Tracking and Mapping in Medical Computer Vision: A Review

As computer vision algorithms are becoming more capable, their applications in clinical systems will become more pervasive. These applications include diagnostics such as colonoscopy and bronchoscopy, guiding biopsies and minimally invasive interventions and surgery, automating instrument motion and providing image guidance using pre-operative scans. Many of these applications depend on the specific visual nature of medical scenes and require designing and applying algorithms to perform in this environment. In this review, we provide an update to the field of camera-based tracking and scene mapping in surgery and diagnostics in medical computer vision. We begin with describing our review process, which results in a final list of 515 papers that we cover. We then give a high-level summary of the state of the art and provide relevant background for those who need tracking and mapping for their clinical applications. We then review datasets provided in the field and the clinical needs therein. Then, we delve in depth into the algorithmic side, and summarize recent developments, which should be especially useful for algorithm designers and to those looking to understand the capability of off-the-shelf methods. We focus on algorithms for deformable environments while also reviewing the essential building blocks in rigid tracking and mapping since there is a large amount of crossover in methods. Finally, we discuss the current state of the tracking and mapping methods along with needs for future algorithms, needs for quantification, and the viability of clinical applications in the field. We conclude that new methods need to be designed or combined to support clinical applications in deformable environments, and more focus needs to be put into collecting datasets for training and evaluation.Comment: 31 pages, 17 figure

Accurate, fast, and robust 3D city-scale reconstruction using wide area motion imagery

Multi-view stereopsis (MVS) is a core problem in computer vision, which takes a set of scene views together with known camera poses, then produces a geometric representation of the underlying 3D model Using 3D reconstruction one can determine any object's 3D profile, as well as knowing the 3D coordinate of any point on the profile. The 3D reconstruction of objects is a generally scientific problem and core technology of a wide variety of fields, such as Computer Aided Geometric Design (CAGD), computer graphics, computer animation, computer vision, medical imaging, computational science, virtual reality, digital media, etc. However, though MVS problems have been studied for decades, many challenges still exist in current state-of-the-art algorithms, for example, many algorithms still lack accuracy and completeness when tested on city-scale large datasets, most MVS algorithms available require a large amount of execution time and/or specialized hardware and software, which results in high cost, and etc... This dissertation work tries to address all the challenges we mentioned, and proposed multiple solutions. More specifically, this dissertation work proposed multiple novel MVS algorithms to automatically and accurately reconstruct the underlying 3D scenes. By proposing a novel volumetric voxel-based method, one of our algorithms achieved near real-time runtime speed, which does not require any special hardware or software, and can be deployed onto power-constrained embedded systems. By developing a new camera clustering module and a novel weighted voting-based surface likelihood estimation module, our algorithm is generalized to process di erent datasets, and achieved the best performance in terms of accuracy and completeness when compared with existing algorithms. This dissertation work also performs the very first quantitative evaluation in terms of precision, recall, and F-score using real-world LiDAR groundtruth data. Last but not least, this dissertation work proposes an automatic workflow, which can stitch multiple point cloud models with limited overlapping areas into one larger 3D model for better geographical coverage. All the results presented in this dissertation work have been evaluated in our wide area motion imagery (WAMI) dataset, and improved the state-of-the-art performances by a large margin.The generated results from this dissertation work have been successfully used in many aspects, including: city digitization, improving detection and tracking performances, real time dynamic shadow detection, 3D change detection, visibility map generating, VR environment, and visualization combined with other information, such as building footprint and roads.Includes bibliographical references

AUTOMATED ANALYSIS OF NEURONAL MORPHOLOGY: DETECTION, MODELING AND RECONSTRUCTION

Ph.DDOCTOR OF PHILOSOPH

From nanometers to centimeters: Imaging across spatial scales with smart computer-aided microscopy

Microscopes have been an invaluable tool throughout the history of the life sciences, as they allow researchers to observe the miniscule details of living systems in space and time. However, modern biology studies complex and non-obvious phenotypes and their distributions in populations and thus requires that microscopes evolve from visual aids for anecdotal observation into instruments for objective and quantitative measurements. To this end, many cutting-edge developments in microscopy are fuelled by innovations in the computational processing of the generated images. Computational tools can be applied in the early stages of an experiment, where they allow for reconstruction of images with higher resolution and contrast or more colors compared to raw data. In the final analysis stage, state-of-the-art image analysis pipelines seek to extract interpretable and humanly tractable information from the high-dimensional space of images. In the work presented in this thesis, I performed super-resolution microscopy and wrote image analysis pipelines to derive quantitative information about multiple biological processes. I contributed to studies on the regulation of DNMT1 by implementing machine learning-based segmentation of replication sites in images and performed quantitative statistical analysis of the recruitment of multiple DNMT1 mutants. To study the spatiotemporal distribution of DNA damage response I performed STED microscopy and could provide a lower bound on the size of the elementary spatial units of DNA repair. In this project, I also wrote image analysis pipelines and performed statistical analysis to show a decoupling of DNA density and heterochromatin marks during repair. More on the experimental side, I helped in the establishment of a protocol for many-fold color multiplexing by iterative labelling of diverse structures via DNA hybridization. Turning from small scale details to the distribution of phenotypes in a population, I wrote a reusable pipeline for fitting models of cell cycle stage distribution and inhibition curves to high-throughput measurements to quickly quantify the effects of innovative antiproliferative antibody-drug-conjugates. The main focus of the thesis is BigStitcher, a tool for the management and alignment of terabyte-sized image datasets. Such enormous datasets are nowadays generated routinely with light-sheet microscopy and sample preparation techniques such as clearing or expansion. Their sheer size, high dimensionality and unique optical properties poses a serious bottleneck for researchers and requires specialized processing tools, as the images often do not fit into the main memory of most computers. BigStitcher primarily allows for fast registration of such many-dimensional datasets on conventional hardware using optimized multi-resolution alignment algorithms. The software can also correct a variety of aberrations such as fixed-pattern noise, chromatic shifts and even complex sample-induced distortions. A defining feature of BigStitcher, as well as the various image analysis scripts developed in this work is their interactivity. A central goal was to leverage the user's expertise at key moments and bring innovations from the big data world to the lab with its smaller and much more diverse datasets without replacing scientists with automated black-box pipelines. To this end, BigStitcher was implemented as a user-friendly plug-in for the open source image processing platform Fiji and provides the users with a nearly instantaneous preview of the aligned images and opportunities for manual control of all processing steps. With its powerful features and ease-of-use, BigStitcher paves the way to the routine application of light-sheet microscopy and other methods producing equally large datasets

Image Registration Workshop Proceedings

Automatic image registration has often been considered as a preliminary step for higher-level processing, such as object recognition or data fusion. But with the unprecedented amounts of data which are being and will continue to be generated by newly developed sensors, the very topic of automatic image registration has become and important research topic. This workshop presents a collection of very high quality work which has been grouped in four main areas: (1) theoretical aspects of image registration; (2) applications to satellite imagery; (3) applications to medical imagery; and (4) image registration for computer vision research

Image Processing and Analysis for Preclinical and Clinical Applications

Radiomics is one of the most successful branches of research in the field of image processing and analysis, as it provides valuable quantitative information for the personalized medicine. It has the potential to discover features of the disease that cannot be appreciated with the naked eye in both preclinical and clinical studies. In general, all quantitative approaches based on biomedical images, such as positron emission tomography (PET), computed tomography (CT) and magnetic resonance imaging (MRI), have a positive clinical impact in the detection of biological processes and diseases as well as in predicting response to treatment. This Special Issue, “Image Processing and Analysis for Preclinical and Clinical Applications”, addresses some gaps in this field to improve the quality of research in the clinical and preclinical environment. It consists of fourteen peer-reviewed papers covering a range of topics and applications related to biomedical image processing and analysis

Multiple layer image analysis for video microscopy

Motion analysis is a fundamental problem that serves as the basis for many other image analysis tasks, such as structure estimation and object segmentation. Many motion analysis techniques assume that objects are opaque and non-reflective, asserting that a single pixel is an observation of a single scene object. This assumption breaks down when observing semitransparent objects--a single pixel is an observation of the object and whatever lies behind it. This dissertation is concerned with methods for analyzing multiple layer motion in microscopy, a domain where most objects are semitransparent. I present a novel approach to estimating the transmission of light through stationary, semitransparent objects by estimating the gradient of the constant transmission observed over all frames in a video. This enables removing the non-moving elements from the video, providing an enhanced view of the moving elements. I present a novel structured illumination technique that introduces a semitransparent pattern layer to microscopy, enabling microscope stage tracking even in the presence of stationary, sparse, or moving specimens. Magnitude comparisons at the frequencies present in the pattern layer provide estimates of pattern orientation and focal depth. Two pattern tracking techniques are examined, one based on phase correlation at pattern frequencies, and one based on spatial correlation using a model of pattern layer appearance based on microscopy image formation. Finally, I present a method for designing optimal structured illumination patterns tuned for constraints imposed by specific microscopy experiments. This approach is based on analysis of the microscope's optical transfer function at different focal depths