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Good question. Maybe it is done that way to allow light to shine thru the sample the same way one illuminates microscope slides from behind?

Maybe further project should do both to allow for making more advanced models? And when one first are taking the photo, maybe one was to do other studies as well? X-ray, ultraviolet, infrared, fluorescence, phase contrast etc. Who knows what one would revile if that data was freely available on the internet.

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Your answer is correct, in order to get any pictures, you typically have to shine light through a sample (unless it is fluorescent, then you can bounce light off of it). Also, in order to stain the sample, it needs to be thin(in this case 20um).Also, for the high mag stuff, you cut the section even thinner (ultra thin sectioning, which is the machine behind the guy under the "path to uploads?" heading). To do this, you need to already work with a thin section. Overall, sectioning brains is a super long, kinda boring process;) Hence why I've watched (listened) to a LOT of netflix.

If you guys are interested in seeing open source brain images, check out http://www.brain-map.org, it's a great resource working on something similar.

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