Deep Lesion Graphs in the Wild: Relationship Learning and Organization of Significant Radiology Image Findings in a Diverse Large-scale Lesion Database

Radiologists in their daily work routinely find and annotate significant abnormalities on a large number of radiology images. Such abnormalities, or lesions, have collected over years and stored in hospitals' picture archiving and communication systems. However, they are basically unsorted and lack semantic annotations like type and location. In this paper, we aim to organize and explore them by learning a deep feature representation for each lesion. A large-scale and comprehensive dataset, DeepLesion, is introduced for this task. DeepLesion contains bounding boxes and size measurements of over 32K lesions. To model their similarity relationship, we leverage multiple supervision information including types, self-supervised location coordinates and sizes. They require little manual annotation effort but describe useful attributes of the lesions. Then, a triplet network is utilized to learn lesion embeddings with a sequential sampling strategy to depict their hierarchical similarity structure. Experiments show promising qualitative and quantitative results on lesion retrieval, clustering, and classification. The learned embeddings can be further employed to build a lesion graph for various clinically useful applications. We propose algorithms for intra-patient lesion matching and missing annotation mining. Experimental results validate their effectiveness.Comment: Accepted by CVPR2018. DeepLesion url adde

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

Regularized Newton Methods for X-ray Phase Contrast and General Imaging Problems

Like many other advanced imaging methods, x-ray phase contrast imaging and tomography require mathematical inversion of the observed data to obtain real-space information. While an accurate forward model describing the generally nonlinear image formation from a given object to the observations is often available, explicit inversion formulas are typically not known. Moreover, the measured data might be insufficient for stable image reconstruction, in which case it has to be complemented by suitable a priori information. In this work, regularized Newton methods are presented as a general framework for the solution of such ill-posed nonlinear imaging problems. For a proof of principle, the approach is applied to x-ray phase contrast imaging in the near-field propagation regime. Simultaneous recovery of the phase- and amplitude from a single near-field diffraction pattern without homogeneity constraints is demonstrated for the first time. The presented methods further permit all-at-once phase contrast tomography, i.e. simultaneous phase retrieval and tomographic inversion. We demonstrate the potential of this approach by three-dimensional imaging of a colloidal crystal at 95 nm isotropic resolution.Comment: (C)2016 Optical Society of America. One print or electronic copy may be made for personal use only. Systematic reproduction and distribution, duplication of any material in this paper for a fee or for commercial purposes, or modifications of the content of this paper are prohibite

Deep learning in computational microscopy

We propose to use deep convolutional neural networks (DCNNs) to perform 2D and 3D computational imaging. Specifically, we investigate three different applications. We first try to solve the 3D inverse scattering problem based on learning a huge number of training target and speckle pairs. We also demonstrate a new DCNN architecture to perform Fourier ptychographic Microscopy (FPM) reconstruction, which achieves high-resolution phase recovery with considerably less data than standard FPM. Finally, we employ DCNN models that can predict focused 2D fluorescent microscopic images from blurred images captured at overfocused or underfocused planes.Published versio

Estimation de l'enveloppe et de la fréquence locales par les opérateurs de Teager-Kaiser en interférométrie en lumière blanche.

In this work, a new method for surface extraction in white light scanning interferometry (WLSI) is introduced. The proposed extraction scheme is based on the Teager-Kaiser energy operator and its extended versions. This non-linear class of operators is helpful to extract the local instantaneous envelope and frequency of any narrow band AM-FM signal. Namely, the combination of the envelope and frequency information, allows effective surface extraction by an iterative re-estimation of the phase in association with a new correlation technique, based on a recent TK crossenergy operator. Through the experiments, it is shown that the proposed method produces substantially effective results in term of surface extraction compared to the peak fringe scanning technique, the five step phase shifting algorithm and the continuous wavelet transform based method. In addition, the results obtained show the robustness of the proposed method to noise and to the fluctuations of the carrier frequency

Automatic 3D bi-ventricular segmentation of cardiac images by a shape-refined multi-task deep learning approach

Deep learning approaches have achieved state-of-the-art performance in cardiac magnetic resonance (CMR) image segmentation. However, most approaches have focused on learning image intensity features for segmentation, whereas the incorporation of anatomical shape priors has received less attention. In this paper, we combine a multi-task deep learning approach with atlas propagation to develop a shape-constrained bi-ventricular segmentation pipeline for short-axis CMR volumetric images. The pipeline first employs a fully convolutional network (FCN) that learns segmentation and landmark localisation tasks simultaneously. The architecture of the proposed FCN uses a 2.5D representation, thus combining the computational advantage of 2D FCNs networks and the capability of addressing 3D spatial consistency without compromising segmentation accuracy. Moreover, the refinement step is designed to explicitly enforce a shape constraint and improve segmentation quality. This step is effective for overcoming image artefacts (e.g. due to different breath-hold positions and large slice thickness), which preclude the creation of anatomically meaningful 3D cardiac shapes. The proposed pipeline is fully automated, due to network's ability to infer landmarks, which are then used downstream in the pipeline to initialise atlas propagation. We validate the pipeline on 1831 healthy subjects and 649 subjects with pulmonary hypertension. Extensive numerical experiments on the two datasets demonstrate that our proposed method is robust and capable of producing accurate, high-resolution and anatomically smooth bi-ventricular 3D models, despite the artefacts in input CMR volumes

SPNet: Deep 3D Object Classification and Retrieval using Stereographic Projection

학위논문(석사)--서울대학교 대학원 :공과대학 전기·컴퓨터공학부,2019. 8. 이경무.본 논문에서는 3D 물체분류 문제를 효율적으로 해결하기위하여 입체화법의 투사를 활용한 모델을 제안한다. 먼저 입체화법의 투사를 사용하여 3D 입력 영상을 2D 평면 이미지로 변환한다. 또한, 객체의 카테고리를 추정하기 위하여 얕은 2D합성곱신셩망(CNN)을 제시하고, 다중시점으로부터 얻은 객체 카테고리의 추정값들을 결합하여 성능을 더욱 향상시키는 앙상블 방법을 제안한다. 이를위해 (1) 입체화법투사를 활용하여 3D 객체를 2D 평면 이미지로 변환하고 (2) 다중시점 영상들의 특징점을 학습 (3) 효과적이고 강인한 시점의 특징점을 선별한 후 (4) 다중시점 앙상블을 통한 성능을 향상시키는 4단계로 구성된 학습방법을 제안한다. 본 논문에서는 실험결과를 통해 제안하는 방법이 매우 적은 모델의 학습 변수와 GPU 메모리를 사용하는과 동시에 객체 분류 및 검색에서의 우수한 성능을 보이고있음을 증명하였다.We propose an efficient Stereographic Projection Neural Network (SPNet) for learning representations of 3D objects. We first transform a 3D input volume into a 2D planar image using stereographic projection. We then present a shallow 2D convolutional neural network (CNN) to estimate the object category followed by view ensemble, which combines the responses from multiple views of the object to further enhance the predictions. Specifically, the proposed approach consists of four stages: (1) Stereographic projection of a 3D object, (2) view-specific feature learning, (3) view selection and (4) view ensemble. The proposed approach performs comparably to the state-of-the-art methods while having substantially lower GPU memory as well as network parameters. Despite its lightness, the experiments on 3D object classification and shape retrievals demonstrate the high performance of the proposed method.1 INTRODUCTION 2 Related Work 2.1 Point cloud-based methods 2.2 3D model-based methods 2.3 2D/2.5D image-based methods 3 Proposed Stereographic Projection Network 3.1 Stereographic Representation 3.2 Network Architecture 3.3 View Selection 3.4 View Ensemble 4 Experimental Evaluation 4.1 Datasets 4.2 Training 4.3 Choice of Stereographic Projection 4.4 Test on View Selection Schemes 4.5 3D Object Classification 4.6 Shape Retrieval 4.7 Implementation 5 ConclusionsMaste