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What are the benefits of CLARITY over this technique that was published more than a year earlier?

Of course the second technique needs a fancier microscope that is likely more expensive and requires more technical ability. But CLARITY requires an objective with a very long working distance. I'm no expert in optics, but I'm pretty sure this results in a significant decrease in numerical aperture and therefore resolution.

It seems as though the other method is simply better than CLARITY, and that a lab serious about doing whole brain imaging could afford to invest in a setup similar to the one described. Yet this technique received none of hype that was bestowed on CLARITY. Am I missing something?

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To start with, CLARITY is a whole-brain imaging technique , there is no need for sectioning which destroys connections and can cause the brain slices to warp as they are being cut. The costs for setting up CLARITY are much lower because all that is needed is chemicals to get the prep ready for imaging whereas in the Nat Methods paper you have to set up an automated slicing and imaging system,not an easy task by any means. Therefore an investigator is more likely to use CLARITY due to its easy of setting up and low start up costs. Also, as with any brain slice technique , you lose patterns of connectivity among neurons that are more than the slice distance apart(i.e in the next slice) and you don't look at the "whole picture". Thus due to the complexity,high start-up costs and specialized machinery STP is a poorer method than CLARITY for whole-brain imaging.As for resolution, I agree with you on principle that CLARITY has worse resolution(I looked through the paper but couldn't find exact figures) although you have to consider this in terms of all the trade-offs.

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I don't think this is fair to the serial two-photon technique. For each Z-stack the sectioning occurs after the optical slice is recorded, so I don't entirely see how the warping is a big issue. Also, even using CLARITY you eventually need to take optical slices, so you don't really get a "whole picture." You get a z-stack that then has to be computationally reconstructed. The same problems with this reconstruction that you point out (loss of connectivity patterns) is a concern in CLARITY as well. – stords Feb 24 '14 at 22:11
This is not quite true. You don't need to section the brain with CLARITY because the how point is you clear away all the fats so you image cells directly in their native configuration without disturbing them. When I said slices I mean physically cutting the tissue which you do for STP but not for CLARITY. Hopefully this clarifies my response. – V_ix Feb 25 '14 at 4:30
You don't need to physically section the brain, but you still need to take optical sections for CLARITY. Unless there is a microscopy technique for creating 3D images that doesn't involve stacking a bunch of 2D images, of which I'm not aware. – stords Feb 25 '14 at 6:31
Right, but optical sectioning does not disturb the tissue like slicing, nor does it destroy connections or cause swelling. – V_ix Feb 25 '14 at 16:38

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