arXiv subjects

Nassir Navab

Publications and source records attributed to Nassir Navab.

At least 325 records · Page 18Linked to original sources

arXiv2022

Y-Net: A Spatiospectral Dual-Encoder Networkfor Medical Image Segmentation

Automated segmentation of retinal optical coherence tomography (OCT) images has become an important recent direction in machine learning for medical applications. We hypothesize that the anatomic structure of layers and their high-frequency variation in OCT images make retinal OCT a fitting choice for extracting spectral-domain features and combining them with spatial domain features. In this work, we present $Υ$-Net, an architecture that combines the frequency domain features with the image domain to improve the segmentation performance of OCT images. The results of this work demonstrate that the introduction of two branches, one for spectral and one for spatial domain features, brings a very significant improvement in fluid segmentation performance and allows outperformance as compared to the well-known U-Net model. Our improvement was 13% on the fluid segmentation dice score and 1.9% on the average dice score. Finally, removing selected frequency ranges in the spectral domain demonstrates the impact of these features on the fluid segmentation outperformance.

eess.IV↗

arXiv2022

Adaptive Personlization in Federated Learning for Highly Non-i.i.d. Data

Federated learning (FL) is a distributed learning method that offers medical institutes the prospect of collaboration in a global model while preserving the privacy of their patients. Although most medical centers conduct similar medical imaging tasks, their differences, such as specializations, number of patients, and devices, lead to distinctive data distributions. Data heterogeneity poses a challenge for FL and the personalization of the local models. In this work, we investigate an adaptive hierarchical clustering method for FL to produce intermediate semi-global models, so clients with similar data distribution have the chance of forming a more specialized model. Our method forms several clusters consisting of clients with the most similar data distributions; then, each cluster continues to train separately. Inside the cluster, we use meta-learning to improve the personalization of the participants' models. We compare the clustering approach with classical FedAvg and centralized training by evaluating our proposed methods on the HAM10k dataset for skin lesion classification with extreme heterogeneous data distribution. Our experiments demonstrate significant performance gain in heterogeneous distribution compared to standard FL methods in classification accuracy. Moreover, we show that the models converge faster if applied in clusters and outperform centralized training while using only a small subset of data.

cs.LG↗

arXiv2022

Unsupervised Cross-Domain Feature Extraction for Single Blood Cell Image Classification

Diagnosing hematological malignancies requires identification and classification of white blood cells in peripheral blood smears. Domain shifts caused by different lab procedures, staining, illumination, and microscope settings hamper the re-usability of recently developed machine learning methods on data collected from different sites. Here, we propose a cross-domain adapted autoencoder to extract features in an unsupervised manner on three different datasets of single white blood cells scanned from peripheral blood smears. The autoencoder is based on an R-CNN architecture allowing it to focus on the relevant white blood cell and eliminate artifacts in the image. To evaluate the quality of the extracted features we use a simple random forest to classify single cells. We show that thanks to the rich features extracted by the autoencoder trained on only one of the datasets, the random forest classifier performs satisfactorily on the unseen datasets, and outperforms published oracle networks in the cross-domain task. Our results suggest the possibility of employing this unsupervised approach in more complicated diagnosis and prognosis tasks without the need to add expensive expert labels to unseen data.

cs.CV↗

arXiv2022

Sonification as a Reliable Alternative to Conventional Visual Surgical Navigation

Despite the undeniable advantages of image-guided surgical assistance systems in terms of accuracy, such systems have not yet fully met surgeons' needs or expectations regarding usability, time efficiency, and their integration into the surgical workflow. On the other hand, perceptual studies have shown that presenting independent but causally correlated information via multimodal feedback involving different sensory modalities can improve task performance. This article investigates an alternative method for computer-assisted surgical navigation, introduces a novel sonification methodology for navigated pedicle screw placement, and discusses advanced solutions based on multisensory feedback. The proposed method comprises a novel sonification solution for alignment tasks in four degrees of freedom based on frequency modulation (FM) synthesis. We compared the resulting accuracy and execution time of the proposed sonification method with visual navigation, which is currently considered the state of the art. We conducted a phantom study in which 17 surgeons executed the pedicle screw placement task in the lumbar spine, guided by either the proposed sonification-based or the traditional visual navigation method. The results demonstrated that the proposed method is as accurate as the state of the art while decreasing the surgeon's need to focus on visual navigation displays instead of the natural focus on surgical tools and targeted anatomy during task execution.

cs.SD↗

arXiv2022

DeStripe: A Self2Self Spatio-Spectral Graph Neural Network with Unfolded Hessian for Stripe Artifact Removal in Light-sheet Microscopy

Light-sheet fluorescence microscopy (LSFM) is a cutting-edge volumetric imaging technique that allows for three-dimensional imaging of mesoscopic samples with decoupled illumination and detection paths. Although the selective excitation scheme of such a microscope provides intrinsic optical sectioning that minimizes out-of-focus fluorescence background and sample photodamage, it is prone to light absorption and scattering effects, which results in uneven illumination and striping artifacts in the images adversely. To tackle this issue, in this paper, we propose a blind stripe artifact removal algorithm in LSFM, called DeStripe, which combines a self-supervised spatio-spectral graph neural network with unfolded Hessian prior. Specifically, inspired by the desirable properties of Fourier transform in condensing striping information into isolated values in the frequency domain, DeStripe firstly localizes the potentially corrupted Fourier coefficients by exploiting the structural difference between unidirectional stripe artifacts and more isotropic foreground images. Affected Fourier coefficients can then be fed into a graph neural network for recovery, with a Hessian regularization unrolled to further ensure structures in the standard image space are well preserved. Since in realistic, stripe-free LSFM barely exists with a standard image acquisition protocol, DeStripe is equipped with a Self2Self denoising loss term, enabling artifact elimination without access to stripe-free ground truth images. Competitive experimental results demonstrate the efficacy of DeStripe in recovering corrupted biomarkers in LSFM with both synthetic and real stripe artifacts.

eess.IV↗

arXiv2022

Conditional Generative Data Augmentation for Clinical Audio Datasets

In this work, we propose a novel data augmentation method for clinical audio datasets based on a conditional Wasserstein Generative Adversarial Network with Gradient Penalty (cWGAN-GP), operating on log-mel spectrograms. To validate our method, we created a clinical audio dataset which was recorded in a real-world operating room during Total Hip Arthroplasty (THA) procedures and contains typical sounds which resemble the different phases of the intervention. We demonstrate the capability of the proposed method to generate realistic class-conditioned samples from the dataset distribution and show that training with the generated augmented samples outperforms classical audio augmentation methods in terms of classification performance. The performance was evaluated using a ResNet-18 classifier which shows a mean Macro F1-score improvement of 1.70% in a 5-fold cross validation experiment using the proposed augmentation method. Because clinical data is often expensive to acquire, the development of realistic and high-quality data augmentation methods is crucial to improve the robustness and generalization capabilities of learning-based algorithms which is especially important for safety-critical medical applications. Therefore, the proposed data augmentation method is an important step towards improving the data bottleneck for clinical audio-based machine learning systems.

cs.SD↗

arXiv2022

Bioelectric Registration of Electromagnetic Tracking and Preoperative Volume Data

For minimally invasive endovascular surgery, the localization of catheters and guidewires inside the human body is essential. Electromagnetic (EM) tracking is one technology that allows localizing such surgical instruments. For localizing intra-operatively EM-tracked instruments with respect to preoperative volume data, it is necessary to bring pre- and intraoperative imaging into the same coordinate frame. In most existing solutions, such registration requires additional interactions, modifying the procedure's original workflow. We propose a new method taking advantage of Bioelectric signals to initialize and register preoperative volumes to the EM tracking system without significantly changing the interventional workflow. We envision the most natural use-case of our concept in cardiac electrophysiology (EP) procedures, in which EP catheters are already equipped with all the necessary sensing, including electric sensing for the measurement of electrophysiological signals and EM tracking for catheter localization. We use EP catheters for Bioelectric sensing to detect local features of the vasculature while advancing the catheter inside the human body. Such features can be automatically labeled before the procedure within the preoperative data. The combination of Bioelectric and EM tracking can localize vascular features such as bifurcations and stenosis within the EM tracking space. Mapping them to preoperative data automatically registers patients' CT space to EM tracking. The proposed registration process is entirely based on Bioelectric sensed features, with no need for external markers or other interventional imaging devices.

physics.med-ph↗

arXiv2022

Wild ToFu: Improving Range and Quality of Indirect Time-of-Flight Depth with RGB Fusion in Challenging Environments

Indirect Time-of-Flight (I-ToF) imaging is a widespread way of depth estimation for mobile devices due to its small size and affordable price. Previous works have mainly focused on quality improvement for I-ToF imaging especially curing the effect of Multi Path Interference (MPI). These investigations are typically done in specifically constrained scenarios at close distance, indoors and under little ambient light. Surprisingly little work has investigated I-ToF quality improvement in real-life scenarios where strong ambient light and far distances pose difficulties due to an extreme amount of induced shot noise and signal sparsity, caused by the attenuation with limited sensor power and light scattering. In this work, we propose a new learning based end-to-end depth prediction network which takes noisy raw I-ToF signals as well as an RGB image and fuses their latent representation based on a multi step approach involving both implicit and explicit alignment to predict a high quality long range depth map aligned to the RGB viewpoint. We test our approach on challenging real-world scenes and show more than 40% RMSE improvement on the final depth map compared to the baseline approach.

cs.CV↗

arXiv2022

U-PET: MRI-based Dementia Detection with Joint Generation of Synthetic FDG-PET Images

Alzheimer's disease (AD) is the most common cause of dementia. An early detection is crucial for slowing down the disease and mitigating risks related to the progression. While the combination of MRI and FDG-PET is the best image-based tool for diagnosis, FDG-PET is not always available. The reliable detection of Alzheimer's disease with only MRI could be beneficial, especially in regions where FDG-PET might not be affordable for all patients. To this end, we propose a multi-task method based on U-Net that takes T1-weighted MR images as an input to generate synthetic FDG-PET images and classifies the dementia progression of the patient into cognitive normal (CN), cognitive impairment (MCI), and AD. The attention gates used in both task heads can visualize the most relevant parts of the brain, guiding the examiner and adding interpretability. Results show the successful generation of synthetic FDG-PET images and a performance increase in disease classification over the naive single-task baseline.

eess.IV↗

arXiv2022

Virtual embeddings and self-consistency for self-supervised learning

Self-supervised Learning (SSL) has recently gained much attention due to the high cost and data limitation in the training of supervised learning models. The current paradigm in the SSL is to utilize data augmentation at the input space to create different views of the same images and train a model to maximize the representations between similar images and minimize them for different ones. While this approach achieves state-of-the-art (SOTA) results in various downstream tasks, it still lakes the opportunity to investigate the latent space augmentation. This paper proposes TriMix, a novel concept for SSL that generates virtual embeddings through linear interpolation of the data, thus providing the model with novel representations. Our strategy focuses on training the model to extract the original embeddings from virtual ones, hence, better representation learning. Additionally, we propose a self-consistency term that improves the consistency between the virtual and actual embeddings. We validate TriMix on eight benchmark datasets consisting of natural and medical images with an improvement of 2.71% and 0.41% better than the second-best models for both data types. Further, our approach outperformed the current methods in semi-supervised learning, particularly in low data regimes. Besides, our pre-trained models showed better transfer to other datasets.

cs.CV↗

arXiv2022

PRO-TIP: Phantom for RObust automatic ultrasound calibration by TIP detection

We propose a novel method to automatically calibrate tracked ultrasound probes. To this end we design a custom phantom consisting of nine cones with different heights. The tips are used as key points to be matched between multiple sweeps. We extract them using a convolutional neural network to segment the cones in every ultrasound frame and then track them across the sweep. The calibration is robustly estimated using RANSAC and later refined employing image based techniques. Our phantom can be 3D-printed and offers many advantages over state-of-the-art methods. The phantom design and algorithm code are freely available online. Since our phantom does not require a tracking target on itself, ease of use is improved over currently used techniques. The fully automatic method generalizes to new probes and different vendors, as shown in our experiments. Our approach produces results comparable to calibrations obtained by a domain expert.

cs.CV↗

arXiv2022

Unsupervised Pre-Training on Patient Population Graphs for Patient-Level Predictions

Pre-training has shown success in different areas of machine learning, such as Computer Vision (CV), Natural Language Processing (NLP) and medical imaging. However, it has not been fully explored for clinical data analysis. Even though an immense amount of Electronic Health Record (EHR) data is recorded, data and labels can be scarce if the data is collected in small hospitals or deals with rare diseases. In such scenarios, pre-training on a larger set of EHR data could improve the model performance. In this paper, we apply unsupervised pre-training to heterogeneous, multi-modal EHR data for patient outcome prediction. To model this data, we leverage graph deep learning over population graphs. We first design a network architecture based on graph transformer designed to handle various input feature types occurring in EHR data, like continuous, discrete, and time-series features, allowing better multi-modal data fusion. Further, we design pre-training methods based on masked imputation to pre-train our network before fine-tuning on different end tasks. Pre-training is done in a fully unsupervised fashion, which lays the groundwork for pre-training on large public datasets with different tasks and similar modalities in the future. We test our method on two medical datasets of patient records, TADPOLE and MIMIC-III, including imaging and non-imaging features and different prediction tasks. We find that our proposed graph based pre-training method helps in modeling the data at a population level and further improves performance on the fine tuning tasks in terms of AUC on average by 4.15% for MIMIC and 7.64% for TADPOLE.

cs.LG↗

arXiv2022

BFS-Net: Weakly Supervised Cell Instance Segmentation from Bright-Field Microscopy Z-Stacks

Despite its broad availability, volumetric information acquisition from Bright-Field Microscopy (BFM) is inherently difficult due to the projective nature of the acquisition process. We investigate the prediction of 3D cell instances from a set of BFM Z-Stack images. We propose a novel two-stage weakly supervised method for volumetric instance segmentation of cells which only requires approximate cell centroids annotation. Created pseudo-labels are thereby refined with a novel refinement loss with Z-stack guidance. The evaluations show that our approach can generalize not only to BFM Z-Stack data, but to other 3D cell imaging modalities. A comparison of our pipeline against fully supervised methods indicates that the significant gain in reduced data collection and labelling results in minor performance difference.

cs.CV↗

arXiv2022

PhoCaL: A Multi-Modal Dataset for Category-Level Object Pose Estimation with Photometrically Challenging Objects

Object pose estimation is crucial for robotic applications and augmented reality. Beyond instance level 6D object pose estimation methods, estimating category-level pose and shape has become a promising trend. As such, a new research field needs to be supported by well-designed datasets. To provide a benchmark with high-quality ground truth annotations to the community, we introduce a multimodal dataset for category-level object pose estimation with photometrically challenging objects termed PhoCaL. PhoCaL comprises 60 high quality 3D models of household objects over 8 categories including highly reflective, transparent and symmetric objects. We developed a novel robot-supported multi-modal (RGB, depth, polarisation) data acquisition and annotation process. It ensures sub-millimeter accuracy of the pose for opaque textured, shiny and transparent objects, no motion blur and perfect camera synchronisation. To set a benchmark for our dataset, state-of-the-art RGB-D and monocular RGB methods are evaluated on the challenging scenes of PhoCaL.

cs.CV↗

arXiv2022

Weakly-supervised Biomechanically-constrained CT/MRI Registration of the Spine

CT and MRI are two of the most informative modalities in spinal diagnostics and treatment planning. CT is useful when analysing bony structures, while MRI gives information about the soft tissue. Thus, fusing the information of both modalities can be very beneficial. Registration is the first step for this fusion. While the soft tissues around the vertebra are deformable, each vertebral body is constrained to move rigidly. We propose a weakly-supervised deep learning framework that preserves the rigidity and the volume of each vertebra while maximizing the accuracy of the registration. To achieve this goal, we introduce anatomy-aware losses for training the network. We specifically design these losses to depend only on the CT label maps since automatic vertebra segmentation in CT gives more accurate results contrary to MRI. We evaluate our method on an in-house dataset of 167 patients. Our results show that adding the anatomy-aware losses increases the plausibility of the inferred transformation while keeping the accuracy untouched.

eess.IV↗

arXiv2022

Latent-Graph Learning for Disease Prediction

Recently, Graph Convolutional Networks (GCNs) have proven to be a powerful machine learning tool for Computer-Aided Diagnosis (CADx) and disease prediction. A key component in these models is to build a population graph, where the graph adjacency matrix represents pair-wise patient similarities. Until now, the similarity metrics have been defined manually, usually based on meta-features like demographics or clinical scores. The definition of the metric, however, needs careful tuning, as GCNs are very sensitive to the graph structure. In this paper, we demonstrate for the first time in the CADx domain that it is possible to learn a single, optimal graph towards the GCN's downstream task of disease classification. To this end, we propose a novel, end-to-end trainable graph learning architecture for dynamic and localized graph pruning. Unlike commonly employed spectral GCN approaches, our GCN is spatial and inductive, and can thus infer previously unseen patients as well. We demonstrate significant classification improvements with our learned graph on two CADx problems in medicine. We further explain and visualize this result using an artificial dataset, underlining the importance of graph learning for more accurate and robust inference with GCNs in medical applications.

cs.LG↗

arXiv2022

Differentiable Graph Module (DGM) for Graph Convolutional Networks

Graph deep learning has recently emerged as a powerful ML concept allowing to generalize successful deep neural architectures to non-Euclidean structured data. Such methods have shown promising results on a broad spectrum of applications ranging from social science, biomedicine, and particle physics to computer vision, graphics, and chemistry. One of the limitations of the majority of current graph neural network architectures is that they are often restricted to the transductive setting and rely on the assumption that the underlying graph is {\em known} and {\em fixed}. Often, this assumption is not true since the graph may be noisy, or partially and even completely unknown. In such cases, it would be helpful to infer the graph directly from the data, especially in inductive settings where some nodes were not present in the graph at training time. Furthermore, learning a graph may become an end in itself, as the inferred structure may provide complementary insights next to the downstream task. In this paper, we introduce Differentiable Graph Module (DGM), a learnable function that predicts edge probabilities in the graph which are optimal for the downstream task. DGM can be combined with convolutional graph neural network layers and trained in an end-to-end fashion. We provide an extensive evaluation of applications from the domains of healthcare (disease prediction), brain imaging (age prediction), computer graphics (3D point cloud segmentation), and computer vision (zero-shot learning). We show that our model provides a significant improvement over baselines both in transductive and inductive settings and achieves state-of-the-art results.

cs.LG↗

arXiv2022

VesNet-RL: Simulation-based Reinforcement Learning for Real-World US Probe Navigation

Ultrasound (US) is one of the most common medical imaging modalities since it is radiation-free, low-cost, and real-time. In freehand US examinations, sonographers often navigate a US probe to visualize standard examination planes with rich diagnostic information. However, reproducibility and stability of the resulting images often suffer from intra- and inter-operator variation. Reinforcement learning (RL), as an interaction-based learning method, has demonstrated its effectiveness in visual navigating tasks; however, RL is limited in terms of generalization. To address this challenge, we propose a simulation-based RL framework for real-world navigation of US probes towards the standard longitudinal views of vessels. A UNet is used to provide binary masks from US images; thereby, the RL agent trained on simulated binary vessel images can be applied in real scenarios without further training. To accurately characterize actual states, a multi-modality state representation structure is introduced to facilitate the understanding of environments. Moreover, considering the characteristics of vessels, a novel standard view recognition approach based on the minimum bounding rectangle is proposed to terminate the searching process. To evaluate the effectiveness of the proposed method, the trained policy is validated virtually on 3D volumes of a volunteer's in-vivo carotid artery, and physically on custom-designed gel phantoms using robotic US. The results demonstrate that proposed approach can effectively and accurately navigate the probe towards the longitudinal view of vessels.

eess.IV↗