26 research outputs found
Modeling 3D cardiac contraction and relaxation with point cloud deformation networks
Global single-valued biomarkers of cardiac function typically used in
clinical practice, such as ejection fraction, provide limited insight on the
true 3D cardiac deformation process and hence, limit the understanding of both
healthy and pathological cardiac mechanics. In this work, we propose the Point
Cloud Deformation Network (PCD-Net) as a novel geometric deep learning approach
to model 3D cardiac contraction and relaxation between the extreme ends of the
cardiac cycle. It employs the recent advances in point cloud-based deep
learning into an encoder-decoder structure, in order to enable efficient
multi-scale feature learning directly on multi-class 3D point cloud
representations of the cardiac anatomy. We evaluate our approach on a large
dataset of over 10,000 cases from the UK Biobank study and find average Chamfer
distances between the predicted and ground truth anatomies below the pixel
resolution of the underlying image acquisition. Furthermore, we observe similar
clinical metrics between predicted and ground truth populations and show that
the PCD-Net can successfully capture subpopulation-specific differences between
normal subjects and myocardial infarction (MI) patients. We then demonstrate
that the learned 3D deformation patterns outperform multiple clinical
benchmarks by 13% and 7% in terms of area under the receiver operating
characteristic curve for the tasks of prevalent MI detection and incident MI
prediction and by 7% in terms of Harrell's concordance index for MI survival
analysis
Multi-objective point cloud autoencoders for explainable myocardial infarction prediction
Myocardial infarction (MI) is one of the most common causes of death in the
world. Image-based biomarkers commonly used in the clinic, such as ejection
fraction, fail to capture more complex patterns in the heart's 3D anatomy and
thus limit diagnostic accuracy. In this work, we present the multi-objective
point cloud autoencoder as a novel geometric deep learning approach for
explainable infarction prediction, based on multi-class 3D point cloud
representations of cardiac anatomy and function. Its architecture consists of
multiple task-specific branches connected by a low-dimensional latent space to
allow for effective multi-objective learning of both reconstruction and MI
prediction, while capturing pathology-specific 3D shape information in an
interpretable latent space. Furthermore, its hierarchical branch design with
point cloud-based deep learning operations enables efficient multi-scale
feature learning directly on high-resolution anatomy point clouds. In our
experiments on a large UK Biobank dataset, the multi-objective point cloud
autoencoder is able to accurately reconstruct multi-temporal 3D shapes with
Chamfer distances between predicted and input anatomies below the underlying
images' pixel resolution. Our method outperforms multiple machine learning and
deep learning benchmarks for the task of incident MI prediction by 19% in terms
of Area Under the Receiver Operating Characteristic curve. In addition, its
task-specific compact latent space exhibits easily separable control and MI
clusters with clinically plausible associations between subject encodings and
corresponding 3D shapes, thus demonstrating the explainability of the
prediction
Multi-class point cloud completion networks for 3D cardiac anatomy reconstruction from cine magnetic resonance images
Cine magnetic resonance imaging (MRI) is the current gold standard for the
assessment of cardiac anatomy and function. However, it typically only acquires
a set of two-dimensional (2D) slices of the underlying three-dimensional (3D)
anatomy of the heart, thus limiting the understanding and analysis of both
healthy and pathological cardiac morphology and physiology. In this paper, we
propose a novel fully automatic surface reconstruction pipeline capable of
reconstructing multi-class 3D cardiac anatomy meshes from raw cine MRI
acquisitions. Its key component is a multi-class point cloud completion network
(PCCN) capable of correcting both the sparsity and misalignment issues of the
3D reconstruction task in a unified model. We first evaluate the PCCN on a
large synthetic dataset of biventricular anatomies and observe Chamfer
distances between reconstructed and gold standard anatomies below or similar to
the underlying image resolution for multiple levels of slice misalignment.
Furthermore, we find a reduction in reconstruction error compared to a
benchmark 3D U-Net by 32% and 24% in terms of Hausdorff distance and mean
surface distance, respectively. We then apply the PCCN as part of our automated
reconstruction pipeline to 1000 subjects from the UK Biobank study in a
cross-domain transfer setting and demonstrate its ability to reconstruct
accurate and topologically plausible biventricular heart meshes with clinical
metrics comparable to the previous literature. Finally, we investigate the
robustness of our proposed approach and observe its capacity to successfully
handle multiple common outlier conditions
3D Shape-Based Myocardial Infarction Prediction Using Point Cloud Classification Networks
Myocardial infarction (MI) is one of the most prevalent cardiovascular
diseases with associated clinical decision-making typically based on
single-valued imaging biomarkers. However, such metrics only approximate the
complex 3D structure and physiology of the heart and hence hinder a better
understanding and prediction of MI outcomes. In this work, we investigate the
utility of complete 3D cardiac shapes in the form of point clouds for an
improved detection of MI events. To this end, we propose a fully automatic
multi-step pipeline consisting of a 3D cardiac surface reconstruction step
followed by a point cloud classification network. Our method utilizes recent
advances in geometric deep learning on point clouds to enable direct and
efficient multi-scale learning on high-resolution surface models of the cardiac
anatomy. We evaluate our approach on 1068 UK Biobank subjects for the tasks of
prevalent MI detection and incident MI prediction and find improvements of ~13%
and ~5% respectively over clinical benchmarks. Furthermore, we analyze the role
of each ventricle and cardiac phase for 3D shape-based MI detection and conduct
a visual analysis of the morphological and physiological patterns typically
associated with MI outcomes.Comment: Accepted at EMBC 202
The Liver Tumor Segmentation Benchmark (LiTS)
In this work, we report the set-up and results of the Liver Tumor
Segmentation Benchmark (LITS) organized in conjunction with the IEEE
International Symposium on Biomedical Imaging (ISBI) 2016 and International
Conference On Medical Image Computing Computer Assisted Intervention (MICCAI)
2017. Twenty four valid state-of-the-art liver and liver tumor segmentation
algorithms were applied to a set of 131 computed tomography (CT) volumes with
different types of tumor contrast levels (hyper-/hypo-intense), abnormalities
in tissues (metastasectomie) size and varying amount of lesions. The submitted
algorithms have been tested on 70 undisclosed volumes. The dataset is created
in collaboration with seven hospitals and research institutions and manually
reviewed by independent three radiologists. We found that not a single
algorithm performed best for liver and tumors. The best liver segmentation
algorithm achieved a Dice score of 0.96(MICCAI) whereas for tumor segmentation
the best algorithm evaluated at 0.67(ISBI) and 0.70(MICCAI). The LITS image
data and manual annotations continue to be publicly available through an online
evaluation system as an ongoing benchmarking resource.Comment: conferenc
One health, une seule santé
One Health, « Une seule santé », est une stratégie mondiale visant à développer les collaborations interdisciplinaires pour la santé humaine, animale et environnementale. Elle promeut une approche intégrée, systémique et unifiée de la santé aux échelles locale, nationale et mondiale, afin de mieux affronter les maladies émergentes à risque pandémique, mais aussi s'adapter aux impacts environnementaux présents et futurs. Bien que ce mouvement s’étende, la littérature en français reste rare. Traduit de l’anglais, coordonné par d’éminents épidémiologistes et s'appuyant sur un large panel d' approches scientifiques rarement réunies autour de la santé, cet ouvrage retrace les origines du concept et présente un contenu pratique sur les outils méthodologiques, la collecte de données, les techniques de surveillance et les plans d’étude. Il combine recherche et pratique en un seul volume et constitue un ouvrage de référence unique pour la santé mondiale
Acoustic orientation in the dark: About how the brain processes naturalistic echolocation sequences in the fruit-eating bat "Carollia perspicillata"
Echolocation allows bats to orientate in darkness without using visual information. Bats emit spatially directed high frequency calls and infer spatial information from echoes coming from call reflections in objects (Simmons 2012; Moss and Surlykke 2001, 2010). The echoes provide momentary snapshots, which have to be integrated to create an acoustic image of the surroundings. The spatial resolution of the computed image increases with the quantity of received echoes. Thus, a high call rate is required for a detailed representation of the surroundings.
One important parameter that the bats extract from the echoes is an object’s distance. The distance is inferred from the echo delay, which represents the duration between call emission and echo arrival (Kössl et al. 2014). The echo delay decreases with decreasing distance and delay-tuned neurons have been characterized in the ascending auditory pathway, which runs from the inferior colliculus (Wenstrup et al. 2012; MacĂas et al. 2016; Wenstrup and Portfors 2011; Dear and Suga 1995) to the auditory cortex (Hagemann et al. 2010; Suga and O'Neill 1979; O'Neill and Suga 1982).
Electrophysiological studies usually characterize neuronal processing by using artificial and simplified versions of the echolocation signals as stimuli (Hagemann et al. 2010; Hagemann et al. 2011; HechavarrĂa and Kössl 2014; HechavarrĂa et al. 2013). The high controllability of artificial stimuli simplifies the inference of the neuronal mechanisms underlying distance processing. But, it remains largely unexplored how the neurons process delay information from echolocation sequences. The main purpose of the thesis is to investigate how natural echolocation sequences are processed in the brain of the bat Carollia perspicillata. Bats actively control the sensory information that it gathers during echolocation. This allows experimenters to easily identify and record the acoustic stimuli that are behaviorally relevant for orientation. For recording echolocation sequences, a bat was placed in the mass of a swinging pendulum (Kobler et al. 1985; Beetz et al. 2016b). During the swing the bat emitted echolocation calls that were reflected in surrounding objects. An ultrasound sensitive microphone traveling with the bat and positioned above the bat’s head recorded the echolocation sequence. The echolocation sequence carried delay information of an approach flight and was used as stimulus for neuronal recordings from the auditory cortex and inferior colliculus of the bats.
Presentation of high stimulus rates to other species, such as rats, guinea pigs, suppresses cortical neuron activity (Wehr and Zador 2005; Creutzfeldt et al. 1980). Therefore, I tested if neurons of bats are suppressed when they are stimulated with high acoustic rates represented in echolocation sequences (sequence situation). Additionally, the bats were stimulated with randomized call echo elements of the sequence and an interstimulus time interval of 400 ms (element situation). To quantify neuronal suppression induced by the sequence, I compared the response pattern to the sequence situation with the concatenated response patterns to the element situation. Surprisingly, although the bats should be adapted for processing high acoustic rates, their cortical neurons are vastly suppressed in the sequence situation (Beetz et al. 2016b). However, instead of being completely suppressed during the sequence situation, the neurons partially recover from suppression at a unit specific call echo element. Multi-electrode recordings from the cortex allow assessment of the representation of echo delays along the cortical surface. At the cortical level, delay-tuned neurons are topographically organized. Cortical suppression improves sharpness of neuronal tuning and decreases the blurriness of the topographic map. With neuronal recordings from the inferior colliculus, I tested whether the echolocation sequence also induced neuronal suppression at subcortical level. The sequence induced suppression was weaker in the inferior colliculus than in the cortex. The collicular response makes the neurons able to track the acoustic events in the echolocation sequence. Collicular suppression mainly improves the signal-to-noise ratio. In conclusion, the results demonstrate that cortical suppression is not necessarily a shortcoming for temporal processing of rapidly occurring stimuli as it has previously been interpreted.
Natural environments are usually composed of multiple objects. Thus, each echolocation call reflects off multiple objects resulting in multiple echoes following the calls. At present, it is largely unexplored how neurons process echolocation sequences containing echo information from more than one object (multi-object sequences). Therefore, I stimulated bats with a multi-object sequence which contained echo information from three objects. The objects were different distances away from each other. I tested the influence of each object on the neuronal tuning by stimulating the bats with different sequences created from filtering object specific echoes from the multi-object sequence. The cortex most reliably processes echo information from the nearest object whereas echo information from distant objects is not processed due to neuronal suppression. Collicular neurons process less selectively echo information from certain objects and respond to each echo.
For proper echolocation, bats have to distinguish between own biosonar signals and the signals coming from conspecifics. This can be quite challenging when many bats echolocate adjacent to each other. In behavioral experiments, the echolocation performance of C. perspicillata was tested in the presence of potentially interfering sounds. In the presence of acoustic noise, the bats increase the sensory acquisition rate which may increase the update rate of sensory processing. Neuronal recordings from the auditory cortex and inferior colliculus could strengthen the hypothesis. Although there were signs of acoustic interference or jamming at neuronal level, the neurons were not completely suppressed and responded to the rest of the echolocation sequence
Multi-domain variational autoencoders for combined modeling of MRI-based biventricular anatomy and ECG-based cardiac electrophysiology
Human cardiac function is characterized by a complex interplay of mechanical deformation and electrophysiological conduction. Similar to the underlying cardiac anatomy, these interconnected physiological patterns vary considerably across the human population with important implications for the effectiveness of clinical decision-making and the accuracy of computerized heart models. While many previous works have investigated this variability separately for either cardiac anatomy or physiology, this work aims to combine both aspects in a single data-driven approach and capture their intricate interdependencies in a multi-domain setting. To this end, we propose a novel multi-domain Variational Autoencoder (VAE) network to capture combined Electrocardiogram (ECG) and Magnetic Resonance Imaging (MRI)-based 3D anatomy information in a single model. Each VAE branch is specifically designed to address the particular challenges of the respective input domain, enabling efficient encoding, reconstruction, and synthesis of multi-domain cardiac signals. Our method achieves high reconstruction accuracy on a United Kingdom Biobank dataset, with Chamfer Distances between reconstructed and input anatomies below the underlying image resolution and ECG reconstructions outperforming multiple single-domain benchmarks by a considerable margin. The proposed VAE is capable of generating realistic virtual populations of arbitrary size with good alignment in clinical metrics between the synthesized and gold standard anatomies and Maximum Mean Discrepancy (MMD) scores of generated ECGs below those of comparable single-domain approaches. Furthermore, we observe the latent space of our VAE to be highly interpretable with separate components encoding different aspects of anatomical and ECG variability. Finally, we demonstrate that the combined anatomy and ECG representation improves the performance in a cardiac disease classification task by 3.9% in terms of Area Under the Receiver Operating Characteristic (AUROC) curve over the best corresponding single-domain modeling approach
Neural processing of naturalistic echolocation signals in bats
Echolocation behavior, a navigation strategy based on acoustic signals, allows scientists to explore neural processing of behaviorally relevant stimuli. For the purpose of orientation, bats broadcast echolocation calls and extract spatial information from the echoes. Because bats control call emission and thus the availability of spatial information, the behavioral relevance of these signals is undiscussable. While most neurophysiological studies, conducted in the past, used synthesized acoustic stimuli that mimic portions of the echolocation signals, recent progress has been made to understand how naturalistic echolocation signals are encoded in the bat brain. Here, we review how does stimulus history affect neural processing, how spatial information from multiple objects and how echolocation signals embedded in a naturalistic, noisy environment are processed in the bat brain. We end our review by discussing the huge potential that state-of-the-art recording techniques provide to gain a more complete picture on the neuroethology of echolocation behavior
Combined generation of electrocardiogram and cardiac anatomy models using multi-modal variational autoencoders
Understanding population-wide variability of the human heart is crucial to detect abnormalities and improve the assessment of both cardiac anatomy and function. While many computational modeling approaches have been developed to capture this variability separately for either cardiac anatomy or physiology, their complex interconnections have rarely been explored together. In this work, we propose a novel multi-modal variational autoencoder (VAE) capable of processing combined physiology and bitemporal anatomy information in the form of electrocardiograms (ECG) and 3D biventricular point clouds. Our method achieves high reconstruction accuracy on a UK Biobank dataset with Chamfer distances between predicted and input anatomies below the underlying image resolution and the ECG reconstructions outperforming a state-of-the-art benchmark approach specialized in ECG generation. We also evaluate its generative ability and find comparable populations of generated and gold standard anatomies, ECGs, and combined anatomy-ECG data in terms of common clinical metrics and maximum mean discrepancies