Method and System for Imaging and Analysis of a Biological Specimen

A method for quantifying an active neuronal population of a subject animal exposed to a stimulant, the method comprising:

• i) delivering a stimulant to the subject animal;
• ii) isolating the brain of the subject animal;
• iii) preparing the brain of the animal to produce a cleared brain by:
• a) fixing the brain with a plurality of hydrogel monomers to produce a hydrogel-fixed brain;
• b) clearing the hydrogel-fixed brain using a flow-assisted clearing device to produce a cleared brain, wherein the clearing is performed by immersing the hydrogel-fixed brain in a buffer and flowing the buffer through the hydrogel-fixed brain, wherein the buffer flow is unidirectional;
• and
• c) contacting the cleared brain with a refractive index matching solution;
• iv) imaging the cleared brain;
• and
• v) identifying the active neuronal population.