Task adapted reconstruction for inverse problems

The paper considers the problem of performing a task defined on a model parameter that is only observed indirectly through noisy data in an ill-posed inverse problem. A key aspect is to formalize the steps of reconstruction and task as appropriate estimators (non-randomized decision rules) in statistical estimation problems. The implementation makes use of (deep) neural networks to provide a differentiable parametrization of the family of estimators for both steps. These networks are combined and jointly trained against suitable supervised training data in order to minimize a joint differentiable loss function, resulting in an end-to-end task adapted reconstruction method. The suggested framework is generic, yet adaptable, with a plug-and-play structure for adjusting both the inverse problem and the task at hand. More precisely, the data model (forward operator and statistical model of the noise) associated with the inverse problem is exchangeable, e.g., by using neural network architecture given by a learned iterative method. Furthermore, any task that is encodable as a trainable neural network can be used. The approach is demonstrated on joint tomographic image reconstruction, classification and joint tomographic image reconstruction segmentation

New Descriptor for Glomerulus Detection in Kidney Microscopy Image

Glomerulus detection is a key step in histopathological evaluation of microscopy images of kidneys. However, the task of automatic detection of glomeruli poses challenges due to the disparity in sizes and shapes of glomeruli in renal sections. Moreover, extensive variations of their intensities due to heterogeneity in immunohistochemistry staining are also encountered. Despite being widely recognized as a powerful descriptor for general object detection, the rectangular histogram of oriented gradients (Rectangular HOG) suffers from many false positives due to the aforementioned difficulties in the context of glomerulus detection. A new descriptor referred to as Segmental HOG is developed to perform a comprehensive detection of hundreds of glomeruli in images of whole kidney sections. The new descriptor possesses flexible blocks that can be adaptively fitted to input images to acquire robustness to deformations of glomeruli. Moreover, the novel segmentation technique employed herewith generates high quality segmentation outputs and the algorithm is assured to converge to an optimal solution. Consequently, experiments using real world image data reveal that Segmental HOG achieves significant improvements in detection performance compared to Rectangular HOG. The proposed descriptor and method for glomeruli detection present promising results and is expected to be useful in pathological evaluation

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Joint Image Reconstruction and Segmentation Using the Potts Model

We propose a new algorithmic approach to the non-smooth and non-convex Potts problem (also called piecewise-constant Mumford-Shah problem) for inverse imaging problems. We derive a suitable splitting into specific subproblems that can all be solved efficiently. Our method does not require a priori knowledge on the gray levels nor on the number of segments of the reconstruction. Further, it avoids anisotropic artifacts such as geometric staircasing. We demonstrate the suitability of our method for joint image reconstruction and segmentation. We focus on Radon data, where we in particular consider limited data situations. For instance, our method is able to recover all segments of the Shepp-Logan phantom from $7$ angular views only. We illustrate the practical applicability on a real PET dataset. As further applications, we consider spherical Radon data as well as blurred data