Vicente Parot

Photometric stereo endoscopy

Abstract. 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. We introduce photometric stereo endoscopy (PSE), a technique which allows high spatial frequency components of surface topography to be acquired simultaneously with conventional two-dimensional color imagery. We implement this technique in an endoscopic form factor and demonstrate that it can acquire the topography of small features with complex geometries and heterogeneous optical properties. PSE imaging of ex vivo human gastrointestinal tissue shows that surface topography measurements enable differentiation of abnormal shapes from surrounding normal tissue. Together, these results confirm that the topographical measurements can be obtained with relatively simple hardware in an endoscopic form factor, and suggest the potential of PSE to improve lesion detection and classification in gastrointestinal imaging.

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

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. In Optopatch-expressing animals, we tested for overall health, genetically targeted expression, and function of the optogenetic components. In offspring of Floxopatch mice crossed with a variety of Cre driver lines, we observed spontaneous and optically evoked activity in vitro in acute brain slices and in vivo in somatosensory ganglia. Cell-type-specific expression allowed classification and characterization of neuronal subtypes based on their firing patterns. The Floxopatch mouse line is a useful tool for fast and sensitive characterization of neural activity in genetically specified cell types in intact tissue. SIGNIFICANCE STATEMENT Optical recordings of neural activity offer the promise of rapid and spatially resolved mapping of neural function. Calcium imaging has been widely applied in this mode, but is insensitive to the details of action potential waveforms and subthreshold events. Simultaneous optical perturbation and optical readout of single-cell electrical activity (“Optopatch”) has been demonstrated in cultured neurons and in organotypic brain slices, but not in acute brain slices or in vivo. Here, we describe a transgenic mouse in which expression of Optopatch constructs is controlled by the Cre-recombinase enzyme. This animal enables fast and robust optical measurements of single-cell electrical excitability in acute brain slices and in somatosensory ganglia in vivo, opening the door to rapid optical mapping of neuronal excitability.

Application of the fractional Fourier transform to image reconstruction in MRI

The classic paradigm for MRI requires a homogeneous B0 field in combination with linear encoding gradients. Distortions are produced when the B0 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 B0 fields. Nonlinear magnetic components can also arise from concomitant fields, particularly in low‐field imaging, or intentionally used for nonlinear encoding. In any of these situations, the second‐order component is key, because it constitutes the first step to approximate higher‐order fields. We propose to use the fractional Fourier transform for analyzing and reconstructing the objects magnetization under the presence of quadratic fields. The fractional fourier transform provides a precise theoretical framework for this. We show how it can be used for reconstruction and for gaining a better understanding of the quadratic field‐induced distortions, including examples of reconstruction for simulated and in vivo data. The obtained images have improved quality compared with standard Fourier reconstructions. The fractional fourier transform opens a new paradigm for understanding the MR signal generated by an object under a quadratic main field or nonlinear encoding. Magn Reson Med, 2012.

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. While 3D imaging has proved beneficial for laparoscopic procedures, more research is needed to assess how it will improve applications of flexible endoscopy. In this editorial, we discuss the possible uses of 3D technologies in colonoscopy and factors that have hindered the translation of 3D imaging to flexible endoscopy. Emerging 3D imaging technologies for flexible endoscopy have the potential to improve sensitivity, lesion resection, training and automated lesion detection. To maximize the likelihood of clinical adoption, these technologies should require minimal hardware modification while maintaining the robustness and quality of regular 2D imaging.

Quantitative assessments of geometric errors for rapid prototyping in medical applications

Purpose – In medical applications, it is crucial to evaluate the geometric accuracy of rapid prototyping (RP) models. Current research on evaluating geometric accuracy has focused on identifying two or more specific anatomical landmarks on the original structure and the RP model, and comparing their corresponding linear distances. Such kind of accuracy metrics is ambiguous and may induce misrepresentations of the actual errors. The purpose of this paper is to propose an alternative method and metrics to measure the accuracy of RP models.Design/methodology/approach – The authors propose an accuracy metric composed of two different approaches: a global accuracy evaluation using volumetric intersection indexes calculated over segmented Computed Tomography scans of the original object and the RP model. Second, a local error metric that is computed from the surfaces of the original object and the RP model. This local error is rendered in a 3D surface using a color code, that allow differentiating regions where...

System for clinical photometric stereo endoscopy

Photometric stereo endoscopy is a technique that captures information about the high-spatial-frequency topography of the field of view simultaneously with a conventional color image. Here we describe a system that will enable photometric stereo endoscopy to be clinically evaluated in the large intestine of human patients. The clinical photometric stereo endoscopy system consists of a commercial gastroscope, a commercial video processor, an image capturing and processing unit, custom synchronization electronics, white light LEDs, a set of four fibers with diffusing tips, and an alignment cap. The custom pieces that come into contact with the patient are composed of biocompatible materials that can be sterilized before use. The components can then be assembled in the endoscopy suite before use. The resulting endoscope has the same outer diameter as a conventional colonoscope (14 mm), plugs into a commercial video processor, captures topography and color images at 15 Hz, and displays the conventional color image to the gastroenterologist in real-time. We show that this system can capture a color and topographical video in a tubular colon phantom, demonstrating robustness to complex geometries and motion. The reported system is suitable for in vivo evaluation of photometric stereo endoscopy in the human large intestine.

Chemical species separation with simultaneous estimation of field map and T 2* 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. In this work, we present a new approach for chemical species separation in MRI with simultaneous estimation of field map and T  2* decay, formulated entirely in k‐space. In this approach, the time map is used to model the phase accrual from off‐resonance precession and also the amplitude decay due to T  2* . Our technique fits the signal model directly in k‐space with the acquired data minimizing the l2‐norm with an interior‐point algorithm. Standard two dimensional gradient echo sequences in the thighs and head were used for demonstrating the technique. With this approach, we were able to obtain excellent estimation for the species, the field inhomogeneity, and T  2* decay images. The results do not suffer from geometric distortions derived from the chemical shift or the field inhomogeneity. Importantly, as the T  2* map is well positioned, the species signal in borders is correctly estimated. Considering intraecho time variations in a complete signal model in k‐space for separating species yields superior estimation of the variables of interest when compared to existing methods. Magn Reson Med, 2012.

The fractional Fourier transform and quadratic field magnetic resonance imaging

The fractional Fourier transform (FrFT) is revisited in the framework of strongly continuous periodic semigroups to restate known results and to explore new properties of the FrFT. We then show how the FrFT can be used to reconstruct Magnetic Resonance (MR) images acquired under the presence of quadratic field inhomogeneity. Particularly, we prove that the order of the FrFT is a measure of the distortion in the reconstructed signal. Moreover, we give a dynamic interpretation to the order as time evolution of a function. We also introduce the notion of @r-@a space as an extension of the Fourier or k-space in MR, and we use it to study the distortions introduced in two common MR acquisition strategies. We formulate the reconstruction problem in the context of the FrFT and show how the semigroup theory allows us to find new reconstruction formulas for discrete sampled signals. Finally, the results are supplemented with numerical examples that show how it performs in a standard 1D MR signal reconstruction.

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. The change in the value of L(c) measures the number of amino acids released by an unfolding protein and can be used as a precise locator of the unfolding transition state. However, manual WLC fits are slow and introduce inevitable operator-driven errors which reduce the accuracy of the L(c) estimates. Here we demonstrate an extended Kalman filter that provides operator-free real time estimates of L(c) from sawtooth pattern data. The filter design is based on a cantilever-protein arrangement modeled by a simple linear time-invariant cantilever model and by a nonlinear force-length relationship function for the protein. The resulting Kalman filter applied to sawtooth pattern data demonstrates its real time, operator-free ability to accurately measure L(c). These results are a marked improvement over the earlier techniques and the procedure is easily extended or modified to accommodate further quantities of interest in force spectroscopy.

All-optical electrophysiology reveals brain-state dependent changes in hippocampal subthreshold dynamics and excitability

A technology to record membrane potential from multiple neurons, simultaneously, in behaving animals will have a transformative impact on neuroscience research1. Parallel recordings could reveal the subthreshold potentials and intercellular correlations that underlie network behavior2. Paired stimulation and recording can further reveal the input-output properties of individual cells or networks in the context of different brain states3. Genetically encoded voltage indicators are a promising tool for these purposes, but were so far limited to single-cell recordings with marginal signal to noise ratio (SNR) in vivo4-6. We developed improved near infrared voltage indicators, high speed microscopes and targeted gene expression schemes which enabled recordings of supra- and subthreshold voltage dynamics from multiple neurons simultaneously in mouse hippocampus, in vivo. The reporters revealed sub-cellular details of back-propagating action potentials, correlations in sub-threshold voltage between multiple cells, and changes in dynamics associated with transitions from resting to locomotion. In combination with optogenetic stimulation, the reporters revealed brain state-dependent changes in neuronal excitability, reflecting the interplay of excitatory and inhibitory synaptic inputs. These tools open the possibility for detailed explorations of network dynamics in the context of behavior.