Multi-stage Suture Detection for Robot Assisted Anastomosis based on Deep Learning

In robotic surgery, task automation and learning from demonstration combined with human supervision is an emerging trend for many new surgical robot platforms. One such task is automated anastomosis, which requires bimanual needle handling and suture detection. Due to the complexity of the surgical environment and varying patient anatomies, reliable suture detection is difficult, which is further complicated by occlusion and thread topologies. In this paper, we propose a multi-stage framework for suture thread detection based on deep learning. Fully convolutional neural networks are used to obtain the initial detection and the overlapping status of suture thread, which are later fused with the original image to learn a gradient road map of the thread. Based on the gradient road map, multiple segments of the thread are extracted and linked to form the whole thread using a curvilinear structure detector. Experiments on two different types of sutures demonstrate the accuracy of the proposed framework.Comment: Submitted to ICRA 201

Automatic segmentation of the left ventricle cavity and myocardium in MRI data

A novel approach for the automatic segmentation has been developed to extract the epi-cardium and endo-cardium boundaries of the left ventricle (lv) of the heart. The developed segmentation scheme takes multi-slice and multi-phase magnetic resonance (MR) images of the heart, transversing the short-axis length from the base to the apex. Each image is taken at one instance in the heart's phase. The images are segmented using a diffusion-based filter followed by an unsupervised clustering technique and the resulting labels are checked to locate the (lv) cavity. From cardiac anatomy, the closest pool of blood to the lv cavity is the right ventricle cavity. The wall between these two blood-pools (interventricular septum) is measured to give an approximate thickness for the myocardium. This value is used when a radial search is performed on a gradient image to find appropriate robust segments of the epi-cardium boundary. The robust edge segments are then joined using a normal spline curve. Experimental results are presented with very encouraging qualitative and quantitative results and a comparison is made against the state-of-the art level-sets method

Search for high-amplitude Delta Scuti and RR Lyrae stars in Sloan Digital Sky Survey Stripe 82 using principal component analysis

We propose a robust principal component analysis (PCA) framework for the exploitation of multi-band photometric measurements in large surveys. Period search results are improved using the time series of the first principal component due to its optimized signal-to-noise ratio.The presence of correlated excess variations in the multivariate time series enables the detection of weaker variability. Furthermore, the direction of the largest variance differs for certain types of variable stars. This can be used as an efficient attribute for classification. The application of the method to a subsample of Sloan Digital Sky Survey Stripe 82 data yielded 132 high-amplitude Delta Scuti variables. We found also 129 new RR Lyrae variables, complementary to the catalogue of Sesar et al., 2010, extending the halo area mapped by Stripe 82 RR Lyrae stars towards the Galactic bulge. The sample comprises also 25 multiperiodic or Blazhko RR Lyrae stars.Comment: 23 pages, 17 figure

Mapping for maximum performance on FPGA DSP blocks

The digital signal processing (DSP) blocks on modern field programmable gate arrays (FPGAs) are highly capable and support a variety of different datapath configurations. Unfortunately, inference in synthesis tools can fail to result in circuits that reach maximum DSP block throughput. We have developed a tool that maps graphs of add/sub/mult nodes to DSP blocks on Xilinx FPGAs, ensuring maximum throughput. This is done by delaying scheduling until after the graph has been partitioned onto DSP blocks and scheduled based on their pipeline structure, resulting in a throughput optimized implementation. Our tool prepares equivalent implementations in a variety of other methods, including high-level synthesis (HLS) for comparison. We show that the proposed approach offers an improvement in frequency of 100% over standard pipelined code, and 23% over Vivado HLS synthesis implementation, while retaining code portability, at the cost of a modest increase in logic resource usage

Biometric Applications Based on Multiresolution Analysis Tools

This dissertation is dedicated to the development of new algorithms for biometric applications based on multiresolution analysis tools. Biometric is a unique, measurable characteristic of a human being that can be used to automatically recognize an individual or verify an individual\u27s identity. Biometrics can measure physiological, behavioral, physical and chemical characteristics of an individual. Physiological characteristics are based on measurements derived from direct measurement of a part of human body, such as, face, fingerprint, iris, retina etc. We focussed our investigations to fingerprint and face recognition since these two biometric modalities are used in conjunction to obtain reliable identification by various border security and law enforcement agencies. We developed an efficient and robust human face recognition algorithm for potential law enforcement applications. A generic fingerprint compression algorithm based on state of the art multiresolution analysis tool to speed up data archiving and recognition was also proposed. Finally, we put forth a new fingerprint matching algorithm by generating an efficient set of fingerprint features to minimize false matches and improve identification accuracy. Face recognition algorithms were proposed based on curvelet transform using kernel based principal component analysis and bidirectional two-dimensional principal component analysis and numerous experiments were performed using popular human face databases. Significant improvements in recognition accuracy were achieved and the proposed methods drastically outperformed conventional face recognition systems that employed linear one-dimensional principal component analysis. Compression schemes based on wave atoms decomposition were proposed and major improvements in peak signal to noise ratio were obtained in comparison to Federal Bureau of Investigation\u27s wavelet scalar quantization scheme. Improved performance was more pronounced and distinct at higher compression ratios. Finally, a fingerprint matching algorithm based on wave atoms decomposition, bidirectional two dimensional principal component analysis and extreme learning machine was proposed and noteworthy improvements in accuracy were realized

Methods for three-dimensional Registration of Multimodal Abdominal Image Data

Multimodal image registration benefits the diagnosis, treatment planning and the performance of image-guided procedures in the liver, since it enables the fusion of complementary information provided by pre- and intrainterventional data about tumor localization and access. Although there exist various registration methods, approaches which are specifically optimized for the registration of multimodal abdominal scans are only scarcely available. The work presented in this thesis aims to tackle this problem by focusing on the development, optimization and evaluation of registration methods specifically for the registration of multimodal liver scans. The contributions to the research field of medical image registration include the development of a registration evaluation methodology that enables the comparison and optimization of linear and non-linear registration algorithms using a point-based accuracy measure. This methodology has been used to benchmark standard registration methods as well as novel approaches that were developed within the frame of this thesis. The results of the methodology showed that the employed similarity measure used during the registration has a major impact on the registration accuracy of the method. Due to this influence, two alternative similarity metrics bearing the potential to be used on multimodal image data are proposed and evaluated. The first metric relies on the use of gradient information in form of Histograms of Oriented Gradients (HOG) whereas the second metric employs a siamese neural network to learn a similarity measure directly on the image data. The evaluation showed, that both metrics could compete with state of the art similarity measures in terms of registration accuracy. The HOG-metric offers the advantage that it does not require ground truth data to learn a similarity estimation, but instead it is applicable to various data sets with the sole requirement of distinct gradients. However, the Siamese metric is characterized by a higher robustness for large rotations than the HOG-metric. To train such a network, registered ground truth data is required which may be critical for multimodal image data. Yet, the results show that it is possible to apply models trained on registered synthetic data on real patient data. The last part of this thesis focuses on methods to learn an entire registration process using neural networks, thereby offering the advantage to replace the traditional, time-consuming iterative registration procedure. Within the frame of this thesis, the so-called VoxelMorph network which was originally proposed for monomodal, non-linear registration learning is extended for affine and multimodal registration learning tasks. This extension includes the consideration of an image mask during metric evaluation as well as loss functions for multimodal data, such as the pretrained Siamese metric and a loss relying on the comparison of deformation fields. Based on the developed registration evaluation methodology, the performance of the original network as well as the extended variants are evaluated for monomodal and multimodal registration tasks using multiple data sets. With the extended network variants, it is possible to learn an entire multimodal registration process for the correction of large image displacements. As for the Siamese metric, the results imply a general transferability of models trained with synthetic data to registration tasks including real patient data. Due to the lack of multimodal ground truth data, this transfer represents an important step towards making Deep Learning based registration procedures clinically usable

Development of low dissipative high order filter schemes for multiscale Navier–Stokes/MHD systems

Recent progress in the development of a class of low dissipative high order (fourth-order or higher) filter schemes for multiscale Navier–Stokes, and ideal and non-ideal magnetohydrodynamics (MHD) systems is described. The four main features of this class of schemes are: (a) multiresolution wavelet decomposition of the computed flow data as sensors for adaptive numerical dissipative control, (b) multistep filter to accommodate efficient application of different numerical dissipation models and different spatial high order base schemes, (c) a unique idea in solving the ideal conservative MHD system (a non-strictly hyperbolic conservation law) without having to deal with an incomplete eigensystem set while at the same time ensuring that correct shock speeds and locations are computed, and (d) minimization of the divergence of the magnetic field numerical error. By design, the flow sensors, different choice of high order base schemes and numerical dissipation models are stand-alone modules. A whole class of low dissipative high order schemes can be derived at ease, making the resulting computer software very flexible with widely applicable. Performance of multiscale and multiphysics test cases are illustrated with many levels of grid refinement and comparison with commonly used schemes in the literature

BEMDEC: An Adaptive and Robust Methodology for Digital Image Feature Extraction

The intriguing study of feature extraction, and edge detection in particular, has, as a result of the increased use of imagery, drawn even more attention not just from the field of computer science but also from a variety of scientific fields. However, various challenges surrounding the formulation of feature extraction operator, particularly of edges, which is capable of satisfying the necessary properties of low probability of error (i.e., failure of marking true edges), accuracy, and consistent response to a single edge, continue to persist. Moreover, it should be pointed out that most of the work in the area of feature extraction has been focused on improving many of the existing approaches rather than devising or adopting new ones. In the image processing subfield, where the needs constantly change, we must equally change the way we think. In this digital world where the use of images, for variety of purposes, continues to increase, researchers, if they are serious about addressing the aforementioned limitations, must be able to think outside the box and step away from the usual in order to overcome these challenges. In this dissertation, we propose an adaptive and robust, yet simple, digital image features detection methodology using bidimensional empirical mode decomposition (BEMD), a sifting process that decomposes a signal into its two-dimensional (2D) bidimensional intrinsic mode functions (BIMFs). The method is further extended to detect corners and curves, and as such, dubbed as BEMDEC, indicating its ability to detect edges, corners and curves. In addition to the application of BEMD, a unique combination of a flexible envelope estimation algorithm, stopping criteria and boundary adjustment made the realization of this multi-feature detector possible. Further application of two morphological operators of binarization and thinning adds to the quality of the operator