151 research outputs found
FetusMapV2: Enhanced Fetal Pose Estimation in 3D Ultrasound
Fetal pose estimation in 3D ultrasound (US) involves identifying a set of
associated fetal anatomical landmarks. Its primary objective is to provide
comprehensive information about the fetus through landmark connections, thus
benefiting various critical applications, such as biometric measurements, plane
localization, and fetal movement monitoring. However, accurately estimating the
3D fetal pose in US volume has several challenges, including poor image
quality, limited GPU memory for tackling high dimensional data, symmetrical or
ambiguous anatomical structures, and considerable variations in fetal poses. In
this study, we propose a novel 3D fetal pose estimation framework (called
FetusMapV2) to overcome the above challenges. Our contribution is three-fold.
First, we propose a heuristic scheme that explores the complementary network
structure-unconstrained and activation-unreserved GPU memory management
approaches, which can enlarge the input image resolution for better results
under limited GPU memory. Second, we design a novel Pair Loss to mitigate
confusion caused by symmetrical and similar anatomical structures. It separates
the hidden classification task from the landmark localization task and thus
progressively eases model learning. Last, we propose a shape priors-based
self-supervised learning by selecting the relatively stable landmarks to refine
the pose online. Extensive experiments and diverse applications on a
large-scale fetal US dataset including 1000 volumes with 22 landmarks per
volume demonstrate that our method outperforms other strong competitors.Comment: 16 pages, 11 figures, accepted by Medical Image Analysis(2023
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
Automatic linear measurements of the fetal brain on MRI with deep neural networks
Timely, accurate and reliable assessment of fetal brain development is
essential to reduce short and long-term risks to fetus and mother. Fetal MRI is
increasingly used for fetal brain assessment. Three key biometric linear
measurements important for fetal brain evaluation are Cerebral Biparietal
Diameter (CBD), Bone Biparietal Diameter (BBD), and Trans-Cerebellum Diameter
(TCD), obtained manually by expert radiologists on reference slices, which is
time consuming and prone to human error. The aim of this study was to develop a
fully automatic method computing the CBD, BBD and TCD measurements from fetal
brain MRI. The input is fetal brain MRI volumes which may include the fetal
body and the mother's abdomen. The outputs are the measurement values and
reference slices on which the measurements were computed. The method, which
follows the manual measurements principle, consists of five stages: 1)
computation of a Region Of Interest that includes the fetal brain with an
anisotropic 3D U-Net classifier; 2) reference slice selection with a
Convolutional Neural Network; 3) slice-wise fetal brain structures segmentation
with a multiclass U-Net classifier; 4) computation of the fetal brain
midsagittal line and fetal brain orientation, and; 5) computation of the
measurements. Experimental results on 214 volumes for CBD, BBD and TCD
measurements yielded a mean difference of 1.55mm, 1.45mm and 1.23mm
respectively, and a Bland-Altman 95% confidence interval () of 3.92mm,
3.98mm and 2.25mm respectively. These results are similar to the manual
inter-observer variability. The proposed automatic method for computing
biometric linear measurements of the fetal brain from MR imaging achieves human
level performance. It has the potential of being a useful method for the
assessment of fetal brain biometry in normal and pathological cases, and of
improving routine clinical practice.Comment: 15 pages, 8 figures, presented in CARS 2020, submitted to IJCAR
Deep learning in medical imaging and radiation therapy
Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146980/1/mp13264_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146980/2/mp13264.pd
Computational Anatomy for Multi-Organ Analysis in Medical Imaging: A Review
The medical image analysis field has traditionally been focused on the
development of organ-, and disease-specific methods. Recently, the interest in
the development of more 20 comprehensive computational anatomical models has
grown, leading to the creation of multi-organ models. Multi-organ approaches,
unlike traditional organ-specific strategies, incorporate inter-organ relations
into the model, thus leading to a more accurate representation of the complex
human anatomy. Inter-organ relations are not only spatial, but also functional
and physiological. Over the years, the strategies 25 proposed to efficiently
model multi-organ structures have evolved from the simple global modeling, to
more sophisticated approaches such as sequential, hierarchical, or machine
learning-based models. In this paper, we present a review of the state of the
art on multi-organ analysis and associated computation anatomy methodology. The
manuscript follows a methodology-based classification of the different
techniques 30 available for the analysis of multi-organs and multi-anatomical
structures, from techniques using point distribution models to the most recent
deep learning-based approaches. With more than 300 papers included in this
review, we reflect on the trends and challenges of the field of computational
anatomy, the particularities of each anatomical region, and the potential of
multi-organ analysis to increase the impact of 35 medical imaging applications
on the future of healthcare.Comment: Paper under revie
Symbiotic deep learning for medical image analysis with applications in real-time diagnosis for fetal ultrasound screening
The last hundred years have seen a monumental rise in the power and capability of machines to
perform intelligent tasks in the stead of previously human operators. This rise is not expected
to slow down any time soon and what this means for society and humanity as a whole remains
to be seen. The overwhelming notion is that with the right goals in mind, the growing influence
of machines on our every day tasks will enable humanity to give more attention to the truly
groundbreaking challenges that we all face together. This will usher in a new age of human
machine collaboration in which humans and machines may work side by side to achieve greater
heights for all of humanity. Intelligent systems are useful in isolation, but the true benefits of
intelligent systems come to the fore in complex systems where the interaction between humans
and machines can be made seamless, and it is this goal of symbiosis between human and machine
that may democratise complex knowledge, which motivates this thesis. In the recent past, datadriven
methods have come to the fore and now represent the state-of-the-art in many different
fields. Alongside the shift from rule-based towards data-driven methods we have also seen a
shift in how humans interact with these technologies. Human computer interaction is changing
in response to data-driven methods and new techniques must be developed to enable the same
symbiosis between man and machine for data-driven methods as for previous formula-driven
technology.
We address five key challenges which need to be overcome for data-driven human-in-the-loop
computing to reach maturity. These are (1) the ’Categorisation Challenge’ where we examine
existing work and form a taxonomy of the different methods being utilised for data-driven
human-in-the-loop computing; (2) the ’Confidence Challenge’, where data-driven methods must
communicate interpretable beliefs in how confident their predictions are; (3) the ’Complexity
Challenge’ where the aim of reasoned communication becomes increasingly important as the
complexity of tasks and methods to solve also increases; (4) the ’Classification Challenge’ in
which we look at how complex methods can be separated in order to provide greater reasoning
in complex classification tasks; and finally (5) the ’Curation Challenge’ where we challenge the
assumptions around bottleneck creation for the development of supervised learning methods.Open Acces
U-Net and its variants for medical image segmentation: theory and applications
U-net is an image segmentation technique developed primarily for medical
image analysis that can precisely segment images using a scarce amount of
training data. These traits provide U-net with a very high utility within the
medical imaging community and have resulted in extensive adoption of U-net as
the primary tool for segmentation tasks in medical imaging. The success of
U-net is evident in its widespread use in all major image modalities from CT
scans and MRI to X-rays and microscopy. Furthermore, while U-net is largely a
segmentation tool, there have been instances of the use of U-net in other
applications. As the potential of U-net is still increasing, in this review we
look at the various developments that have been made in the U-net architecture
and provide observations on recent trends. We examine the various innovations
that have been made in deep learning and discuss how these tools facilitate
U-net. Furthermore, we look at image modalities and application areas where
U-net has been applied.Comment: 42 pages, in IEEE Acces
Automated analysis and visualization of preclinical whole-body microCT data
In this thesis, several strategies are presented that aim to facilitate the analysis and visualization of whole-body in vivo data of small animals. Based on the particular challenges for image processing, when dealing with whole-body follow-up data, we addressed several aspects in this thesis. The developed methods are tailored to handle data of subjects with significantly varying posture and address the large tissue heterogeneity of entire animals. In addition, we aim to compensate for lacking tissue contrast by relying on approximation of organs based on an animal atlas. Beyond that, we provide a solution to automate the combination of multimodality, multidimensional data.* Advanced School for Computing and Imaging (ASCI), Delft, NL * Bontius Stichting inz Doelfonds Beeldverwerking, Leiden, NL * Caliper Life Sciences, Hopkinton, USA * Foundation Imago, Oegstgeest, NLUBL - phd migration 201
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State of the Art of Level Set Methods in Segmentation and Registration of Medical Imaging Modalities
Segmentation of medical images is an important step in various applications such as visualization, quantitative analysis and image-guided surgery. Numerous segmentation methods have been developed in the past two decades for extraction of organ contours on medical images. Low-level segmentation methods, such as pixel-based clustering, region growing, and filter-based edge detection, require additional pre-processing and post-processing as well as considerable amounts of expert intervention or information of the objects of interest. Furthermore the subsequent analysis of segmented objects is hampered by the primitive, pixel or voxel level representations from those region-based segmentation. Deformable models, on the other hand, provide an explicit representation of the boundary and the shape of the object. They combine several desirable features such as inherent connectivity and smoothness, which counteract noise and boundary irregularities, as well as the ability to incorporate knowledge about the object of interest. However, parametric deformable models have two main limitations. First, in situations where the initial model and desired object boundary differ greatly in size and shape, the model must be re-parameterized dynamically to faithfully recover the object boundary. The second limitation is that it has difficulty dealing with topological adaptation such as splitting or merging model parts, a useful property for recovering either multiple objects or objects with unknown topology. This difficulty is caused by the fact that a new parameterization must be constructed whenever topology change occurs, which requires sophisticated schemes. Level set deformable models, also referred to as geometric deformable models, provide an elegant solution to address the primary limitations of parametric deformable models. These methods have drawn a great deal of attention since their introduction in 1988. Advantages of the contour implicit formulation of the deformable model over parametric formulation include: (1) no parameterization of the contour, (2) topological flexibility, (3) good numerical stability, (4) straightforward extension of the 2D formulation to n-D. Recent reviews on the subject include papers from Suri. In this chapter we give a general overview of the level set segmentation methods with emphasize on new frameworks recently introduced in the context of medical imaging problems. We then introduce novel approaches that aim at combining segmentation and registration in a level set formulation. Finally we review a selective set of clinical works with detailed validation of the level set methods for several clinical applications
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