Despite its wide use in medicine, ultrasound imaging faces several challenges related to its poor signal-to-noise ratio and several sources of noise and artefacts. Enhancing ultrasound image quality involves balancing concurrent factors like contrast, resolution, and speckle preservation. In recent years, there has been progress both in model-based and learning-based approaches to improve ultrasound image reconstruction. Bringing the best from both worlds, we propose a hybrid approach leveraging advances in diffusion models. To this end, we adapt Denoising Diffusion Restoration Models (DDRM) to incorporate ultrasound physics through a linear direct model and an unsupervised fine-tuning of the prior diffusion model. We conduct comprehensive experiments on simulated, in-vitro, and in-vivo data, demonstrating the efficacy of our approach in achieving high-quality image reconstructions from a single plane wave input and in comparison to state-of-the-art methods. Finally, given the stochastic nature of the method, we analyse in depth the statistical properties of single and multiple-sample reconstructions, experimentally show the informativeness of their variance, and provide an empirical model relating this behaviour to speckle noise. The code and data are available at: (upon acceptance).
Muscle volume is a useful quantitative biomarker in sports, but also for the follow-up of degenerative musculo-skelletal diseases. In addition to volume, other shape biomarkers can be extracted by segmenting the muscles of interest from medical images. Manual segmentation is still today the gold standard for such measurements despite being very time-consuming. We propose a method for automatic segmentation of 18 muscles of the lower limb on 3D Magnetic Resonance Images to assist such morphometric analysis. By their nature, the tissue of different muscles is undistinguishable when observed in MR Images. Thus, muscle segmentation algorithms cannot rely on appearance but only on contour cues. However, such contours are hard to detect and their thickness varies across subjects. To cope with the above challenges, we propose a segmentation approach based on a hybrid architecture, combining convolutional and visual transformer blocks. We investigate for the first time the behaviour of such hybrid architectures in the context of muscle segmentation for shape analysis. Considering the consistent anatomical muscle configuration, we rely on transformer blocks to capture the longrange relations between the muscles. To further exploit the anatomical priors, a second contribution of this work consists in adding a regularisation loss based on an adjacency matrix of plausible muscle neighbourhoods estimated from the training data. Our experimental results on a unique database of elite athletes show it is possible to train complex hybrid models from a relatively small database of large volumes, while the anatomical prior regularisation favours better predictions.
Diffuse Large B-cell Lymphoma (DLBCL) is a lymphatic cancer involving one or more lymph nodes and extranodal sites. Its diagnostic and follow-up rely on Positron Emission Tomography (PET) and Computed Tomography (CT). After diagnosis, the number of nonresponding patients to standard front-line therapy remains significant (30-40%). This work aims to develop a computer-aided approach to identify high-risk patients requiring adapted treatment by efficiently exploiting all the information available for each patient, including both clinical and image data. We propose a method based on recent graph neural networks that combine imaging information from multiple lesions, and a cross-attention module to integrate different data modalities efficiently. The model is trained and evaluated on a private prospective multicentric dataset of 583 patients. Experimental results show that our proposed method outperforms classical supervised methods based on either clinical, imaging or both clinical and imaging data for the 2-year progression-free survival (PFS) classification accuracy.
Measuring cross-sectional areas in ultrasound images is a standard tool to evaluate disease progress or treatment response. Often addressed today with supervised deep-learning segmentation approaches, existing solutions highly depend upon the quality of experts' annotations. However, the annotation quality in ultrasound is anisotropic and position-variant due to the inherent physical imaging principles, including attenuation, shadows, and missing boundaries, commonly exacerbated with depth. This work proposes a novel approach that guides ultrasound segmentation networks to account for sonographers' uncertainties and generate predictions with variability similar to the experts. We claim that realistic variability can reduce overconfident predictions and improve physicians' acceptance of deep-learning cross-sectional segmentation solutions. Our method provides CM's certainty for each pixel for minimal computational overhead as it can be precalculated directly from the image. We show that there is a correlation between low values in the confidence maps and expert's label uncertainty. Therefore, we propose to give the confidence maps as additional information to the networks. We study the effect of the proposed use of ultrasound CMs in combination with four state-of-the-art neural networks and in two configurations: as a second input channel and as part of the loss. We evaluate our method on 3D ultrasound datasets of the thyroid and lower limb muscles. Our results show ultrasound CMs increase the Dice score, improve the Hausdorff and Average Surface Distances, and decrease the number of isolated pixel predictions. Furthermore, our findings suggest that ultrasound CMs improve the penalization of uncertain areas in the ground truth data, thereby improving problematic interpolations. Our code and example data will be made public at https://github.com/IFL-CAMP/Confidence-segmentation.
Ultrasound image reconstruction can be approximately cast as a linear inverse problem that has traditionally been solved with penalized optimization using the $l_1$ or $l_2$ norm, or wavelet-based terms. However, such regularization functions often struggle to balance the sparsity and the smoothness. A promising alternative is using learned priors to make the prior knowledge closer to reality. In this paper, we rely on learned priors under the framework of Denoising Diffusion Restoration Models (DDRM), initially conceived for restoration tasks with natural images. We propose and test two adaptions of DDRM to ultrasound inverse problem models, DRUS and WDRUS. Our experiments on synthetic and PICMUS data show that from a single plane wave our method can achieve image quality comparable to or better than DAS and state-of-the-art methods. The code is available at: https://github.com/Yuxin-Zhang-Jasmine/DRUS-v1.
Longitudinal image registration is challenging and has not yet benefited from major performance improvements thanks to deep-learning. Inspired by Deep Image Prior, this paper introduces a different use of deep architectures as regularizers to tackle the image registration question. We propose a subject-specific deformable registration method called MIRRBA, relying on a deep pyramidal architecture to be the prior parametric model constraining the deformation field. Diverging from the supervised learning paradigm, MIRRBA does not require a learning database, but only the pair of images to be registered to optimize the network's parameters and provide a deformation field. We demonstrate the regularizing power of deep architectures and present new elements to understand the role of the architecture in deep learning methods for registration. Hence, to study the impact of the network parameters, we ran our method with different architectural configurations on a private dataset of 110 metastatic breast cancer full-body PET images with manual segmentations of the brain, bladder and metastatic lesions. We compared it against conventional iterative registration approaches and supervised deep learning-based models. Global and local registration accuracies were evaluated using the detection rate and the Dice score respectively, while registration realism was evaluated using the Jacobian's determinant. Moreover, we computed the ability of the different methods to shrink vanishing lesions with the disappearing rate. MIRRBA significantly improves the organ and lesion Dice scores of supervised models. Regarding the disappearing rate, MIRRBA more than doubles the best performing conventional approach SyNCC score. Our work therefore proposes an alternative way to bridge the performance gap between conventional and deep learning-based methods and demonstrates the regularizing power of deep architectures.
For early breast cancer detection, regular screening with mammography imaging is recommended. Routinary examinations result in datasets with a predominant amount of negative samples. A potential solution to such class-imbalance is joining forces across multiple institutions. Developing a collaborative computer-aided diagnosis system is challenging in different ways. Patient privacy and regulations need to be carefully respected. Data across institutions may be acquired from different devices or imaging protocols, leading to heterogeneous non-IID data. Also, for learning-based methods, new optimization strategies working on distributed data are required. Recently, federated learning has emerged as an effective tool for collaborative learning. In this setting, local models perform computation on their private data to update the global model. The order and the frequency of local updates influence the final global model. Hence, the order in which samples are locally presented to the optimizers plays an important role. In this work, we define a memory-aware curriculum learning method for the federated setting. Our curriculum controls the order of the training samples paying special attention to those that are forgotten after the deployment of the global model. Our approach is combined with unsupervised domain adaptation to deal with domain shift while preserving data privacy. We evaluate our method with three clinical datasets from different vendors. Our results verify the effectiveness of federated adversarial learning for the multi-site breast cancer classification. Moreover, we show that our proposed memory-aware curriculum method is beneficial to further improve classification performance. Our code is publicly available at: https://github.com/ameliajimenez/curriculum-federated-learning.
We address the problem of 3D shape registration and we propose a novel technique based on spectral graph theory and probabilistic matching. The task of 3D shape analysis involves tracking, recognition, registration, etc. Analyzing 3D data in a single framework is still a challenging task considering the large variability of the data gathered with different acquisition devices. 3D shape registration is one such challenging shape analysis task. The main contribution of this chapter is to extend the spectral graph matching methods to very large graphs by combining spectral graph matching with Laplacian embedding. Since the embedded representation of a graph is obtained by dimensionality reduction we claim that the existing spectral-based methods are not easily applicable. We discuss solutions for the exact and inexact graph isomorphism problems and recall the main spectral properties of the combinatorial graph Laplacian; We provide a novel analysis of the commute-time embedding that allows us to interpret the latter in terms of the PCA of a graph, and to select the appropriate dimension of the associated embedded metric space; We derive a unit hyper-sphere normalization for the commute-time embedding that allows us to register two shapes with different samplings; We propose a novel method to find the eigenvalue-eigenvector ordering and the eigenvector signs using the eigensignature (histogram) which is invariant to the isometric shape deformations and fits well in the spectral graph matching framework, and we present a probabilistic shape matching formulation using an expectation maximization point registration algorithm which alternates between aligning the eigenbases and finding a vertex-to-vertex assignment.
This paper addresses the domain shift problem for segmentation. As a solution, we propose OLVA, a novel and lightweight unsupervised domain adaptation method based on a Variational Auto-Encoder (VAE) and Optimal Transport (OT) theory. Thanks to the VAE, our model learns a shared cross-domain latent space that follows a normal distribution, which reduces the domain shift. To guarantee valid segmentations, our shared latent space is designed to model the shape rather than the intensity variations. We further rely on an OT loss to match and align the remaining discrepancy between the two domains in the latent space. We demonstrate OLVA's effectiveness for the segmentation of multiple cardiac structures on the public Multi-Modality Whole Heart Segmentation (MM-WHS) dataset, where the source domain consists of annotated 3D MR images and the unlabelled target domain of 3D CTs. Our results show remarkable improvements with an additional margin of 12.5\% dice score over concurrent generative training approaches.
Matching articulated shapes represented by voxel-sets reduces to maximal sub-graph isomorphism when each set is described by a weighted graph. Spectral graph theory can be used to map these graphs onto lower dimensional spaces and match shapes by aligning their embeddings in virtue of their invariance to change of pose. Classical graph isomorphism schemes relying on the ordering of the eigenvalues to align the eigenspaces fail when handling large data-sets or noisy data. We derive a new formulation that finds the best alignment between two congruent $K$-dimensional sets of points by selecting the best subset of eigenfunctions of the Laplacian matrix. The selection is done by matching eigenfunction signatures built with histograms, and the retained set provides a smart initialization for the alignment problem with a considerable impact on the overall performance. Dense shape matching casted into graph matching reduces then, to point registration of embeddings under orthogonal transformations; the registration is solved using the framework of unsupervised clustering and the EM algorithm. Maximal subset matching of non identical shapes is handled by defining an appropriate outlier class. Experimental results on challenging examples show how the algorithm naturally treats changes of topology, shape variations and different sampling densities.