Leland Stanford Junior University

Li Ye

Karl A Deisseroth

William E Allen

Brian Hsueh

Jennifer McNab

Qiyuan Tian

The present disclosure provides methods of preparing a biological specimen for imaging analysis, comprising fixing and clearing the biological specimen and subsequently analyzing the cleared biological specimen using microscopy. Also included are methods of quantifying cells, for example, active populations of cells in response to a stimulant. The present disclosure also provides devices for practicing the described methods. A flow-assisted clearing device provides rapid clearing of hydrogel-embedded biological specimens without the need of specialized equipment such as electrophoresis or perfusion devices.

Method and system for imaging and analysis of a biological specimen

Aspects of the present disclosure include a method for visualizing a fiber-like structure in a biological specimen, the method comprising: clearing the biological specimen comprising a fiber-like structure, wherein the fiber-like structure is detectably labeled; illuminating the cleared biological specimen with two light sheets from a first side and a second side to produce an image volume, wherein the second side is opposite to the first side and wherein the image volume comprises a representation of the fiber-like structure; defining a plurality of voxels within the representation of the fiber-like structure; processing each of the plurality of voxels to estimate a plurality of principal fiber-like structure orientations; and defining a starting point on the representation of the fiber-like structure and propagating a plurality of streamlines from the starting point, according to the plurality of principal fiber-like structure.

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Mountain View, CA, United States of America

Li Ye