Engineering a Less Artificial Intelligence

Neuron
Despite enormous progress in machine learning, artificial neural networks still lag behind brains in their ability to generalize to new situations. Differences in generalization are caused by many defining features of a learning algorithm, such as network architecture and learning rule.

The BioLuminescent‐OptoGenetic in vivo response to coelenterazine is proportional, sensitive, and specific in neocortex

Journal of Neuroscience Research
BioLuminescent (BL) light production can modulate neural activity and behavior through co‐expressed OptoGenetic (OG) elements, an approach termed “BL‐OG.” Yet, the relationship between BL‐OG effects and bioluminescent photon emission has not been characterized in vivo.

The Visual Cortex in Context

Annual Review of Vision Science
In this article, we review the anatomical inputs and outputs to the mouse primary visual cortex, area V1. Our survey of data from the Allen Institute Mouse Connectivity project indicates that mouse V1 is highly interconnected with both cortical and subcortical brain areas.
preprint

Restoring Function After Severe Spinal Cord Injury Through Bioluminescence-Driven Optogenetics

BioRxiv
The ability to manipulate specific neuronal populations of the spinal cord following spinal cord injury (SCI) could prove highly beneficial for rehabilitation in patients through maintaining and strengthening still existing neuronal connections and/or facilitating the formation of new connections.
preprint

The BioLuminescent-OptoGenetic in vivo Response to Coelenterazine is Proportional, Sensitive and Specific in Neocortex

BioRxiv
BioLuminescent (BL) light production can modulate neural activity and behavior through co-expressed OptoGenetic (OG) elements, an approach termed "BL-OG". Yet, the relationship between BL-OG effects and bioluminescent photon emission has not been characterized in vivo.
preprint

Aequorea Victoria’s Secrets

bioRxiv
Using mRNA-Seq and de novo transcriptome assembly, we identified, cloned and characterized nine previously undiscovered fluorescent protein (FP) homologs from Aequorea victoria and a related Aequorea species, with most sequences highly divergent from avGFP.

Fluorescent coherent diffractive imaging with accelerating light sheets

Optics Express
We recently introduced coherent holographic image reconstruction by phase transfer (CHIRPT), a single-pixel imaging method that significantly improves the depth of field in fluorescence microscopy and enables holographic refocusing of fluorescent light.

Spectral phase and amplitude retrieval and compensation technique for measurement of pulses

Optics Letters
In this Letter, an in-line, compact, and efficient quantitative pulse compensation and measurement scheme is demon- strated. This simple system can be readily deployed in multiphoton imaging systems and advanced manufacturing where multiphoton processes are exploited.
preprint

Spectral Phase and Amplitude Retrieval and Compensation for Random Access Microscopy

Programmable, two-dimensional, spatial frequency modulation linear and non- linear imaging combined with a novel and remarkably simple, in-situ quantitative pulse compensation and measurement scheme is demonstrated for the first time.

Magnetic Entropy as a Proposed Gating Mechanism for Magnetogenetic Ion Channels

Biophysical Journal
Magnetically sensitive ion channels would allow researchers to better study how specific brain cells affect behavior in freely moving animals; however, recent reports of “magnetogenetic” ion channels based on biogenic ferritin nanoparticles have been questioned.

Temporal Evolution of Cortical Ensembles Promoting Remote Memory Retrieval

Nature Neuroscience
Studies of amnesic patients and animal models support a systems consolidation model, which posits that explicit memories formed in hippocampus are transferred to cortex over time. Prelimbic cortex is required for the expression of learned fear memories from hours after learning until weeks later.

Interacting neural ensembles in orbitofrontal cortex for social and feeding behaviour

Nature
Categorically distinct basic drives can exert potent influences on each other; such interactions are likely to have important adaptive consequences and can become maladaptive.

Systemic AAV vectors for targeted gene delivery

Nature Protocols
Multicolor labeling of cardiac muscle with systemic AAVs.

Circuit Models of Low-Dimensional Shared Variability in Cortical Networks

Neuron
Trial-to-trial variability is a reflection of the circuitry and cellular physiology that make up a neuronal network. A pervasive yet puzzling feature of cortical circuits is that despite their complex wiring, population-wide shared spiking variability is low dimensional.

An adaptive excitation source for multiphoton imaging

Conference on Lasers and Electro-Optics, OSA Technical Digest (online)
We demonstrate an adaptive femtosecond laser source that improves the imaging speed by >10 times for multiphoton imaging of brain activity in awake mouse, achieving 30 frames/s, 734×734 µm field-of-view (FOV) at 700 µm depth.

Interferometric spatial frequency modulation imaging

Optics Letters
Interferometric spatial frequency modulation for imaging (I-SPIFI) is demonstrated for the first time, to our knowledge. Significantly, this imaging modality can be seamlessly combined with nonlinear SPIFI imaging and operates through single-element detection.

Interferometric spatial frequency modulation imaging

Optics Letters
Interferometric spatial frequency modulation for imaging (I-SPIFI) is demonstrated for the first time, to our knowledge. Significantly, this imaging modality can be seamlessly combined with nonlinear SPIFI imaging and operates through single-element detection.

Inferring single-trial neural population dynamics using sequential auto-encoders

Nature Methods
Neuroscience is experiencing a revolution in which simultaneous recording of thousands of neurons is revealing population dynamics that are not apparent from single-neuron responses. Deeper understanding of this structure requires studying phenomena detected in single trials, which is challenging.

Three-photon imaging of mouse brain structure and function through the intact skull

Nature Methods
Optical imaging through the intact mouse skull is challenging because of skull-induced aberrations and scattering. We found that three-photon excitation provided improved optical sectioning compared with that obtained with two-photon excitation.

How biological attention mechanisms improve task performance in a large-scale visual system model

eLife
How does attentional modulation of neural activity enhance performance? Here we use a deep convolutional neural network as a large-scale model of the visual system to address this question.

Crystal structure of the natural anion- conducting channelrhodopsin GtACR1

Nature
The naturally occurring channelrhodopsin variant anion channelrhodopsin-1 (ACR1) exhibits large light-gated anion conductance and high anion selectivity when expressed in heterologous settings.

Three-dimensional single-pixel imaging of incoherent light with spatiotemporally modulated illumination

Journal of the Optical Society of America A
We derive analytic expressions for the three-dimensional coherent transfer function (CTF) and coherent spread function (CSF) for coherent holographic image reconstruction by phase transfer (CHIRPT) microscopy with monochromatic and broadband illumination sources.

Investigation of the long wavelength limit of soliton self-frequency shift in a silica fiber

Optics Express
We explore the long wavelength limit of soliton self-frequency shift in silica-based fibers experimentally and using numerical simulation. We found that the longest wavelength soliton generated by soliton self-frequency shift is approximately 2500 nm.

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

Science
Retrieving high-content gene-expression information while retaining three-dimensional (3D) positional anatomy at cellular resolution has been difficult, limiting integrative understanding of structure and function in complex biological tissues.

Fabrication and characterization of modulation masks for multimodal spatial frequency modulated microscopy

Applied Optics
Spatial frequency modulated imaging (SPIFI) is a powerful imaging method that when used in conjunction with multiphoton contrast mechanisms has the potential to improve the spatial and temporal scales that can be explored within a single nonlinear optical microscope platform.

Fabrication and characterization of modulation masks for multimodal spatial frequency modulated microscopy

Applied Optics
Spatial frequency modulated imaging (SPIFI) is a powerful imaging method that when used in conjunction with multiphoton contrast mechanisms has the potential to improve the spatial and temporal scales that can be explored within a single nonlinear optical microscope platform.

Fiber-based tunable repetition rate source for deep tissue two-photon fluorescence microscopy

Biomedical Optics Express
Deep tissue multiphoton imaging requires high peak power to enhance signal and low average power to prevent thermal damage. Both goals can be advantageously achieved through laser repetition rate tuning instead of simply adjusting the average power.

Comparison of excitation wavelengths for in vivo deep imaging of mouse brain

SPIE
The attenuation of excitation power reaching the focus is the main issue that limits the depth penetration of highresolution imaging of biological tissue. The attenuation is caused by a combination of tissue scattering and absorption.

In vivo three-photon imaging of deep cerebellum

SPIE
We demonstrate three-photon microscopy (3PM) of mouse cerebellum at 1 mm depth by imaging both blood vessels and neurons. We compared 3PM and 2PM in the mouse cerebellum for imaging green and red fluorescence.

Long-term potentiation expands information content of hippocampal dentate gyrus synapses

PNAS
An approach combining signal detection theory and precise 3D reconstructions from serial section electron microscopy (3DEM) was used to investigate synaptic plasticity and information storage capacity at medial perforant path synapses in adult hippocampal dentate gyrus in vivo.

Balanced excitation and inhibition are required for high-capacity, noise-robust neuronal selectivity

PNAS
Neurons and networks in the cerebral cortex must operate reliably despite multiple sources of noise. To evaluate the impact of noise, we determine the robustness of single-neuron stimulus selective responses and the robustness of attractor states of networks of neurons performing memory tasks.

Thirst-associated preoptic neurons encode an aversive motivational drive

Science
Water deprivation produces a drive to seek and consume water. How neural activity creates this motivation remains poorly understood.

Fast two-photon imaging of subcellular voltage dynamics in neuronal tissue with genetically encoded indicators

eLife
Monitoring voltage dynamics in defined neurons deep in the brain is critical for unraveling the function of neuronal circuits but is challenging due to the limited performance of existing tools.