Publications related to Automated Detection and Delineation of Tree Structures in Noisy Micrographs

Aggregating Spatial and Photometric Context for Photometric Stereo

Photometric stereo, a computer vision technique for estimating the 3D shape of objects through images captured under varying illumination conditions, has been a topic of research for nearly four decades. In its general formulation, photometric stereo is an ...

EPFL2024

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets

Martin Weigert

Volume electron microscopy is the method of choice for the in situ interrogation of cellular ultrastructure at the nanometer scale, and with the increase in large raw image datasets generated, improving computational strategies for image segmentation and s ...

Nature Portfolio2024

Semantic Shape Editing with Parametric Implicit Templates

Uday Kusupati

We propose a semantic shape editing method to edit 3D triangle meshes using parametric implicit surface templates, benefiting from the many advantages offered by analytical implicit representations, such as infinite resolution and boolean or blending opera ...

ACM Association for Computing Machinery2024

Advancing Self-Supervised Deep Learning for 3D Scene Understanding

Seyed Mohammad Mahdi Johari

Recent advancements in deep learning have revolutionized 3D computer vision, enabling the extraction of intricate 3D information from 2D images and video sequences. This thesis explores the application of deep learning in three crucial challenges of 3D com ...

EPFL2024

Incorporating Projective Geometry into Deep Learning

Michal Jan Tyszkiewicz

In this thesis we explore the applications of projective geometry, a mathematical theory of the relation between 3D scenes and their 2D images, in modern learning-based computer vision systems. This is an interesting research question which contradicts the ...

EPFL2024

3D reconstruction of curvilinear one-dimensional objects viewed in transmission electron microscopy

Gulnaz Ganeeva

To obtain a more complete understanding of material microstructure at the nanoscale and to gain profound insights into their properties, there is a growing need for more efficient and precise methods that can streamline the process of 3D imaging using a tr ...

EPFL2023

Deep Learning for 3D Surface Modelling and Reconstruction

Benoît Alain René Guillard

In recent years, there has been a significant revolution in the field of deep learning, which has demonstrated its effectiveness in automatically capturing intricate patterns from large datasets. However, the majority of these successes in Computer Vision ...

EPFL2023

Automated neuron tracking inside moving and deforming C. elegans using deep learning and targeted augmentation

Sahand Jamal Rahi, Kseniia Korchagina

Reading out neuronal activity from three-dimensional (3D) functional imaging requires segmenting and tracking individual neurons. This is challenging in behaving animals if the brain moves and deforms. The traditional approach is to train a convolutional n ...

Nature Portfolio2023

Self-supervised Dense Representation Learning for Live-Cell Microscopy with Time Arrow Prediction

Max Stieber, Martin Weigert, Benjamin Tobias Gallusser

State-of-the-art object detection and segmentation methods for microscopy images rely on supervised machine learning, which requires laborious manual annotation of training data. Here we present a self-supervised method based on time arrow prediction pre-t ...

Springer International Publishing Ag2023

Multi-site, Multi-domain Airway Tree Modeling

Boyu Zhang, Jiancheng Yang, Ying Zhu, Yi Wu

Open international challenges are becoming the de facto standard for assessing computer vision and image analysis algorithms. In recent years, new methods have extended the reach of pulmonary airway segmentation that is closer to the limit of image resolut ...

Elsevier2023

SAGTTA: SALIENCY GUIDED TEST TIME AUGMENTATION FOR MEDICAL IMAGE SEGMENTATION ACROSS VENDOR DOMAIN SHIFT

Seyedbehzad Bozorgtabar, Devavrat Tomar

Test time augmentation has been shown to be an effective approach to combat domain shifts in deep learning. Despite their promising performance levels, the interpretability of the underlying used models is however low. Saliency maps have been widely used i ...

IEEE2023

Self-Supervised Learning for Patient Stratification and Survival Analysis in Computational Pathology: An Application to Colorectal Cancer

Christian Robert Abbet

Over the years, clinical institutes accumulated large amounts of digital slides from resected tissue specimens. These digital images, called whole slide images (WSIs), are high-resolution tissue snapshots that depict the complex interaction of cells at the ...

EPFL2023

Detecting Anomalies and Obstacles in Road Scenes

Krzysztof Maciej Lis

We address the problem of segmenting anomalies and unusual obstacles in road scenes for the purpose of self-driving safety. The objects in question are not present in the common training sets as it is not feasible to collect and annotate examples for every ...

EPFL2023

Synthesis and Analysis of 3D shapes with Geometric Deep Learning in Computer-Aided Engineering

Edoardo Remelli

In this thesis, we advocate that Computer-Aided Engineering could benefit from a Geometric Deep Learning revolution, similarly to the way that Deep Learning revolutionized Computer Vision. To do so, we consider a variety of Computer-Aided Engineering pr ...

EPFL2022

GALET: A deep learning image segmentation model for drone-based grain size analysis of gravel bars

Giovanni De Cesare, Christian Mörtl

In this study, we present the deep learning image segmentation model for drone-based grain size analysis of gravel bars called GALET. The objectives are to quantify the performance of the code and to test its applicability in river research and management. ...

International Association for Hydro-Environment Engineering and Research (IAHR)2022

Robust Isometric Non-Rigid Structure-From-Motion

Shaifali Parashar

Non-Rigid Structure-from-Motion (NRSfM) reconstructs a deformable 3D object from keypoint correspondences established between monocular 2D images. Current NRSfM methods lack statistical robustness, which is the ability to cope with correspondence errors. T ...

IEEE COMPUTER SOC2022

Digital twins for post-earthquake damage assessment of free-standing buildings including damage information

Radhakrishna Achanta, Katrin Beyer, Amir Rezaie, Bryan German Pantoja Rosero

We present a pipeline for the automatic generation of digital twins of free-standing buildings for damage assessment. Our method takes multiple view images of the target building as input and processes them to produce a 3D model in levels of detail (LOD) f ...

2022

Self-supervised Segmentation via Background Inpainting

Pascal Fua, Mathieu Salzmann, Victor Constantin, Isinsu Katircioglu, Helge Jochen Rhodin

While supervised object detection and segmentation methods achieve impressive accuracy, they generalize poorly to images whose appearance significantly differs from the data they have been trained on. To address this when annotating data is prohibitively e ...

2022

Weakly Supervised Volumetric Image Segmentation with Deformed Templates

Pascal Fua, Pamuditha Udaranga Wickramasinghe, Patrick Moller Jensen, Mian Akbar Shah

There are many approaches to weakly-supervised training of networks to segment 2D images. By contrast, existing approaches to segmenting volumetric images rely on full-supervision of a subset of 2D slices of the 3D volume. We propose an approach to volume ...

Springer2022

Unsupervised Visual Entity Abstraction towards 2D and 3D Compositional Models

Beril Besbinar

Object-centric learning has gained significant attention over the last years as it can serve as a powerful tool to analyze complex scenes as a composition of simpler entities. Well-established tasks in computer vision, such as object detection or instance ...

EPFL2022