Jonathan Fabrizio

Minh On Vu Ngoc, Yizi Chen, Nicolas Boutry et al.

Capturing the global topology of an image is essential for proposing an accurate segmentation of its domain. However, most of existing segmentation methods do not preserve the initial topology of the given input, which is detrimental for numerous downstream object-based tasks. This is all the more true for deep learning models which most work at local scales. In this paper, we propose a new topology-preserving deep image segmentation method which relies on a new leakage loss: the Pathloss. Our method is an extension of the BALoss [1], in which we want to improve the leakage detection for better recovering the closeness property of the image segmentation. This loss allows us to correctly localize and fix the critical points (a leakage in the boundaries) that could occur in the predictions, and is based on a shortest-path search algorithm. This way, loss minimization enforces connectivity only where it is necessary and finally provides a good localization of the boundaries of the objects in the image. Moreover, according to our research, our Pathloss learns to preserve stronger elongated structure compared to methods without using topology-preserving loss. Training with our topological loss function, our method outperforms state-of-the-art topology-aware methods on two representative datasets of different natures: Electron Microscopy and Historical Map.

Spyridon Bakas, Mauricio Reyes, Andras Jakab et al.

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset.