Synapse Resolution Whole-Brain Atlases

It is well-known that the highest resolution whole brain atlases are currently at BrainMaps.org, which has been compared to a Google Maps for the brain. However, these atlases are 0.46 microns per pixel, and are not sufficient to discern individual synapses, which require nanometer resolution. So in this post, I will consider the problems associated with constructing a synapse resolution (nanometer resolution) whole-brain atlas.

There seem to be two fundamental hurdles to constructing a synapse resolution whole-brain atlas: 1) image acquisition, and 2) digital technologies for working with the images and serving them over a network.

The first hurdle encompasses the time bottleneck and section preparation. If each section is 50 nm thick, then for a 10 mm mouse brain, 20,000 sections are needed, thus requiring some type of automation for section preparation. If we consider the time to scan a single 10mmx10mm section at 1MHz, it comes out to 46 days, which is unacceptable. Even with 20,000 TEMs (transmission electron microscopes) in parallel, one for each section, it will take 46 days for the complete scan. An alternative is offered by way of virtual microscopy solutions offered for light microscopy. One way would be to scan over the section, acquiring one column at a time instead of a patchwork of small images for montaging. Another alternative would be to construct a TEM with parallel scanning capabilities (having parallel magnetic lenses and electron beams), so that the entire section could be scanned at once, instead of scanning each little image patch in serial. This solution requires constructing a special type of TEM which implements certain features found in current day virtual microscopy systems for LM (light microscopy), and thus requires a team of hardware and software specialists to specially design, in addition to some physicists who are intimately acquianted with the physics behind TEM.

The second hurdle involves digital technologies, and the observation that even if a whole mouse brain was able to be acquired through TEM, that digital technologies currently would not be able to deal with that much data (8 x 10^17 pixels, or 2.4 10^18 megabytes (uncompressed)). A single section is 4 x 10^12 pixels, which comes out to 12 x 10^12 megabytes or 12,000 petabytes (uncompressed), which is still not feasible using today's digital technologies.

Let's consider a less ambitious proposal: TEM montaging of a 1mm x 2mm area at 2.5 nm resolution. TEMs typically acquire images in 2kx2k patches, which means that each patch is 5 microns x 5 microns. So for 2mmx1mm, it's 80,000 patches, and the montaged image size would be 800k x 400k, which is already a problem since there are file format size limitations on common formats like TIFF and JPG, and so to acquire such a large image would necessitate using a non-standard file format, which makes the issue of making the images web accessible more problematic. The largest images, say at BrainMaps.org, are 120k x 100k, which works out to 3 GB as a JPG-compressed TIFF file (or 30 GB uncompressed), and which is already near the limit for the TIFF file format (which is 4 GB), which means that images much exceeding 120k x 100k are already going to present a problem.

In conclusion, for purposes of obtaining information about whole-brain connectivity, a nanometer-resolution whole-brain scan is required, and current-day tracer experiments are suboptimal and will always leave room for ambiguities that can only be resolved by completely mapping every synapse and axon in the brain. However, constructing a synapse resolution (or nanometer resolution) whole-brain atlas for even a mouse brain is so formidable as to be seemingly beyond today's technological capabilities. Maybe in 10-20 years.

Virtual Microscopy a Disruptive Technology?

Virtual microscopy is a method of posting microscope images on, and transmitting them over, computer networks. This allows independent viewing of images by large numbers of people in diverse locations.

Prior to recent advances in virtual microscopy, slides were commonly digitized by various forms of film scanner and image resolutions rarely exceeded 5000 dpi. Nowadays, it is possible to achieve more than 100,000 dpi and thus resolutions approaching that visible under the optical microscope. This increase in scanning resolution comes at a price; whereas a typical flatbed or film scanner ranges in cost from $200 to $600, a 100,000 dpi slide scanner will range from $80,000 to $200,000.

Virtual microscopy has been characterized as potentially a disruptive technology. A disruptive technology is a new technological innovation, product, or service that eventually overturns the existing dominant technology in the market, which in this case would be real (i.e., conventional) microscopy. Our experience with virtual microscopy suggests that it is unlikely to replace real microscopy any time soon, but for the time being, it nicely complements and extends the capabilities of real microscopes. Specifically, we find a three-fold extension of virtual microscopy over real microscopy in the following areas: 1) data-sharing and remote access, 2) data-management and annotation, and 3) data-mining. Data management and data-mining of virtual (digitized) slides are capabilities that cannot be directly applied to real slides. In addition, the online distribution and sharing of virtual slides with anyone with an internet connection ensures the rapid dissemination of neuroanatomical data that otherwise would not be possible. While largely emphasizing the pros of virtual slides in this article, it is worthwhile to point out the cons. Namely, it is not possible to change focus in a virtual slide as it is in a real slide. Normally, this is not a problem since virtual slides tend to be completely in focus. However, the inability to change the plane of focus in a virtual slide rules out their use in unbiased stereological estimation methods that require optical dissectors. Nonetheless, biased sterelogical estimation methods, or unbiased methods not using optical dissectors, are still possible. Another drawback is that the resolution of the virtual slide is limited to the optical lens used in the scanner. For example, if we generate a virtual slide at 20x and subsequently want to examine part of the slide at 40x, then it is necessary to rescan the entire slide using the higher objective, which in some cases, is not possible due to file size restrictions or hardware issues. Finally, at the time of writing, virtual microscopy does not deal well with fluorescence, and is only recommended for light microscopy.

Virtual microscopy-based digital brain atlases are superior to conventional print atlases in five respects: 1) resolution, 2) annotation, 3) interaction, 4) data integration, and 5) data-mining. The resolution of conventional print brain atlases typically does not exceed 7200 dpi, whereas virtual microscopy-based digital brain atlases attain 100,000 dpi and offer the ability to zoom in and out. Annotation can be more complete in virtual microscopy-based digital brain atlases, with options to display some types of annotations and make the rest invisible. Greater interactivity means that the user can zoom in/out and pan through brain image data, which is not possible in print-based atlases. Data-integration capabilities, including the integration of connectivity and gene expression data, are superior for the virtual microscopy-based digital brain atlases. And finally, the ability to data-mine virtual microscopy-based digital brain atlases is a feature not available for print-based atlases. While we do not foresee virtual microscopy-based digital brain atlases completely replacing conventional print-based brain atlases, we expect that they will be progressively more commonly used in place of print-based atlases.

What I'd like to know is, how likely is virtual microscopy to overtake regular microscopy and print atlases in the near future? In my opinion, conventional print brain atlases are a ripoff, often costing over $200 each. The idea of having this information freely available online is very tantalizing and welcome.

In other news, Society for Neuroscience 2006 is fast approaching! Hope to see you all in Atlanta this Oct 14-18.