits set by the wavelength of light (≈0.2 μm). The main 
benefit is that they go well together with various spectrometric methods (see below) for 
determining the composition of tissues. 
 
Sub‐diffraction optical microscopy is possible, if limited. Various fluorescence‐based methods 
have been developed that could be applicable if fluorophores could be attached to the brain 
tissue in a way that provided the relevant information. Structured illumination techniques 
use patterned illumination and post‐collection analysis of the interference fringes between the 
illumination and sample image together with optical nonlinearities to break the diffraction 
limit. This way, 50 nm resolving power can be achieved in a wide field, at the price of 
photodamage due to the high power levels (Gustafsson, 2005). Near‐field scanning optical 
microscopy (NSOM) uses a multinanometre optic fiber to scan the substrate using near‐field 
optics, gaining resolution (down to the multi‐nanometer scale) and freedom from using 
fluorescent markers at the expense of speed and depth of field. It can also be extended into 
near field spectroscopy.  
 
Confocal microscopy suffers from having to scan through the entire region of interest and 
quality degrades away from the focal plane. Using inverse scattering methods depth‐
independent focus can be achieved (Ralston, Marks et al., 2007).  

==== Optical Histology ====

All‐optical histology uses femtosecond laser pulses to ablate tissue samples, avoiding the 
need for mechanical removal of the surface layer (Tsai, Friedman et al., 2003). This treatment 
appears to change the tissue 2‐10 μm from the surface. However, Tsai et al. were optimistic 
about being able to scan a fluorescence labelled entire mouse brain into 2 terapixels at the 
diffraction limit of spatial resolution.  
 
Another interesting application of femtosecond laser pulses is microdissection (Sakakura, 
Kajiyama et al., 2007; Colombelli, Grill et al., 2004). The laser was able to remove 100 μm 
samples from plant and animal material, modifying a ~10 μm border. This form of optical 
dissection might be an important complement for EM methods, in that, after scanning the 
geometry of the tissue at a high resolution, relevant pieces can be removed and analyzed 
microchemically. This could enable gaining both the EM connectivity data and detailed 
biochemistry information. Platforms already exist that can both inject biomolecules into 
individual cells, perform microdissection, isolate and collect individual cells using laser 
catapulting, and set up complex optical force patterns (Stuhrmann, Jahnke et al., 2006).