Abstract: Apparatus and methods for 3D-Scanless Holographic Optogenetics with Temporal focusing (3D-SHOT), which allows precise, simultaneous photo-activation of arbitrary sets of neurons anywhere within the addressable volume of the microscope. Soma-targeted (ST) optogenetic tools, ST-ChroME and IRES-ST-eGtACR1, optimized for multiphoton activation and suppression are also provided. The methods use point-cloud holography to place multiple copies of a temporally focused disc matching the dimensions of a designated neuron's cell body. Experiments in cultured cells, brain slices, and in living mice demonstrate single-neuron spatial resolution even when optically targeting randomly distributed groups of neurons in 3D.

Abstract: Apparatus and methods for 3D-Scanless Holographic Optogenetics with Temporal focusing (3D-SHOT), which allows precise, simultaneous photo-activation of arbitrary sets of neurons anywhere within the addressable volume of the microscope. Soma-targeted (ST) optogenetic tools, ST-ChroME and IRES-ST-eGtACR1, optimized for multiphoton activation and suppression are also provided. The methods use point-cloud holography to place multiple copies of a temporally focused disc matching the dimensions of a designated neuron's cell body. Experiments in cultured cells, brain slices, and in living mice demonstrate single-neuron spatial resolution even when optically targeting randomly distributed groups of neurons in 3D.

Abstract: Systems and methods are disclosed for recovering both phase and amplitude of an arbitrary sample in an optical microscope from a single image, using patterned partially coherent illumination. This is realized through the use of a encoded light source which embeds several different illumination patterns into color channels. The sample is modulated by each illumination wavelength separately and independently of each other, but all of the channels are sensed by the imaging device in a single step. This color image contains information about the phase and amplitude of a sample encoded in each channel, and can be used to recover both amplitude and phase from this single image, at the incoherent resolution limit. Further, extensions of this method are shown which allow the same recovery of a sample whilst it is moving during a single exposure using a motion deblurring algorithm.

Abstract: Apparatus and methods for 3D-Scanless Holographic Optogenetics with Temporal focusing (3D-SHOT), which allows precise, simultaneous photo-activation of arbitrary sets of neurons anywhere within the addressable volume of the microscope. Soma-targeted (ST) optogenetic tools, ST-ChroME and IRES-ST-eGtACR 1, optimized for multiphoton activation and suppression are also provided. The methods use point-cloud holography to place multiple copies of a temporally focused disc matching the dimensions of a designated neuron's cell body. Experiments in cultured cells, brain slices, and in living mice demonstrate single-neuron spatial resolution even when optically targeting randomly distributed groups of neurons in 3D.

Abstract: Apparatus and methods for 3D-Scanless Holographic Optogenetics with Temporal focusing (3D-SHOT), which allows precise, simultaneous photo-activation of arbitrary sets of neurons anywhere within the addressable volume of the microscope. Soma-targeted (ST) optogenetic tools, ST-ChroME and IRES-ST-eGtACR 1, optimized for multiphoton activation and suppression are also provided. The methods use point-cloud holography to place multiple copies of a temporally focused disc matching the dimensions of a designated neuron's cell body. Experiments in cultured cells, brain slices, and in living mice demonstrate single-neuron spatial resolution even when optically targeting randomly distributed groups of neurons in 3D.

Abstract: A system and method for quantitative functional neuroimaging through thick brain tissue in live animals. A computational imaging method is disclosed that uses plenoptic image acquisition including a first initialization step that identifies individual neurons by their optical signature and provides a reliable estimate of their position in space and a second stimulation-based image processing step that used acquired calibration data to quickly quantify activity in each identified neuron at video frame-rate.

Abstract: Systems and methods are disclosed for recovering both phase and amplitude of an arbitrary sample in an optical microscope from a single image, using patterned partially coherent illumination. This is realized through the use of a encoded light source which embeds several different illumination patterns into color channels. The sample is modulated by each illumination wavelength separately and independently of each other, but all of the channels are sensed by the imaging device in a single step. This color image contains information about the phase and amplitude of a sample encoded in each channel, and can be used to recover both amplitude and phase from this single image, at the incoherent resolution limit. Further, extensions of this method are shown which allow the same recovery of a sample whilst it is moving during a single exposure using a motion deblurring algorithm.

Abstract: A system and method for incorporating partially coherent illumination models into the problem of phase and amplitude retrieval from a stack of intensity images. The recovery of phase could be realized by many methods, including Kalman filters or other nonlinear optimization algorithms that provide least squares error between the measurement and estimation.

Abstract: A method and apparatus for increasing sample image resolution using patterned illumination. An array of optical emitters is selectively activated as a programmable light source, directed to a patterned mask which selectively changes amplitude or phase characteristics of optical energy received onto a sample. A sequence of images are captured of the sample, each being captured in response to a different spatial arrangement of optical outputs from the optical emitter array. These sample images are then post processed into a reconstructed image which has increased resolution over the separately collected images of the sample.

Abstract: A system and methods for wide field of view, high resolution Fourier ptychographic microscopic imaging with a programmable LED array light source. The individual lights in the LED array can be actuated according to random, non-random and hybrid random and non-random illumination strategies to produce high resolution images with fast acquisition speeds. The methods greatly reduce the acquisition time and number of images captured compared to conventional sequential scans. The methods also provide for fast, wide field 3D imaging of thick biological samples.

Abstract: A system and method for incorporating partially coherent illumination models into the problem of phase and amplitude retrieval from a stack of intensity images. The recovery of phase could be realized by many methods, including Kalman filters or other nonlinear optimization algorithms that provide least squares error between the measurement and estimation.

Abstract: A system and method for quantitative functional neuroimaging through thick brain tissue in live animals. A computational imaging method is disclosed that uses plenoptic image acquisition including a first initialization step that identifies individual neurons by their optical signature and provides a reliable estimate of their position in space and a second stimulation-based image processing step that used acquired calibration data to quickly quantify activity in each identified neuron at video frame-rate.

Abstract: Phase differences associated with a defocused wavefront can be determined from a single color image. The color image, which is a measurement of intensity as a function of wavelength, is used to calculate the change in intensity with respect to wavelength over the image plane. The change in intensity can then be used to estimate a phase difference associated with the defocused wavefront using two-dimensional fast Fourier transform solvers. The phase difference can be used to infer information about objects in the path of the defocused wavefront. For example, it can be used to determine an object's shape, surface profile, or refractive index profile. It can also be used to calculate path length differences for actuating adaptive optical systems. Compared to other techniques, deriving phase from defocused color images is faster, simpler, and can be implemented using standard color filters.

Abstract: Phase differences associated with a defocused wavefront can be determined from a single color image. The color image, which is a measurement of intensity as a function of wavelength, is used to calculate the change in intensity with respect to wavelength over the image plane. The change in intensity can then be used to estimate a phase difference associated with the defocused wavefront using two-dimensional fast Fourier transform solvers. The phase difference can be used to infer information about objects in the path of the defocused wavefront. For example, it can be used to determine an object's shape, surface profile, or refractive index profile. It can also be used to calculate path length differences for actuating adaptive optical systems. Compared to other techniques, deriving phase from defocused color images is faster, simpler, and can be implemented using standard color filters.