To efficiently establish training databases for machine learning methods, collaborative and crowdsourcing platforms have been investigated to collectively tackle the annotation effort. However, when this concept is ported to the medical imaging domain, reading expertise will have a direct impact on the annotation accuracy. In this study, we examine the impact of expertise and the amount of available annotations on the accuracy outcome of a liver segmentation problem in an abdominal computed tomography (CT) image database. In controlled experiments, we study this impact for different types of weak annotations. To address the decrease in accuracy associated with lower expertise, we propose a method for outlier correction making use of a weakly labelled atlas. Using this approach, we demonstrate that weak annotations subject to high error rates can achieve a similarly high accuracy as state-of-the-art multi-atlas segmentation approaches relying on a large amount of expert manual segmentations. Annotations of this nature can realistically be obtained from a non-expert crowd and can potentially enable crowdsourcing of weak annotation tasks for medical image analysis.
To reduce the annotation effort, many well-known studies propose segmentation methods employing simple forms of user annotations to obtain voxel-wise segmentations . While adjusting hyperparameters can be considered an interaction, in this study we concentrate on simplified forms of pictorial input , called weak annotations (WA). Such annotations have been extensively used in the literature, particularly in the context of medical object segmentation problems. @cite_5 used user-provided scribbles (SC) or brush strokes as input and hard constraints to an interactive graphical segmentation problem. Similarly, @cite_6 , @cite_2 and @cite_7 expressed this problem in a spatially continuous setting by using prior region ordering constraints and exploiting parallelism via GPU computing. The GrabCut algorithm employs rectangular regions (RR) as bounding boxes to both compute a colour appearance model and spatially constrain the search for an object. These spatial constraints further allow to reduce the computational effort . The segmentation platform ITK-SNAP combines RR with SC and employs a pre-segmentation (PS) to initialise an active contour model.
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In this paper, we propose DeepCut, a method to obtain pixelwise object segmentations given an image dataset labelled weak annotations, in our case bounding boxes. It extends the approach of the well-known GrabCut[1] method to include machine learning by training a neural network classifier from bounding box annotations. We formulate the problem as an energy minimisation problem over a densely-connected conditional random field and iteratively update the training targets to obtain pixelwise object segmentations. Additionally, we propose variants of the DeepCut method and compare those to a naive approach to CNN training under weak supervision. We test its applicability to solve brain and lung segmentation problems on a challenging fet al magnetic resonance dataset and obtain encouraging results in terms of accuracy. In this paper, we propose DeepCut, a method to obtain pixelwise object segmentations given an image dataset labelled with bounding box annotations. It extends the approach of the well-known GrabCut method to include machine learning by training a neural network classifier from bounding box annotations. We formulate the problem as an energy minimisation problem over a densely-connected conditional random field and iteratively update the training targets to obtain pixelwise object segmentations. Additionally, we propose variants of the DeepCut method and compare those to a naive approach to CNN training under weak supervision. We test its applicability to solve brain and lung segmentation problems on a challenging fet al magnetic resonance dataset and obtain encouraging results in terms of accuracy. Extracting 3D shape of deforming objects in monocular videos, a task known as non-rigid structure-from-motion (NRSfM), has so far been studied only on synthetic datasets and controlled environments. Typically, the objects to reconstruct are pre-segmented, they exhibit limited rotations and occlusions, or full-length trajectories are assumed. In order to integrate NRSfM into current video analysis pipelines, one needs to consider as input realistic -thus incomplete- tracking, and perform spatio-temporal grouping to segment the objects from their surroundings. Furthermore, NRSfM needs to be robust to noise in both segmentation and tracking, e.g., drifting, segmentation "leaking", optical flow "bleeding" etc. In this paper, we make a first attempt towards this goal, and propose a method that combines dense optical flow tracking, motion trajectory clustering and NRSfM for 3D reconstruction of objects in videos. For each trajectory cluster, we compute multiple reconstructions by minimizing the reprojection error and the rank of the 3D shape under different rank bounds of the trajectory matrix. We show that dense 3D shape is extracted and trajectories are completed across occlusions and low textured regions, even under mild relative motion between the object and the camera. We achieve competitive results on a public NRSfM benchmark while using fixed parameters across all sequences and handling incomplete trajectories, in contrast to existing approaches. We further test our approach on popular video segmentation datasets. To the best of our knowledge, our method is the first to extract dense object models from realistic videos, such as those found in Youtube or Hollywood movies, without object-specific priors. In this paper, we propose a non-local structured prior for volumetric multi-view 3D reconstruction. Towards this goal, we present a novel Markov random field model based on ray potentials in which assumptions about large 3D surface patches such as planarity or Manhattan world constraints can be efficiently encoded as probabilistic priors. We further derive an inference algorithm that reasons jointly about voxels, pixels and image segments, and estimates marginal distributions of appearance, occupancy, depth, normals and planarity. Key to tractable inference is a novel hybrid representation that spans both voxel and pixel space and that integrates non-local information from 2D image segmentations in a principled way. We compare our non-local prior to commonly employed local smoothness assumptions and a variety of state-of-the-art volumetric reconstruction baselines on challenging outdoor scenes with textureless and reflective surfaces. Our experiments indicate that regularizing over larger distances has the potential to resolve ambiguities where local regularizers fail.