Three-Dimensional GPU-Accelerated Active Contours for Automated Localization of Cells in Large Images

Cell segmentation in microscopy is a challenging problem, since cells are often asymmetric and densely packed. This becomes particularly challenging for extremely large images, since manual intervention and processing time can make segmentation intractable. In this paper, we present an efficient and highly parallel formulation for symmetric three-dimensional (3D) contour evolution that extends previous work on fast two-dimensional active contours. We provide a formulation for optimization on 3D images, as well as a strategy for accelerating computation on consumer graphics hardware. The proposed software takes advantage of Monte-Carlo sampling schemes in order to speed up convergence and reduce thread divergence. Experimental results show that this method provides superior performance for large 2D and 3D cell segmentation tasks when compared to existing methods on large 3D brain images

Vision Based Position Control For Vertical Take-Off And Landing (VTOL) Using One Singular Landmark

This project presents a vision based position control for Vertical Take-off and Landing (VTOL) to recognise a singular landmark for landing and take-off. Position control can provide safe flight and an accurate navigation. The circle landmark which used is an artificial landmark at known locations in an environment. Initially, a camera mounted on VTOL facing downward detecting landmarks in environments. A single circle used as landmark and VTOL will be control the position to reach the landmark. The images from the down-looking camera provided vision data to estimates position of VTOL from landmark. A mathematical method based on projective geometry using to locate VTOL on desired landmark from projected point in capture image. By compute the x-y coordinates of the VTOL with respect to landmark, height of camera above landmark will be obtained. VTOL can localize itself in known environment with pose estimation from landmark. The graphic user interface system (GUI) generate by MATLAB software is used to communicate with VTOL to control the VTOL positio

Cell Type-Specific Arousal-Dependent Modulation of Thalamic Activity in the Lateral Geniculate Nucleus

State-dependent thalamocortical activity is important for sensory coding, oscillations, and cognition. The lateral geniculate nucleus (LGN) relays visual information to the cortex, but the state-dependent spontaneous activity of LGN neurons in awake behaving animals remains controversial. Using a combination of pupillometry, extracellular, and intracellular recordings from identified LGN neurons in behaving mice, we show that thalamocortical (TC) neurons and interneurons are distinctly correlated to arousal forming two complementary coalitions. Intracellular recordings indicated that the membrane potential of LGN TC neurons was tightly correlated to fluctuations in pupil size. Inactivating the corticothalamic feedback to the LGN suppressed the arousal dependency of LGN neurons. Taken together, our results show that LGN neuronal membrane potential and action potential output are dynamically linked to arousal-dependent brain states in awake mice, and this might have important functional implications.Peer reviewe

Accurate pupil center detection in off-the-shelf eye tracking systems using convolutional neural networks

Remote eye tracking technology has suffered an increasing growth in recent years due to its applicability in many research areas. In this paper, a video-oculography method based on convolutional neural networks (CNNs) for pupil center detection over webcam images is proposed. As the first contribution of this work and in order to train the model, a pupil center manual labeling procedure of a facial landmark dataset has been performed. The model has been tested over both real and synthetic databases and outperforms state-of-the-art methods, achieving pupil center estimation errors below the size of a constricted pupil in more than 95% of the images, while reducing computing time by a 8 factor. Results show the importance of use high quality training data and well-known architectures to achieve an outstanding performance.This research was funded by Public University of Navarra (Pre-doctoral research grant) and by the Spanish Ministry of Science and Innovation under Contract 'Challenges of Eye Tracking Off-the-Shelf (ChETOS)' with reference: PID2020-118014RB-I0

Brain State Dependent Activity in the Lateral Geniculate Nucleus

Brain state dependent thalamocortical (TC) activity plays and important role in sensory coding, oscillations and cognition. The lateral geniculate nucleus (LGN) relays visual information to the cortex, but the state dependent spontaneous and visually evoked activity of LGN neurons in awake behaving animals remains controversial. In awake head-restrained mice, using a combination of pupillometry, extracellular and intracellular recordings from morphologically and physiologically identified LGN neurons we show that TC neurons and putative local interneurons are inversely related to arousal forming two complementary coalitions with TC cells being positively correlates with wakefulness, while local interneuron activity is negatively correlated. Additionally, the orientation tuning of visually evoked thalamic cell responses is altered during various brain states. Intracellular recordings indicated that the membrane potential of LGN TC neurons was tightly correlated to fluctuations in pupil size. Inactivating the corticothalamic feedback by GABAA agonist muscimol applied on the dural surface significantly diminishes the correlation between brain states and thalamic neuronal activity. Additional investigations show that by photostimulating GABAergic axons (expressing Channelrhodopsin-2 in a Cre-dependent manner) that project from the lateral hypothalamus (LH) to the dorsal raphe nucleus (DRN), neurons in the DRN increase their action potential output, presumably through disinhibition. Taken together our results show that LGN neuronal membrane potential and action potential output are dynamically linked to arousal dependent brain states in awake mice and this fact might have important functional implications

A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis.

BACKGROUND: The yeast Schizosaccharomyces pombe is frequently used as a model for studying the cell cycle. The cells are rod-shaped and divide by medial fission. The process of cell division, or cytokinesis, is controlled by a network of signaling proteins called the Septation Initiation Network (SIN); SIN proteins associate with the SPBs during nuclear division (mitosis). Some SIN proteins associate with both SPBs early in mitosis, and then display strongly asymmetric signal intensity at the SPBs in late mitosis, just before cytokinesis. This asymmetry is thought to be important for correct regulation of SIN signaling, and coordination of cytokinesis and mitosis. In order to study the dynamics of organelles or large protein complexes such as the spindle pole body (SPB), which have been labeled with a fluorescent protein tag in living cells, a number of the image analysis problems must be solved; the cell outline must be detected automatically, and the position and signal intensity associated with the structures of interest within the cell must be determined. RESULTS: We present a new 2D and 3D image analysis system that permits versatile and robust analysis of motile, fluorescently labeled structures in rod-shaped cells. We have designed an image analysis system that we have implemented as a user-friendly software package allowing the fast and robust image-analysis of large numbers of rod-shaped cells. We have developed new robust algorithms, which we combined with existing methodologies to facilitate fast and accurate analysis. Our software permits the detection and segmentation of rod-shaped cells in either static or dynamic (i.e. time lapse) multi-channel images. It enables tracking of two structures (for example SPBs) in two different image channels. For 2D or 3D static images, the locations of the structures are identified, and then intensity values are extracted together with several quantitative parameters, such as length, width, cell orientation, background fluorescence and the distance between the structures of interest. Furthermore, two kinds of kymographs of the tracked structures can be established, one representing the migration with respect to their relative position, the other representing their individual trajectories inside the cell. This software package, called "RodCellJ", allowed us to analyze a large number of S. pombe cells to understand the rules that govern SIN protein asymmetry. CONCLUSIONS: "RodCell" is freely available to the community as a package of several ImageJ plugins to simultaneously analyze the behavior of a large number of rod-shaped cells in an extensive manner. The integration of different image-processing techniques in a single package, as well as the development of novel algorithms does not only allow to speed up the analysis with respect to the usage of existing tools, but also accounts for higher accuracy. Its utility was demonstrated on both 2D and 3D static and dynamic images to study the septation initiation network of the yeast Schizosaccharomyces pombe. More generally, it can be used in any kind of biological context where fluorescent-protein labeled structures need to be analyzed in rod-shaped cells. AVAILABILITY: RodCellJ is freely available under http://bigwww.epfl.ch/algorithms.html, (after acceptance of the publication)

ATMAD : robust image analysis for Automatic Tissue MicroArray De-arraying

International audienceBackground. Over the last two decades, an innovative technology called Tissue Microarray (TMA),which combines multi-tissue and DNA microarray concepts, has been widely used in the field ofhistology. It consists of a collection of several (up to 1000 or more) tissue samples that are assembledonto a single support – typically a glass slide – according to a design grid (array) layout, in order toallow multiplex analysis by treating numerous samples under identical and standardized conditions.However, during the TMA manufacturing process, the sample positions can be highly distorted fromthe design grid due to the imprecision when assembling tissue samples and the deformation of theembedding waxes. Consequently, these distortions may lead to severe errors of (histological) assayresults when the sample identities are mismatched between the design and its manufactured output.The development of a robust method for de-arraying TMA, which localizes and matches TMAsamples with their design grid, is therefore crucial to overcome the bottleneck of this prominenttechnology.Results. In this paper, we propose an Automatic, fast and robust TMA De-arraying (ATMAD)approach dedicated to images acquired with bright field and fluorescence microscopes (or scanners).First, tissue samples are localized in the large image by applying a locally adaptive thresholdingon the isotropic wavelet transform of the input TMA image. To reduce false detections, a parametricshape model is considered for segmenting ellipse-shaped objects at each detected position.Segmented objects that do not meet the size and the roundness criteria are discarded from thelist of tissue samples before being matched with the design grid. Sample matching is performed byestimating the TMA grid deformation under the thin-plate model. Finally, thanks to the estimateddeformation, the true tissue samples that were preliminary rejected in the early image processingstep are recognized by running a second segmentation step.Conclusions. We developed a novel de-arraying approach for TMA analysis. By combining waveletbaseddetection, active contour segmentation, and thin-plate spline interpolation, our approach isable to handle TMA images with high dynamic, poor signal-to-noise ratio, complex background andnon-linear deformation of TMA grid. In addition, the deformation estimation produces quantitativeinformation to asset the manufacturing quality of TMAs

A single-camera gaze tracking system under natural light

Gaze tracking is a human-computer interaction technology, and it has been widely studied in the academic and industrial fields. However, constrained by the performance of the specific sensors and algorithms, it has not been popularized for everyone. This paper proposes a single-camera gaze tracking system under natural light to enable its versatility. The iris center and anchor point are the most crucial factors for the accuracy of the system. The accurate iris center is detected by the simple active contour snakuscule, which is initialized by the prior knowledge of eye anatomical dimensions. After that, a novel anchor point is computed by the stable facial landmarks. Next, second-order mapping functions use the eye vectors and the head pose to estimate the points of regard. Finally, the gaze errors are improved by implementing a weight coefficient on the points of regard of the left and right eyes. The feature position of the iris center achieves an accuracy of 98.87% on the GI4E database when the normalized error is lower than 0.05. The accuracy of the gaze tracking method is superior to the-state-of-the-art appearance-based and feature-based methods on the EYEDIAP database