Tracing in 2D to reduce the annotation effort for 3D deep delineation of linear structures

The difficulty of obtaining annotations to build training databases still slows down the adoption of recent deep learning approaches for biomedical image analysis. In this paper, we show that we can train a Deep Net to perform 3D volumetric delineation given only 2D annotations in Maximum Intensity Projections (MIP) of the training volumes. This significantly reduces the annotation time: We conducted a user study that suggests that annotating 2D projections is on average twice as fast as annotating the original 3D volumes. Our technical contribution is a loss function that evaluates a 3D prediction against annotations of 2D projections. It is inspired by space carving, a classical approach to reconstructing complex 3D shapes from arbitrarily-positioned cameras. It can be used to train any deep network with volumetric output, without the need to change the network's architecture. Substituting the loss is all it takes to enable 2D annotations in an existing training setup. In extensive experiments on 3D light microscopy images of neurons and retinal blood vessels, and on Magnetic Resonance Angiography (MRA) brain scans, we show that, when trained on projection annotations, deep delineation networks perform as well as when they are trained using costlier 3D annotations. (C) 2019 Elsevier B.V. All rights reserved.

Learning Approach to Delineation of Curvilinear Structures in 2D and 3D Images

Agata Justyna Mosinska

Detection of curvilinear structures has long been of interest due to its wide range of applications. Large amounts of imaging data could be readily used in many fields, but it is practically not possible to analyze them manually. Hence, the need for automated delineation approaches. In the recent years Computer Vision witnessed a paradigm shift from mathematical modelling to data-driven methods based on Machine Learning. This led to improvements in performance and robustness of the detection algorithms. Nonetheless, most Machine Learning methods are general-purpose and they do not exploit the specificity of the delineation problem. In this thesis, we present learning methods suited for this task and we apply them to various kinds of microscopic and natural images, proving the general applicability of the presented solutions. First, we introduce a topology loss - a new training loss term, which captures higher-level features of curvilinear networks such as smoothness, connectivity and continuity. This is in contrast to most Deep Learning segmentation methods that do not take into account the geometry of the resulting prediction. In order to compute the new loss term, we extract topology features of prediction and ground-truth using a pre-trained network, whose filters are activated by structures at different scales and orientations. We show that this approach yields better results in terms of conventional segmentation metrics and overall topology of the resulting delineation. Although segmentation of curvilinear structures provides useful information, it is not always sufficient. In many cases, such as neuroscience and cartography, it is crucial to estimate the network connectivity. In order to find the graph representation of the structure depicted in the image, we propose an approach for joint segmentation and connection classification. Apart from pixel probabilities, this approach also returns the likelihood of a proposed path being a part of the reconstructed network. We show that segmentation and path classification are closely related tasks and can benefit from the synergy. The aforementioned methods rely on Machine Learning, which requires significant amounts of annotated ground-truth data to train models. The labelling process often requires expertise, it is costly and tiresome. To alleviate this problem, we introduce an Active Learning method that significantly decreases the time spent on annotating images. It queries the annotator only about the most informative examples, in this case the hypothetical paths belonging to the structure of interest. Contrary to conventional Active Learning methods, our approach exploits local consistency of linear paths to pick the ones that stand out from their neighborhood. Our final contribution is a method suited for both Active Learning and proofreading the result, which often requires more time than the automated delineation itself. It investigates edges of the delineation graph and determines the ones that are especially significant for the global reconstruction by perturbing their weights. Our Active Learning and proofreading strategies are combined with a new efficient formulation of an optimal subgraph computation and reduce the annotation effort by up to 80%.

EPFL2019

GarNet: A Two-Stream Network for Fast and Accurate 3D Cloth Draping

Victor Constantin, Pascal Fua, Erhan Gündogdu, Mathieu Salzmann

While Physics-Based Simulation (PBS) can accurately drape a 3D garment on a 3D body, it remains too costly for real-time applications, such as virtual try-on. By contrast, inference in a deep network, requiring a single forward pass, is much faster. Taking advantage of this, we propose a novel architecture to fit a 3D garment template to a 3D body. Specifically, we build upon the recent progress in 3D point cloud processing with deep networks to extract garment features at varying levels of detail, including point-wise, patch-wise and global features. We fuse these features with those extracted in parallel from the 3D body, so as to model the cloth-body interactions. The resulting two-stream architecture, which we call as GarNet, is trained using a loss function inspired by physics-based modeling, and delivers visually plausible garment shapes whose 3D points are, on average, less than 1 cm away from those of a PBS method, while running 100 times faster. Moreover, the proposed method can model various garment types with different cutting patterns when parameters of those patterns are given as input to the network.

IEEE2019

Learning to Segment 3D Linear Structures Using Only 2D Annotations

Pascal Fua, Mateusz Kozinski, Agata Justyna Mosinska, Mathieu Salzmann

We propose a loss function for training a Deep Neural Network (DNN) to segment volumetric data, that accommodates ground truth annotations of 2D projections of the training volumes, instead of annotations of the 3D volumes themselves. In consequence, we significantly decrease the amount of annotations needed for a given training set. We apply the proposed loss to train DNNs for segmentation of vascular and neural networks in microscopy images and demonstrate only a marginal accuracy loss associated to the significant reduction of the annotation effort. The lower labor cost of deploying DNNs, brought in by our method, can contribute to a wide adoption of these techniques for analysis of 3D images of linear structures.

SPRINGER INTERNATIONAL PUBLISHING AG2018

Learning Approach to Delineation of Curvilinear Structures in 2D and 3D Images

Agata Justyna Mosinska

EPFL2019