1,230 research outputs found
Automated Segmentation of Pulmonary Lobes using Coordination-Guided Deep Neural Networks
The identification of pulmonary lobes is of great importance in disease
diagnosis and treatment. A few lung diseases have regional disorders at lobar
level. Thus, an accurate segmentation of pulmonary lobes is necessary. In this
work, we propose an automated segmentation of pulmonary lobes using
coordination-guided deep neural networks from chest CT images. We first employ
an automated lung segmentation to extract the lung area from CT image, then
exploit volumetric convolutional neural network (V-net) for segmenting the
pulmonary lobes. To reduce the misclassification of different lobes, we
therefore adopt coordination-guided convolutional layers (CoordConvs) that
generate additional feature maps of the positional information of pulmonary
lobes. The proposed model is trained and evaluated on a few publicly available
datasets and has achieved the state-of-the-art accuracy with a mean Dice
coefficient index of 0.947 0.044.Comment: ISBI 2019 (Oral
PadChest: A large chest x-ray image dataset with multi-label annotated reports
We present a labeled large-scale, high resolution chest x-ray dataset for the
automated exploration of medical images along with their associated reports.
This dataset includes more than 160,000 images obtained from 67,000 patients
that were interpreted and reported by radiologists at Hospital San Juan
Hospital (Spain) from 2009 to 2017, covering six different position views and
additional information on image acquisition and patient demography. The reports
were labeled with 174 different radiographic findings, 19 differential
diagnoses and 104 anatomic locations organized as a hierarchical taxonomy and
mapped onto standard Unified Medical Language System (UMLS) terminology. Of
these reports, 27% were manually annotated by trained physicians and the
remaining set was labeled using a supervised method based on a recurrent neural
network with attention mechanisms. The labels generated were then validated in
an independent test set achieving a 0.93 Micro-F1 score. To the best of our
knowledge, this is one of the largest public chest x-ray database suitable for
training supervised models concerning radiographs, and the first to contain
radiographic reports in Spanish. The PadChest dataset can be downloaded from
http://bimcv.cipf.es/bimcv-projects/padchest/
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From Fully-Supervised, Single-Task to Scarcely-Supervised, Multi-Task Deep Learning for Medical Image Analysis
Image analysis based on machine learning has gained prominence with the advent of deep learning, particularly in medical imaging. To be effective in addressing challenging image analysis tasks, however, conventional deep neural networks require large corpora of annotated training data, which are unfortunately scarce in the medical domain, thus often rendering fully-supervised learning strategies ineffective.This thesis devises for use in a variety of medical image analysis applications a series of novel deep learning methods, ranging from fully-supervised, single-task learning to scarcely-supervised, multi-task learning that makes efficient use of annotated training data. Specifically, its main contributions include (1) fully-supervised, single-task learning for the segmentation of pulmonary lobes from chest CT scans and the analysis of scoliosis from spine X-ray images; (2) supervised, single-task, domain-generalized pulmonary segmentation in chest X-ray images and retinal vasculature segmentation in fundoscopic images; (3) largely-unsupervised, multiple-task learning via deep generative modeling for the joint synthesis and classification of medical image data; and (4) partly-supervised, multiple-task learning for the combined segmentation and classification of chest and spine X-ray images
Dimensionality Reduction in Deep Learning for Chest X-Ray Analysis of Lung Cancer
Efficiency of some dimensionality reduction techniques, like lung
segmentation, bone shadow exclusion, and t-distributed stochastic neighbor
embedding (t-SNE) for exclusion of outliers, is estimated for analysis of chest
X-ray (CXR) 2D images by deep learning approach to help radiologists identify
marks of lung cancer in CXR. Training and validation of the simple
convolutional neural network (CNN) was performed on the open JSRT dataset
(dataset #01), the JSRT after bone shadow exclusion - BSE-JSRT (dataset #02),
JSRT after lung segmentation (dataset #03), BSE-JSRT after lung segmentation
(dataset #04), and segmented BSE-JSRT after exclusion of outliers by t-SNE
method (dataset #05). The results demonstrate that the pre-processed dataset
obtained after lung segmentation, bone shadow exclusion, and filtering out the
outliers by t-SNE (dataset #05) demonstrates the highest training rate and best
accuracy in comparison to the other pre-processed datasets.Comment: 6 pages, 14 figure
Deep Learning of Unified Region, Edge, and Contour Models for Automated Image Segmentation
Image segmentation is a fundamental and challenging problem in computer
vision with applications spanning multiple areas, such as medical imaging,
remote sensing, and autonomous vehicles. Recently, convolutional neural
networks (CNNs) have gained traction in the design of automated segmentation
pipelines. Although CNN-based models are adept at learning abstract features
from raw image data, their performance is dependent on the availability and
size of suitable training datasets. Additionally, these models are often unable
to capture the details of object boundaries and generalize poorly to unseen
classes. In this thesis, we devise novel methodologies that address these
issues and establish robust representation learning frameworks for
fully-automatic semantic segmentation in medical imaging and mainstream
computer vision. In particular, our contributions include (1) state-of-the-art
2D and 3D image segmentation networks for computer vision and medical image
analysis, (2) an end-to-end trainable image segmentation framework that unifies
CNNs and active contour models with learnable parameters for fast and robust
object delineation, (3) a novel approach for disentangling edge and texture
processing in segmentation networks, and (4) a novel few-shot learning model in
both supervised settings and semi-supervised settings where synergies between
latent and image spaces are leveraged to learn to segment images given limited
training data.Comment: PhD dissertation, UCLA, 202
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