Abstract: Provided herein is a macroscope comprising an objective apparatus comprising a multifocal widefield optics comprising a plurality of optical components configured to focus on a plurality of planes. Also provided herein are methods for analyzing a three-dimensional specimen, the method comprising obtaining, via a macroscope, synchronous multifocal optical images of a plurality of planes of the three-dimensional specimen, wherein the macroscope comprises an objective apparatus comprising a multifocal widefield optics comprising a plurality of optical components configured to focus on a plurality of planes. The three-dimensional specimen can be a biological specimen, such as brain.

Abstract: Methods of modulating dissociative and associative states in a subject are provided. In particular, neuromodulation of rhythmic neural activity in the posteromedial cortex can be used to induce or inhibit dissociative states in a subject.

Abstract: The present disclosure provides variant light-responsive polypeptides, and nucleic acids comprising nucleotide sequences encoding the light-responsive polypeptides. The present disclosure provides methods, devices, and systems for controlling the activity of a cell expressing a variant light-responsive polypeptide of the present disclosure.

Abstract: Methods of treating a subject for a dissociative disorder and methods of screening agents for the ability to modulate dissociative and associative states in a subject are provided. In particular, agents that alter rhythmic neural activity in the posteromedial cortex can be used to modulate dissociative and associative states in a subject.

Abstract: Methods for selectively stimulating a plurality of light-responsive neurons in a sample are provided. Methods according to certain embodiments include irradiating a sample comprising a plurality of light-responsive neurons with a plurality of holographic images that are each configured to stimulate one or more light-responsive neurons in the sample, wherein the holographic images are created by light projection system that includes a plurality of light sources; a plurality of optical adjustment components; a plurality of spatial light modulators; a controller; a processor; and a computer-readable medium comprising instructions that, when executed by the processor, cause the controller to operate the light sources, optical adjustment components and spatial light modulators to generate and display a plurality of holographic images; direct each of the holographic images to a projection location; and project the holographic images onto the sample at a rate greater than 1 kHz.

Abstract: 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.

Abstract: 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.

Abstract: Provided herein are devices, methods, and systems for in situ gene sequencing of a target nucleic acid in a cell in an intact tissue. Methods of screening a candidate agent to determine whether the candidate agent modulates gene expression of a nucleic acid in a cell in an intact tissue are also provided herein.

Abstract: Compositions and methods are provided for genetically modifying cells to guide in situ chemical synthesis of electroactive, conductive, or insulating polymers on plasma membranes, organelle membranes, or subcellular surfaces of cells. In particular, compositions and methods are provided for genetically modifying excitable cells such as neurons, muscle cells, and endocrine cells to guide in situ chemical synthesis of polymers on the extracellular side of the plasma membrane. The subject methods can be used in various applications, for example, to assemble polymers in vivo at targeted locations to modulate electrical conduction and create new electrical conduction pathways, allow cell-type-specific neuromodulation, provide a conductive structure on cells for connection to electrodes, sensors, or other external electronic and electrochemical devices, and create a durable structure to replace damaged tissue for use in regenerative medicine.

Abstract: The present disclosure provides recombinant expression vectors for modulating production of polypeptides of interest in a target cell or target cell population. Aspects of the disclosure include recombinant expression vectors having coding sequences encoding portions of a polypeptide of interest, where the coding sequences are flanked by recombinase recognition sites. Also provided are methods for using the recombinant expression vectors as well as a device for monitoring expression of the polypeptide of interest.

Abstract: The present disclosure provides a genetically encoded calcium indicator (GECI), nucleic acids encoding the GECI, and host cells comprising the GECI. The present disclosure also provides methods of detecting a change in the intracellular concentration of a cell expressing a GECI of the present disclosure.

Abstract: Methods, kits, and systems for fixation of RNA permitting its detection in intact tissue, such as, large volume of mammalian tissue are disclosed. The methods, kits, and systems util-ize carbodiimide-based chemistry to stably retain RNAs in tissue clarified using CLARITY. Also provided herein are methods, kits, and systems for detection of RNAs ire clarified tissue.

Abstract: The present disclosure provides light-responsive polypeptides, and nucleic acids comprising nucleotide sequences encoding the light-responsive polypeptides. The present disclosure provides methods, devices, and systems for controlling the activity of a cell expressing a light-responsive polypeptide of the present disclosure.

Abstract: The present disclosure provides optical image acquisition methods and devices for microscopy systems that enhance the field-of-view during image acquisition. According to aspects of the present disclosure, the methods and devices for enhancing the field-of-view of a sample during image acquisition in an optical imaging system include directing an incident electromagnetic field through a plurality of polarization-selective gratings, where each of the polarization-selective gratings is configured to apply a discrete amount of angular displacement to the incident electromagnetic field in a direction transverse or axial to the optical system's electromagnetic axis, resulting in an enhanced field-of-view during image acquisition.

Abstract: Methods, kits, and systems for fixation of RNA permitting its detection in intact tissue, such as, large volume of mammalian tissue are disclosed. The methods, kits, and systems utilize carbodiimide-based chemistry to stably retain RNAs in tissue clarified using CLARITY. Also provided herein are methods, kits, and systems for detection of RNAs in clarified tissue.

Abstract: Provided herein is a method of optically recording neural activity in one or more regions of a target tissue. Also provided is a method of optically modulating the activity of a neural tissue. Further provided is a system that finds use in performing the present methods.

Abstract: Provided herein is a macroscope comprising an objective apparatus comprising a multifocal widefield optics comprising a plurality of optical components configured to focus on a plurality of planes. Also provided herein are methods for analyzing a three-dimensional specimen, the method comprising obtaining, via a macroscope, synchronous multifocal optical images of a plurality of planes of the three-dimensional specimen, wherein the macroscope comprises an objective apparatus comprising a multifocal widefield optics comprising a plurality of optical components configured to focus on a plurality of planes. The three-dimensional specimen can be a biological specimen, such as brain.

Abstract: Provided herein is a method of optically recording neural activity in one or more regions of a target tissue. Also provided is a method of optically modulating the activity of a neural tissue. Further provided is a system that finds use in performing the present methods.

Abstract: Provided herein are methods for the treatment of bladder dysfunction, including detrusor hyperreflexia and detrusor external sphincter dyssynergia, fecal incontinence, and/or sexual dysfunction in an individual via the use of stably expressed light-responsive opsin proteins capable of selective hyperpolarization or depolarization of the neural cells that innervate the muscles responsible for physiologic functioning of urinary bladder, external urinary sphincter, external anal sphincter, and the male and female genitalia.

Abstract: Methods and compositions are provided for preparing a biological specimen for microscopic analysis. These methods find many uses, for example in medicine and research, e.g., to diagnose or monitor disease or graft transplantation, to study healthy or diseased tissue, to screen candidate agents for toxicity and efficacy in disease modification. Also provided are reagents, devices, kits and systems thereof that find use in practicing the subject methods.