A Deep-Learning Based Pipeline for Estimating the Abundance and Size of Aquatic Organisms in an Unconstrained Underwater Environment from Continuously Captured Stereo Video.

The utilization of stationary underwater cameras is a modern and well-adapted approach to provide a continuous and cost-effective long-term solution to monitor underwater habitats of particular interest. A common goal of such monitoring systems is to gain better insight into the dynamics and condition of populations of various marine organisms, such as migratory or commercially relevant fish taxa. This paper describes a complete processing pipeline to automatically determine the abundance, type and estimate the size of biological taxa from stereoscopic video data captured by the stereo camera of a stationary Underwater Fish Observatory (UFO). A calibration of the recording system was carried out in situ and, afterward, validated using the synchronously recorded sonar data. The video data were recorded continuously for nearly one year in the Kiel Fjord, an inlet of the Baltic Sea in northern Germany. It shows underwater organisms in their natural behavior, as passive low-light cameras were used instead of active lighting to dampen attraction effects and allow for the least invasive recording possible. The recorded raw data are pre-filtered by an adaptive background estimation to extract sequences with activity, which are then processed by a deep detection network, i.e., Yolov5. This provides the location and type of organisms detected in each video frame of both cameras, which are used to calculate stereo correspondences following a basic matching scheme. In a subsequent step, the size and distance of the depicted organisms are approximated using the corner coordinates of the matched bounding boxes. The Yolov5 model employed in this study was trained on a novel dataset comprising 73,144 images and 92,899 bounding box annotations for 10 categories of marine animals. The model achieved a mean detection accuracy of 92.4%, a mean average precision (mAP) of 94.8% and an F1 score of 93%.

Discriminative generalized Hough transform for object localization in medical images.

PURPOSE: This paper proposes the discriminative generalized Hough transform (DGHT) as an efficient and reliable means for object localization in medical images. It is meant to give a deeper insight into the underlying theory and a comprehensive overview of the methodology and the scope of applications. METHODS: The DGHT combines the generalized Hough transform (GHT) with a discriminative training technique for the GHT models to obtain more efficient and robust localization results. To this end, the model points are equipped with individual weights, which are trained discriminatively with respect to a minimal localization error. Through this weighting, the models become more robust since the training focuses on common features of the target object over a set of training images. Unlike other weighting strategies, our training algorithm focuses on the error rate and allows for negative weights, which can be employed to encode rivaling structures into the model. The basic algorithm is presented here in conjunction with several extensions for fully automatic and faster processing. These include: (1) the automatic generation of models from training images and their iterative refinement, (2) the training of joint models for similar objects, and (3) a multi-level approach. RESULTS: The algorithm is tested successfully for the knee in long-leg radiographs (97.6 % success rate), the vertebrae in C-arm CT (95.5 % success rate), and the femoral head in whole-body MR (100 % success rate). In addition, it is compared to Hough forests (Gall et al. in IEEE Trans Pattern Anal Mach Intell 33(11):2188-2202, 2011) for the task of knee localization (97.8 % success rate). Conclusion The DGHT has proven to be a general procedure, which can be easily applied to various tasks with high success rates.

Automatic model-based segmentation of the heart in CT images.

Automatic image processing methods are a prerequisite to efficiently analyze the large amount of image data produced by computed tomography (CT) scanners during cardiac exams. This paper introduces a model-based approach for the fully automatic segmentation of the whole heart (four chambers, myocardium, and great vessels) from 3-D CT images. Model adaptation is done by progressively increasing the degrees-of-freedom of the allowed deformations. This improves convergence as well as segmentation accuracy. The heart is first localized in the image using a 3-D implementation of the generalized Hough transform. Pose misalignment is corrected by matching the model to the image making use of a global similarity transformation. The complex initialization of the multicompartment mesh is then addressed by assigning an affine transformation to each anatomical region of the model. Finally, a deformable adaptation is performed to accurately match the boundaries of the patient's anatomy. A mean surface-to-surface error of 0.82 mm was measured in a leave-one-out quantitative validation carried out on 28 images. Moreover, the piecewise affine transformation introduced for mesh initialization and adaptation shows better interphase and interpatient shape variability characterization than commonly used principal component analysis.

Automatic whole heart segmentation in static magnetic resonance image volumes.

We present a fully automatic segmentation algorithm for the whole heart (four chambers, left ventricular myocardium and trunks of the aorta, the pulmonary artery and the pulmonary veins) in cardiac MR image volumes with nearly isotropic voxel resolution, based on shape-constrained deformable models. After automatic model initialization and reorientation to the cardiac axes, we apply a multi-stage adaptation scheme with progressively increasing degrees of freedom. Particular attention is paid to the calibration of the MR image intensities. Detailed evaluation results for the various anatomical heart regions are presented on a database of 42 patients. On calibrated images, we obtain an average segmentation error of 0.76mm.