Optogenetic control of Nodal signaling patterns.

A crucial step in early embryogenesis is the establishment of spatial patterns of signaling activity. Tools to perturb morphogen signals with high resolution in space and time can help reveal how embryonic cells decode these signals to make appropriate fate decisions. Here, we present new optogenetic reagents and an experimental pipeline for creaHng designer Nodal signaling patterns in live zebrafish embryos.

Efficient dispersion modeling in optical multimode fiber.

Dispersion remains an enduring challenge for the characterization of wavelength-dependent transmission through optical multimode fiber (MMF). Beyond a small spectral correlation width, a change in wavelength elicits a seemingly independent distribution of the transmitted field. Here we report on a parametric dispersion model that describes mode mixing in MMF as an exponential map and extends the concept of principal modes to describe the fiber's spectrally resolved transmission matrix (TM).

Video-based pooled screening yields improved far-red genetically encoded voltage indicators.

Video-based screening of pooled libraries is a powerful approach for directed evolution of biosensors because it enables selection along multiple dimensions simultaneously from large libraries. Here we develop a screening platform, Photopick, which achieves precise phenotype-activated photoselection over a large field of view (2.3 × 2.

Confocal 3D reflectance imaging through multimode fiber without wavefront shaping.

Imaging through optical multimode fiber (MMF) has the potential to enable hair-thin endoscopes that reduce the invasiveness of imaging deep inside tissues and organs. Active wavefront shaping and fluorescent labeling have recently been exploited to overcome modal scrambling and enable MMF imaging. Here, we present a computational approach that circumvents the need for active wavefront control and exogenous fluorophores.

Reciprocity-induced symmetry in the round-trip transmission through complex systems.

Reciprocity is a fundamental principle of wave physics and directly relates to the symmetry in the transmission through a system when interchanging the input and output. The coherent transmission matrix (TM) is a convenient method to characterize wave transmission through general media. Here, we demonstrate the optical reciprocal nature of complex media by exploring their TM properties.

All-Optical Electrophysiology Reveals the Role of Lateral Inhibition in Sensory Processing in Cortical Layer 1.

Cortical layer 1 (L1) interneurons have been proposed as a hub for attentional modulation of underlying cortex, but the transformations that this circuit implements are not known. We combined genetically targeted voltage imaging with optogenetic activation and silencing to study the mechanisms underlying sensory processing in mouse barrel cortex L1. Whisker stimuli evoked precisely timed single spikes in L1 interneurons, followed by strong lateral inhibition.

Voltage imaging and optogenetics reveal behaviour-dependent changes in hippocampal dynamics.

A technology that simultaneously records membrane potential from multiple neurons in behaving animals will have a transformative effect on neuroscience research. Genetically encoded voltage indicators are a promising tool for these purposes; however, these have so far been limited to single-cell recordings with a marginal signal-to-noise ratio in vivo. Here we developed improved near-infrared voltage indicators, high-speed microscopes and targeted gene expression schemes that enabled simultaneous in vivo recordings of supra- and subthreshold voltage dynamics in multiple neurons in the hippocampus of behaving mice.

Wide-Area All-Optical Neurophysiology in Acute Brain Slices.

Optical tools for simultaneous perturbation and measurement of neural activity open the possibility of mapping neural function over wide areas of brain tissue. However, spectral overlap of actuators and reporters presents a challenge for their simultaneous use, and optical scattering and out-of-focus fluorescence in tissue degrade resolution. To minimize optical crosstalk, we combined an optimized variant (eTsChR) of the most blue-shifted channelrhodopsin reported to-date with a nuclear-localized red-shifted Ca indicator, H2B-jRGECO1a.

Genetically Targeted All-Optical Electrophysiology with a Transgenic Cre-Dependent Optopatch Mouse.

Unlabelled: Recent advances in optogenetics have enabled simultaneous optical perturbation and optical readout of membrane potential in diverse cell types. Here, we develop and characterize a Cre-dependent transgenic Optopatch2 mouse line that we call Floxopatch. The animals expressed a blue-shifted channelrhodopsin, CheRiff, and a near infrared Archaerhodopsin-derived voltage indicator, QuasAr2, via targeted knock-in at the rosa26 locus.

Recovery and normalization of triple coincidences in PET.

Purpose: Triple coincidences in positron emission tomography (PET) are events in which three γ-rays are detected simultaneously. These events, though potentially useful for enhancing the sensitivity of PET scanners, are discarded or processed without special consideration in current systems, because there is not a clear criterion for assigning them to a unique line-of-response (LOR). Methods proposed for recovering such events usually rely on the use of highly specialized detection systems, hampering general adoption, and/or are based on Compton-scatter kinematics and, consequently, are limited in accuracy by the energy resolution of standard PET detectors.

Feature space optimization for virtual chromoendoscopy augmented by topography.

Optical colonoscopy is the preferred modality for the screening and prevention of colorectal cancer. Chromoendoscopy can increase lesion detection rate by highlighting tissue topography with a colored dye, but is too time-consuming to be adopted in routine colonoscopy screening. We developed a fast and dye-free technique that generates virtual chromoendoscopy images that incorporate topography features acquired from photometric stereo endoscopy.

3D imaging techniques for improved colonoscopy.

Colonoscopy screening with a conventional 2D colonoscope is known to reduce mortality due to colorectal cancer by half. Unfortunately, the protective value of this procedure is limited by missed lesions. To improve the sensitivity of colonoscopy to precancerous lesions, 3D imaging techniques could be used to highlight their characteristic morphology.

Photometric stereo endoscopy.

While color video endoscopy has enabled wide-field examination of the gastrointestinal tract, it often misses or incorrectly classifies lesions. Many of these missed lesions exhibit characteristic three-dimensional surface topographies. An endoscopic system that adds topographical measurements to conventional color imagery could therefore increase lesion detection and improve classification accuracy.

Chemical species separation with simultaneous estimation of field map and T2* using a k-space formulation.

Chemical species separation techniques in image space are prone to incorporate several distortions. Some of these are signal accentuation in borders and geometrical warping from field inhomogeneity. These errors come from neglecting intraecho time variations.

Application of the fractional Fourier transform to image reconstruction in MRI.

The classic paradigm for MRI requires a homogeneous B(0) field in combination with linear encoding gradients. Distortions are produced when the B(0) is not homogeneous, and several postprocessing techniques have been developed to correct them. Field homogeneity is difficult to achieve, particularly for short-bore magnets and higher B(0) fields.

Extended Kalman filter estimates the contour length of a protein in single molecule atomic force microscopy experiments.

Atomic force microscopy force spectroscopy has become a powerful biophysical technique for probing the dynamics of proteins at the single molecule level. Extending a polyprotein at constant velocity produces the now familiar sawtooth pattern force-length relationship. Customarily, manual fits of the wormlike chain (WLC) model of polymer elasticity to sawtooth pattern data have been used to measure the contour length L(c) of the protein as it unfolds one module at a time.