469 citations · 1k across the 24 of their papers we have counts for
25 papers
Bag-of-Visual-Words for Spatial Mapping of Lung Adenocarcinoma Growth Patterns
Darya Ardan, Valentin Oreiller, Henning Müller
Spatial mapping of lung adenocarcinoma (LUAD) growth patterns across whole slide images (WSIs) requires resolving architectural context at the region level, yet existing methods op…
Comparing Baseline and Day-1 Diffusion MRI Using Multimodal Deep Embeddings for Stroke Outcome Prediction
Sina Raeisadigh, Myles Joshua Toledo Tan, Henning Müller +1
This study compares baseline (J0) and 24-hour (J1) diffusion magnetic resonance imaging (MRI) for predicting three-month functional outcomes after acute ischemic stroke (AIS). Seve…
Towards the Automatic Segmentation, Modeling and Meshing of the Aortic Vessel Tree from Multicenter Acquisitions: An Overview of the SEG.A. 2023 Segmentation of the Aorta Challenge
Yuan Jin, Antonio Pepe, Gian Marco Melito +36
The automated analysis of the aortic vessel tree (AVT) from computed tomography angiography (CTA) holds immense clinical potential, but its development has been impeded by a lack o…
Learn2Reg 2024: New Benchmark Datasets Driving Progress on New Challenges
Lasse Hansen, Wiebke Heyer, Christoph Großbröhmer +51
Medical image registration is critical for clinical applications, and fair benchmarking of different methods is essential for monitoring ongoing progress in the field. To date, the…
3-D Image-to-Image Fusion in Lightsheet Microscopy by Two-Step Adversarial Network: Contribution to the FuseMyCells Challenge
Marek Wodzinski, Henning Müller
Lightsheet microscopy is a powerful 3-D imaging technique that addresses limitations of traditional optical and confocal microscopy but suffers from a low penetration depth and red…
Automatic Registration of SHG and H&E Images with Feature-based Initial Alignment and Intensity-based Instance Optimization: Contribution to the COMULIS Challenge
Marek Wodzinski, Henning Müller
The automatic registration of noninvasive second-harmonic generation microscopy to hematoxylin and eosin slides is a highly desired, yet still unsolved problem. The task is challen…
Lymphoid Infiltration Assessment of the Tumor Margins in H&E Slides
Zhuxian Guo, Amine Marzouki, Jean-François Emile +3
Lymphoid infiltration at tumor margins is a key prognostic marker in solid tumors, playing a crucial role in guiding immunotherapy decisions. Current assessment methods, heavily re…
Automatic Labels are as Effective as Manual Labels in Biomedical Images Classification with Deep Learning
Niccolò Marini, Stefano Marchesin, Lluis Borras Ferris +12
The increasing availability of biomedical data is helping to design more robust deep learning (DL) algorithms to analyze biomedical samples. Currently, one of the main limitations…
ROCOv2: Radiology Objects in COntext Version 2, an Updated Multimodal Image Dataset
Johannes Rückert, Louise Bloch, Raphael Brüngel +11
Automated medical image analysis systems often require large amounts of training data with high quality labels, which are difficult and time consuming to generate. This paper intro…
Improving Quality Control of Whole Slide Images by Explicit Artifact Augmentation
Artur Jurgas, Marek Wodzinski, Marina D'Amato +3
The problem of artifacts in whole slide image acquisition, prevalent in both clinical workflows and research-oriented settings, necessitates human intervention and re-scanning. Ove…
Patch-Based Encoder-Decoder Architecture for Automatic Transmitted Light to Fluorescence Imaging Transition: Contribution to the LightMyCells Challenge
Marek Wodzinski, Henning Müller
Automatic prediction of fluorescently labeled organelles from label-free transmitted light input images is an important, yet difficult task. The traditional way to obtain fluoresce…
RegWSI: Whole Slide Image Registration using Combined Deep Feature- and Intensity-Based Methods: Winner of the ACROBAT 2023 Challenge
Marek Wodzinski, Niccolò Marini, Manfredo Atzori +1
The automatic registration of differently stained whole slide images (WSIs) is crucial for improving diagnosis and prognosis by fusing complementary information emerging from diffe…
DeeperHistReg: Robust Whole Slide Images Registration Framework
Marek Wodzinski, Niccolò Marini, Manfredo Atzori +1
DeeperHistReg is a software framework dedicated to registering whole slide images (WSIs) acquired using multiple stains. It allows one to perform the preprocessing, initial alignme…
Automatic Aorta Segmentation with Heavily Augmented, High-Resolution 3-D ResUNet: Contribution to the SEG.A Challenge
Marek Wodzinski, Henning Müller
Automatic aorta segmentation from 3-D medical volumes is an important yet difficult task. Several factors make the problem challenging, e.g. the possibility of aortic dissection or…
A Hierarchical Transformer Encoder to Improve Entire Neoplasm Segmentation on Whole Slide Image of Hepatocellular Carcinoma
Zhuxian Guo, Qitong Wang, Henning Müller +3
In digital histopathology, entire neoplasm segmentation on Whole Slide Image (WSI) of Hepatocellular Carcinoma (HCC) plays an important role, especially as a preprocessing filter t…
The ACROBAT 2022 Challenge: Automatic Registration Of Breast Cancer Tissue
Philippe Weitz, Masi Valkonen, Leslie Solorzano +38
The alignment of tissue between histopathological whole-slide-images (WSI) is crucial for research and clinical applications. Advances in computing, deep learning, and availability…
Evaluating Post-hoc Interpretability with Intrinsic Interpretability
José Pereira Amorim, Pedro Henriques Abreu, João Santos +1
Despite Convolutional Neural Networks having reached human-level performance in some medical tasks, their clinical use has been hindered by their lack of interpretability. Two majo…
Unsupervised Method for Intra-patient Registration of Brain Magnetic Resonance Images based on Objective Function Weighting by Inverse Consistency: Contribution to the BraTS-Reg Challenge
Marek Wodzinski, Artur Jurgas, Niccolo Marini +2
Registration of brain scans with pathologies is difficult, yet important research area. The importance of this task motivated researchers to organize the BraTS-Reg challenge, joint…
Frobenius integrability of certain -forms on singular spaces
Junyan Cao, Andreas Höring
Demailly proved that on a smooth compact Kähler manifold the distribution defined by a holomorphic -form with values in an anti-pseudoeffective line bundle is always integrable.…
Metrics reloaded: Recommendations for image analysis validation
Lena Maier-Hein, Annika Reinke, Patrick Godau +71
Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. Particularly in automatic biomedical image analysis, chosen…
H&E-adversarial network: a convolutional neural network to learn stain-invariant features through Hematoxylin & Eosin regression
Niccoló Marini, Manfredo Atzori, Sebastian Otálora +2
Computational pathology is a domain that aims to develop algorithms to automatically analyze large digitized histopathology images, called whole slide images (WSI). WSIs are produc…
The Brain Tumor Sequence Registration (BraTS-Reg) Challenge: Establishing Correspondence Between Pre-Operative and Follow-up MRI Scans of Diffuse Glioma Patients
Bhakti Baheti, Satrajit Chakrabarty, Hamed Akbari +70
Registration of longitudinal brain MRI scans containing pathologies is challenging due to dramatic changes in tissue appearance. Although there has been progress in developing gene…
Learning Interpretable Microscopic Features of Tumor by Multi-task Adversarial CNNs To Improve Generalization
Mara Graziani, Sebastian Otalora, Stephane Marchand-Maillet +2
Adopting Convolutional Neural Networks (CNNs) in the daily routine of primary diagnosis requires not only near-perfect precision, but also a sufficient degree of generalization to…
Standardised convolutional filtering for radiomics
Adrien Depeursinge, Vincent Andrearczyk, Philip Whybra +5
The Image Biomarker Standardisation Initiative (IBSI) aims to improve reproducibility of radiomics studies by standardising the computational process of extracting image biomarkers…