Pierre Rougé

Pierre Rougé, Nicolas Passat, Odyssée Merveille

Vessel segmentation and centerline extraction are two crucial preliminary tasks for many computer-aided diagnosis tools dealing with vascular diseases. Recently, deep-learning based methods have been widely applied to these tasks. However, classic deep-learning approaches struggle to capture the complex geometry and specific topology of vascular networks, which is of the utmost importance in most applications. To overcome these limitations, the clDice loss, a topological loss that focuses on the vessel centerlines, has been recently proposed. This loss requires computing, with a proposed soft-skeleton algorithm, the skeletons of both the ground truth and the predicted segmentation. However, the soft-skeleton algorithm provides suboptimal results on 3D images, which makes the clDice hardly suitable on 3D images. In this paper, we propose to replace the soft-skeleton algorithm by a U-Net which computes the vascular skeleton directly from the segmentation. We show that our method provides more accurate skeletons than the soft-skeleton algorithm. We then build upon this network a cascaded U-Net trained with the clDice loss to embed topological constraints during the segmentation. The resulting model is able to predict both the vessel segmentation and centerlines with a more accurate topology.

Pierre Rougé, Pierre-Henri Conze, Nicolas Passat et al.

Segmentation in medical imaging is an essential and often preliminary task in the image processing chain, driving numerous efforts towards the design of robust segmentation algorithms. Supervised learning methods achieve excellent performances when fed with a sufficient amount of labeled data. However, such labels are typically highly time-consuming, error-prone and expensive to produce. Alternatively, semi-supervised learning approaches leverage both labeled and unlabeled data, and are very useful when only a small fraction of the dataset is labeled. They are particularly useful for cerebrovascular segmentation, given that labeling a single volume requires several hours for an expert. In addition to the challenge posed by insufficient annotations, there are concerns regarding annotation consistency. The task of annotating the cerebrovascular tree is inherently ambiguous. Due to the discrete nature of images, the borders and extremities of vessels are often unclear. Consequently, annotations heavily rely on the expert subjectivity and on the underlying clinical objective. These discrepancies significantly increase the complexity of the segmentation task for the model and consequently impair the results. Consequently, it becomes imperative to provide clinicians with precise guidelines to improve the annotation process and construct more uniform datasets. In this article, we investigate the data dependency of deep learning methods within the context of imperfect data and semi-supervised learning, for cerebrovascular segmentation. Specifically, this study compares various state-of-the-art semi-supervised methods based on unsupervised regularization and evaluates their performance in diverse quantity and quality data scenarios. Based on these experiments, we provide guidelines for the annotation and training of cerebrovascular segmentation models.

Méghane Decroocq, Carole Frindel, Pierre Rougé et al.

Computational fluid dynamics (CFD) simulation provides valuable information on blood flow from the vascular geometry. However, it requires extracting precise models of arteries from low-resolution medical images, which remains challenging. Centerline-based representation is widely used to model large vascular networks with small vessels, as it encodes both the geometric and topological information and facilitates manual editing. In this work, we propose an automatic method to generate a structured hexahedral mesh suitable for CFD directly from centerlines. We addressed both the modeling and meshing tasks. We proposed a vessel model based on penalized splines to overcome the limitations inherent to the centerline representation, such as noise and sparsity. The bifurcations are reconstructed using a parametric model based on the anatomy that we extended to planar n-furcations. Finally, we developed a method to produce a volume mesh with structured, hexahedral, and flow-oriented cells from the proposed vascular network model. The proposed method offers better robustness to the common defects of centerlines and increases the mesh quality compared to state-of-the-art methods. As it relies on centerlines alone, it can be applied to edit the vascular model effortlessly to study the impact of vascular geometry and topology on hemodynamics. We demonstrate the efficiency of our method by entirely meshing a dataset of 60 cerebral vascular networks. 92% of the vessels and 83% of the bifurcations were meshed without defects needing manual intervention, despite the challenging aspect of the input data. The source code is released publicly.