Nadja Gruber

Nadja Gruber, Johannes Schwab, Noémie Debroux et al.

We develop Self2Seg, a self-supervised method for the joint segmentation and denoising of a single image. To this end, we combine the advantages of variational segmentation with self-supervised deep learning. One major benefit of our method lies in the fact, that in contrast to data-driven methods, where huge amounts of labeled samples are necessary, Self2Seg segments an image into meaningful regions without any training database. Moreover, we demonstrate that self-supervised denoising itself is significantly improved through the region-specific learning of Self2Seg. Therefore, we introduce a novel self-supervised energy functional in which denoising and segmentation are coupled in a way that both tasks benefit from each other. We propose a unified optimisation strategy and numerically show that for noisy microscopy images our proposed joint approach outperforms its sequential counterpart as well as alternative methods focused purely on denoising or segmentation.

Nadja Gruber, Johannes Schwab, Sebastien Court et al.

We propose an unsupervised image segmentation approach, that combines a variational energy functional and deep convolutional neural networks. The variational part is based on a recent multichannel multiphase Chan-Vese model, which is capable to extract useful information from multiple input images simultaneously. We implement a flexible multiclass segmentation method that divides a given image into $K$ different regions. We use convolutional neural networks (CNNs) targeting a pre-decomposition of the image. By subsequently minimising the segmentation functional, the final segmentation is obtained in a fully unsupervised manner. Special emphasis is given to the extraction of informative feature maps serving as a starting point for the segmentation. The initial results indicate that the proposed method is able to decompose and segment the different regions of various types of images, such as texture and medical images and compare its performance with another multiphase segmentation method.

Markus Haltmeier, Nadja Gruber, Gyeongha Hwang

Photoacoustic tomography (PAT) is an emerging imaging modality that combines the complementary strengths of optical contrast and ultrasonic resolution. A central task is image reconstruction, where measured acoustic signals are used to recover the initial pressure distribution. For ideal point-like or line-like detectors, several efficient and fast reconstruction algorithms exist, including Fourier methods, filtered backprojection, and time reversal. However, when applied to data acquired with finite-size detectors, these methods yield systematically blurred images. Although sharper images can be obtained by compensating for finite-detector effects, supervised learning approaches typically require ground-truth images that may not be available in practice. We propose a self-supervised reconstruction method based on Noisier2Inverse that addresses finite-size detector effects without requiring ground-truth data. Our approach operates directly on noisy measurements and learns to recover high-quality PAT images in a ground-truth-free manner. Its key components are: (i) PAT-specific modeling that recasts the problem as angular deblurring; (ii) a Noisier2Inverse formulation in the polar domain that leverages the known angular point-spread function; and (iii) a novel, statistically grounded early-stopping rule. In experiments, the proposed method consistently outperforms alternative approaches that do not use supervised data and achieves performance close to supervised benchmarks, while remaining practical for real acquisitions with finite-size detectors.

Nadja Gruber, Johannes Schwab, Sebastien Court et al.

We propose, analyze and realize a variational multiclass segmentation scheme that partitions a given image into multiple regions exhibiting specific properties. Our method determines multiple functions that encode the segmentation regions by minimizing an energy functional combining information from different channels. Multichannel image data can be obtained by lifting the image into a higher dimensional feature space using specific multichannel filtering or may already be provided by the imaging modality under consideration, such as an RGB image or multimodal medical data. Experimental results show that the proposed method performs well in various scenarios. In particular, promising results are presented for two medical applications involving classification of brain abscess and tumor growth, respectively. As main theoretical contributions, we prove the existence of global minimizers of the proposed energy functional and show its stability and convergence with respect to noisy inputs. In particular, these results also apply to the special case of binary segmentation, and these results are also novel in this particular situation.

Nadja Gruber, Stephan Antholzer, Werner Jaschke et al.

Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer in adults, and the most common cause of death of people suffering from cirrhosis. The segmentation of liver lesions in CT images allows assessment of tumor load, treatment planning, prognosis and monitoring of treatment response. Manual segmentation is a very time-consuming task and in many cases, prone to inaccuracies and automatic tools for tumor detection and segmentation are desirable. In this paper, we compare two network architectures, one that is composed of one neural network and manages the segmentation task in one step and one that consists of two consecutive fully convolutional neural networks. The first network segments the liver whereas the second network segments the actual tumor inside the liver. Our networks are trained on a subset of the LiTS (Liver Tumor Segmentation) Challenge and evaluated on data.