Current deep learning based detection models tackle detection and segmentation tasks by casting them to pixel or patch-wise classification. To automate the initial mass lesion detection and segmentation on the whole mammographic images and avoid the computational redundancy of patch-based and sliding window approaches, the conditional generative adversarial network (cGAN) was used in this study. Subsequently, feeding the detected regions to the trained densely connected network (DenseNet), the binary classification of benign versus malignant was predicted. We used a combination of publicly available mammographic data repositories to train the pipeline, while evaluating the model's robustness toward our clinically collected repository, which was unseen to the pipeline.
Université de Bretagne Occidentale（西布列塔尼大学）；Inserm（法国国家健康与医学研究院）；IMT Atlantique（大西洋国立高等矿业电信学院）；University Hospital of Brest（布雷斯特大学医院）
Mammography is the primary imaging modality used for early detection and diagnosis of breast cancer. X-ray mammogram analysis mainly refers to the localization of suspicious regions of interest followed by segmentation, towards further lesion classification into benign versus malignant. Among diverse types of breast abnormalities, masses are the most important clinical findings of breast carcinomas. However, manually segmenting breast masses from native mammograms is time-consuming and error-prone. Therefore, an integrated computer-aided diagnosis system is required to assist clinicians for au…
Invasive ductal carcinoma is a prevalent, potentially deadly disease associated with a high rate of morbidity and mortality. Its malignancy is the second leading cause of death from cancer in women. The mammogram is an extremely useful resource for mass detection and invasive ductal carcinoma diagnosis. We are proposing a method for Invasive ductal carcinoma that will use convolutional neural networks (CNN) on mammograms to assist radiologists in diagnosing the disease. Due to the varying image clarity and structure of certain mammograms, it is difficult to observe major cancer characteristics…
SSN College of Engineering（SSN工程学院）；RMK College of Engineering and Technology（RMK工程技术学院）
In the existing research of mammogram image classification, either clinical data or image features of a specific type is considered along with the supervised classifiers such as Neural Network (NN) and Support Vector Machine (SVM). This paper considers automated classification of breast tissue type as benign or malignant using Weighted Feature Support Vector Machine (WFSVM) through constructing the precomputed kernel function by assigning more weight to relevant features using the principle of maximizing deviations. Initially, MIAS dataset of mammogram images is divided into training and test …
VRVis Zentrum für Virtual Reality und Visualisierung Forschungs-GmbH（VRVis虚拟现实与可视化研究中心有限公司）
Machine learning and deep learning methods have become essential for computer-assisted prediction in medicine, with a growing number of applications also in the field of mammography. Typically these algorithms are trained for a specific task, e.g., the classification of lesions or the prediction of a mammogram's pathology status. To obtain a comprehensive view of a patient, models which were all trained for the same task(s) are subsequently ensembled or combined. In this work, we propose a pipeline approach, where we first train a set of individual, task-specific models and subsequently invest…
Breast density estimation is one of the key tasks in recognizing individuals predisposed to breast cancer. It is often challenging because of low contrast and fluctuations in mammograms' fatty tissue background. Most of the time, the breast density is estimated manually where a radiologist assigns one of the four density categories decided by the Breast Imaging and Reporting Data Systems (BI-RADS). There have been efforts in the direction of automating a breast density classification pipeline. Breast density estimation is one of the key tasks performed during a screening exam. Dense breasts ar…
The development of automated tools for brain morphometric analysis in infants has lagged significantly behind analogous tools for adults. This gap reflects the greater challenges in this domain due to: 1) a smaller-scaled region of interest, 2) increased motion corruption, 3) regional changes in geometry due to heterochronous growth, and 4) regional variations in contrast properties corresponding to ongoing myelination and other maturation processes. Nevertheless, there is a great need for automated image-processing tools to quantify differences between infant groups and other individuals, bec…
In the WHO glioma classification guidelines grade, IDH mutation and 1p19q co-deletion play a central role as they are important markers for prognosis and optimal therapy planning. Therefore, we propose a fully automatic, MRI based, 3D pipeline for glioma segmentation and classification. The designed segmentation network was a 3D U-Net achieving an average whole tumor dice score of 90%. After segmentation, the 3D tumor ROI is extracted and fed into the multi-task classification network. The network was trained and evaluated on a large heterogeneous dataset of 628 patients, collected from The Ca…
We present a fully modular and scalable software pipeline for processing electron microscope (EM) images of brain slices into 3D visualization of individual neurons and demonstrate an end-to-end segmentation of a large EM volume using a supercomputer. Our pipeline scales multiple packages used by the EM community with minimal changes to the original source codes. We tested each step of the pipeline individually, on a workstation, a cluster, and a supercomputer. Furthermore, we can compose workflows from these operations using a Balsam database that can be triggered during the data acquisition …
Artifacts are a common occurrence in Diffusion MRI (dMRI) scans. Identifying and removing them is essential to ensure the accuracy and viability of any post processing carried out on these scans. This makes QC (quality control) a crucial first step prior to any analysis of dMRI data. Several QC methods for artifact detection exist, however they suffer from problems like requiring manual intervention and the inability to generalize across different artifacts and datasets. In this paper, we propose an automated deep learning (DL) pipeline that utilizes a 3D-Densenet architecture to train a model…
A Comprehensive Dataset and Automated Pipeline for Nailfold Capillary Analysis
Tsinghua University（清华大学）；University College London（伦敦大学学院）；Shanghai General Hospital（上海交通大学医学院附属第一人民医院）；Beijing University of Posts and Telecommunications（北京邮电大学）
Postoperative glioblastoma segmentation: Development of a fully automated pipeline using deep convolutional neural networks and comparison with currently available models
Río Hortega University Hospital（里奥·奥尔特加大学医院）；Universidad de Valladolid（巴利亚多利德大学）；Center for Biomedical Research in Network of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN)（生物工程、生物材料和纳米医学网络生物医学研究中心）；Albacete University Hospital（阿尔瓦塞特大学医院）；La Princesa University Hospital（拉普林塞萨大学医院）；UiT The Arctic University of Norway（挪威北极大学）；University Hospital of North Norway（北挪威大学医院）；St. Olavs University Hospital（圣奥拉夫大学医院）；Norwegian University of Science and Technology（挪威科技大学）；St. Olavs Hospital, Trondheim University Hospital（圣奥拉夫医院，特隆赫姆大学医院）；de Octubre University Hospital (i + 12)（10月12日大学医院）；Complutense University（马德里康普顿斯大学）；Instituto de Investigación Sanitaria, 12 de Octubre University Hospital (i + 12)（10月12日大学医院卫生研究所）；Institute for Research in Mathematics (IMUVA), University of Valladolid（巴利亚多利德大学数学研究所）
RIKEN Center for Brain Science（理化学研究所脑科学中心）；Keio University School of Medicine（庆应义塾大学医学院）；Okinawa Institute of Science and Technology（冲绳科学技术大学院大学）；Kyoto University（京都大学）；Janelia Farm Research Campus（珍妮莉亚农场研究园区）
Understanding the connectivity in the brain is an important prerequisite for understanding how the brain processes information. In the Brain/MINDS project, a connectivity study on marmoset brains uses two-photon microscopy fluorescence images of axonal projections to collect the neuron connectivity from defined brain regions at the mesoscopic scale. The processing of the images requires the detection and segmentation of the axonal tracer signal. The objective is to detect as much tracer signal as possible while not misclassifying other background structures as the signal. This can be challengi…
Surgical resections are the most prevalent curative treatment for primary liver cancer. Tumors located in critical positions are known to complexify liver resections (LR). While experienced surgeons in specialized medical centers may have the necessary expertise to accurately anticipate LR complexity, and prepare accordingly, an objective method able to reproduce this behavior would have the potential to improve the standard routine of care, and avoid intra- and postoperative complications. In this article, we propose CoRe, an automated medical image processing pipeline for the prediction of p…
Action recognition is an important task for video understanding with broad applications. However, developing an effective action recognition solution often requires extensive engineering efforts in building and testing different combinations of the modules and their hyperparameters. In this demo, we present AutoVideo, a Python system for automated video action recognition. AutoVideo is featured for 1) highly modular and extendable infrastructure following the standard pipeline language, 2) an exhaustive list of primitives for pipeline construction, 3) data-driven tuners to save the efforts of …
The University of Winnipeg（温尼伯大学）；Qatar University（卡塔尔大学）；Hamad Medical Corporation（哈马德医疗公司）
Cardiac imaging known as echocardiography is a non-invasive tool utilized to produce data including images and videos, which cardiologists use to diagnose cardiac abnormalities in general and myocardial infarction (MI) in particular. Echocardiography machines can deliver abundant amounts of data that need to be quickly analyzed by cardiologists to help them make a diagnosis and treat cardiac conditions. However, the acquired data quality varies depending on the acquisition conditions and the patient's responsiveness to the setup instructions. These constraints are challenging to doctors especi…
