Real-time in vivo optogenetic neuromodulation and multielectrode electrophysiologic recording with NeuroRighter

Optogenetic channels have greatly expanded neuroscience’s experimental capabilities, enabling precise genetic targeting and manipulation of neuron subpopulations in awake and behaving animals. However, many barriers to entry remain for this technology – including low-cost and effective hardware for combined optical stimulation and electrophysiologic recording. To address this, we adapted the open-source NeuroRighter multichannel electrophysiology platform for use in awake and behaving rodents in both open and closed-loop stimulation experiments. Here, we present these cost-effective adaptations, including commercially available LED light sources; custom-made optical ferrules; 3D printed ferrule hardware and software to calibrate and standardize output intensity; and modifications to commercially available electrode arrays enabling stimulation proximally and distally to the recording target. We then demonstrate the capabilities and versatility of these adaptations in several open and closed-loop experiments, demonstrate spectrographic methods of analyzing the results, as well as discuss artifacts of stimulation.Emory University. School of Medicine (Emory Neurosciences Initiative seed grant)American Epilepsy SocietyEpilepsy Foundation of America (Predoctoral fellowship)National Science Foundation (U.S.) (NSF GRFP Fellowship 08-593)National Science Foundation (U.S.) (NSF IGERT Fellowship DGE-0333411)National Science Foundation (U.S.) (NSF EFRI #1238097)National Institutes of Health (U.S.) (NIH 1R01NS079757-01)American Society for Engineering Education (SMART Fellowship

Unwind: Interactive Fish Straightening

The ScanAllFish project is a large-scale effort to scan all the world's 33,100 known species of fishes. It has already generated thousands of volumetric CT scans of fish species which are available on open access platforms such as the Open Science Framework. To achieve a scanning rate required for a project of this magnitude, many specimens are grouped together into a single tube and scanned all at once. The resulting data contain many fish which are often bent and twisted to fit into the scanner. Our system, Unwind, is a novel interactive visualization and processing tool which extracts, unbends, and untwists volumetric images of fish with minimal user interaction. Our approach enables scientists to interactively unwarp these volumes to remove the undesired torque and bending using a piecewise-linear skeleton extracted by averaging isosurfaces of a harmonic function connecting the head and tail of each fish. The result is a volumetric dataset of a individual, straight fish in a canonical pose defined by the marine biologist expert user. We have developed Unwind in collaboration with a team of marine biologists: Our system has been deployed in their labs, and is presently being used for dataset construction, biomechanical analysis, and the generation of figures for scientific publication

Transient Receptor Potential Ion Channels Control Thermoregulatory Behaviour in Reptiles

Biological functions are governed by thermodynamics, and animals regulate their body temperature to optimise cellular performance and to avoid harmful extremes. The capacity to sense environmental and internal temperatures is a prerequisite for the evolution of thermoregulation. However, the mechanisms that enable ectothermic vertebrates to sense heat remain unknown. The recently discovered thermal characteristics of transient receptor potential ion channels (TRP) render these proteins suitable to act as temperature sensors. Here we test the hypothesis that TRPs are present in reptiles and function to control thermoregulatory behaviour. We show that the hot-sensing TRPV1 is expressed in a crocodile (Crocodylus porosus), an agamid (Amphibolurus muricatus) and a scincid (Pseudemoia entrecasteauxii) lizard, as well as in the quail and zebrafinch (Coturnix chinensis and Poephila guttata). The TRPV1 genes from all reptiles form a unique clade that is delineated from the mammalian and the ancestral Xenopus sequences by an insertion of two amino acids. TRPV1 and the cool-sensing TRPM8 are expressed in liver, muscle (transversospinalis complex), and heart tissues of the crocodile, and have the potential to act as internal thermometer and as external temperatures sensors. Inhibition of TRPV1 and TRPM8 in C. porosus abolishes the typically reptilian shuttling behaviour between cooling and heating environments, and leads to significantly altered body temperature patterns. Our results provide the proximate mechanism of thermal selection in terrestrial ectotherms, which heralds a fundamental change in interpretation, because TRPs provide the mechanism for a tissue-specific input into the animals' thermoregulatory response

Perceptual models of viewpoint preference

The question of what are good views of a 3D object has been addressed by numerous researchers in perception, computer vision and computer graphics. This has led to a large variety of measures for the goodness of views as well as some special-case viewpoint selection algorithms. In this paper, we leverage the results of a large user study to optimize the parameters of a general model for viewpoint goodness, such that the fitted model can predict people’s preferred views for a broad range of objects. Our model is represented as a combination of attributes known to be important for view selection, such as projected model area and silhouette length. Moreover, this framework can easily incorporate new attributes in the future, based on the data from our existing study. We demonstrate our combined goodness measure in a number of applications, such as automatically selecting a good set of representative views, optimizing camera orbits to pass through good views and avoid bad views, and trackball controls that gently guide the viewer towards better views

Sparse Deformable Models with Application to Cardiac Motion Analysis

Abstract. Deformable models have been widely used with success in medical image analysis. They combine bottom-up information derived from image appearance cues, with top-down shape-based constraints within a physics-based formulation. However, in many real world problems the observations extracted from the image data often contain gross errors, which adversely affect the deformation accuracy. To alleviate this issue, we introduce a new family of deformable models that are inspired from compressed sensing, a technique for efficiently reconstructing a signal based on its sparseness in some domain. In this problem, we employ sparsity to represent the outliers or gross errors, and combine it seamlessly with deformable models. The proposed new formulation is applied to the analysis of cardiac motion, using tagged magnetic resonance imaging (tMRI), where the automated tagging line tracking results are very noisy due to the poor image quality. Our new deformable models track the heart motion robustly, and the resulting strains are consistent with those calculated from manual labels.

Frame-based interactive simulation of complex deformable objects

Abstract We present a new type of deformable model which combines the realism of physically based continuum mechanics models and the usability of framebased skinning methods, allowing the interactive simulation of objects with heterogeneous material properties and complex geometries. The degrees of freedom are coordinate frames. In contrast with traditional skinning, frame positions are not scripted but move in reaction to internal body forces. The deformation gradient and its derivatives are computed at each sample point of a deformed object and used in the equations of Lagrangian mechanics to achieve physical realism. We introduce novel material-aware shape functions in place of the traditional radial basis functions used in meshless frameworks, allowing coarse deformation functions to efficiently resolve non-uniform stiffnesses. Complex models can thus be simulated at high frame rates using a small number of control nodes. 1.