arXiv subjects

Reinhard Koch

Publications and source records attributed to Reinhard Koch.

24 records · Page 2Linked to original sources

arXiv2020

Panoptic Instance Segmentation on Pigs

The behavioural research of pigs can be greatly simplified if automatic recognition systems are used. Especially systems based on computer vision have the advantage that they allow an evaluation without affecting the normal behaviour of the animals. In recent years, methods based on deep learning have been introduced and have shown pleasingly good results. Especially object and keypoint detectors have been used to detect the individual animals. Despite good results, bounding boxes and sparse keypoints do not trace the contours of the animals, resulting in a lot of information being lost. Therefore this work follows the relatively new definition of a panoptic segmentation and aims at the pixel accurate segmentation of the individual pigs. For this a framework of a neural network for semantic segmentation, different network heads and postprocessing methods is presented. With the resulting instance segmentation masks further information like the size or weight of the animals could be estimated. The method is tested on a specially created data set with 1000 hand-labeled images and achieves detection rates of around 95% (F1 Score) despite disturbances such as occlusions and dirty lenses.

cs.CV↗

arXiv2020

MorphoCluster: Efficient Annotation of Plankton images by Clustering

In this work, we present MorphoCluster, a software tool for data-driven, fast and accurate annotation of large image data sets. While already having surpassed the annotation rate of human experts, volume and complexity of marine data will continue to increase in the coming years. Still, this data requires interpretation. MorphoCluster augments the human ability to discover patterns and perform object classification in large amounts of data by embedding unsupervised clustering in an interactive process. By aggregating similar images into clusters, our novel approach to image annotation increases consistency, multiplies the throughput of an annotator and allows experts to adapt the granularity of their sorting scheme to the structure in the data. By sorting a set of 1.2M objects into 280 data-driven classes in 71 hours (16k objects per hour), with 90% of these classes having a precision of 0.889 or higher. This shows that MorphoCluster is at the same time fast, accurate and consistent, provides a fine-grained and data-driven classification and enables novelty detection. MorphoCluster is available as open-source software at https://github.com/morphocluster.

cs.CV↗

arXiv2020

DRST: Deep Residual Shearlet Transform for Densely Sampled Light Field Reconstruction

The Image-Based Rendering (IBR) approach using Shearlet Transform (ST) is one of the most effective methods for Densely-Sampled Light Field (DSLF) reconstruction. The ST-based DSLF reconstruction typically relies on an iterative thresholding algorithm for Epipolar-Plane Image (EPI) sparse regularization in shearlet domain, involving dozens of transformations between image domain and shearlet domain, which are in general time-consuming. To overcome this limitation, a novel learning-based ST approach, referred to as Deep Residual Shearlet Transform (DRST), is proposed in this paper. Specifically, for an input sparsely-sampled EPI, DRST employs a deep fully Convolutional Neural Network (CNN) to predict the residuals of the shearlet coefficients in shearlet domain in order to reconstruct a densely-sampled EPI in image domain. The DRST network is trained on synthetic Sparsely-Sampled Light Field (SSLF) data only by leveraging elaborately-designed masks. Experimental results on three challenging real-world light field evaluation datasets with varying moderate disparity ranges (8 - 16 pixels) demonstrate the superiority of the proposed learning-based DRST approach over the non-learning-based ST method for DSLF reconstruction. Moreover, DRST provides a 2.4x speedup over ST, at least.

cs.MM↗

arXiv2019

2D and 3D Segmentation of uncertain local collagen fiber orientations in SHG microscopy

Collagen fiber orientations in bones, visible with Second Harmonic Generation (SHG) microscopy, represent the inner structure and its alteration due to influences like cancer. While analyses of these orientations are valuable for medical research, it is not feasible to analyze the needed large amounts of local orientations manually. Since we have uncertain borders for these local orientations only rough regions can be segmented instead of a pixel-wise segmentation. We analyze the effect of these uncertain borders on human performance by a user study. Furthermore, we compare a variety of 2D and 3D methods such as classical approaches like Fourier analysis with state-of-the-art deep neural networks for the classification of local fiber orientations. We present a general way to use pretrained 2D weights in 3D neural networks, such as Inception-ResNet-3D a 3D extension of Inception-ResNet-v2. In a 10 fold cross-validation our two stage segmentation based on Inception-ResNet-3D and transferred 2D ImageNet weights achieves a human comparable accuracy.

cs.CV↗

arXiv2018

An Analysis by Synthesis Approach for Automatic Vertebral Shape Identification in Clinical QCT

Quantitative computed tomography (QCT) is a widely used tool for osteoporosis diagnosis and monitoring. The assessment of cortical markers like cortical bone mineral density (BMD) and thickness is a demanding task, mainly because of the limited spatial resolution of QCT. We propose a direct model based method to automatically identify the surface through the center of the cortex of human vertebra. We develop a statistical bone model and analyze its probability distribution after the imaging process. Using an as-rigid-as-possible deformation we find the cortical surface that maximizes the likelihood of our model given the input volume. Using the European Spine Phantom (ESP) and a high resolution μCT scan of a cadaveric vertebra, we show that the proposed method is able to accurately identify the real center of cortex ex-vivo. To demonstrate the in-vivo applicability of our method we use manually obtained surfaces for comparison.

eess.IV↗

arXiv2017

Restoration of Images with Wavefront Aberrations

This contribution deals with image restoration in optical systems with coherent illumination, which is an important topic in astronomy, coherent microscopy and radar imaging. Such optical systems suffer from wavefront distortions, which are caused by imperfect imaging components and conditions. Known image restoration algorithms work well for incoherent imaging, they fail in case of coherent images. In this paper a novel wavefront correction algorithm is presented, which allows image restoration under coherent conditions. In most coherent imaging systems, especially in astronomy, the wavefront deformation is known. Using this information, the proposed algorithm allows a high quality restoration even in case of severe wavefront distortions. We present two versions of this algorithm, which are an evolution of the Gerchberg-Saxton and the Hybrid-Input-Output algorithm. The algorithm is verified on simulated and real microscopic images.

astro-ph.IM↗