Deformable Registration through Learning of Context-Specific Metric Aggregation

We propose a novel weakly supervised discriminative algorithm for learning context specific registration metrics as a linear combination of conventional similarity measures. Conventional metrics have been extensively used over the past two decades and therefore both their strengths and limitations are known. The challenge is to find the optimal relative weighting (or parameters) of different metrics forming the similarity measure of the registration algorithm. Hand-tuning these parameters would result in sub optimal solutions and quickly become infeasible as the number of metrics increases. Furthermore, such hand-crafted combination can only happen at global scale (entire volume) and therefore will not be able to account for the different tissue properties. We propose a learning algorithm for estimating these parameters locally, conditioned to the data semantic classes. The objective function of our formulation is a special case of non-convex function, difference of convex function, which we optimize using the concave convex procedure. As a proof of concept, we show the impact of our approach on three challenging datasets for different anatomical structures and modalities.Comment: Accepted for publication in the 8th International Workshop on Machine Learning in Medical Imaging (MLMI 2017), in conjunction with MICCAI 201

Geometric Multi-Model Fitting with a Convex Relaxation Algorithm

We propose a novel method to fit and segment multi-structural data via convex relaxation. Unlike greedy methods --which maximise the number of inliers-- this approach efficiently searches for a soft assignment of points to models by minimising the energy of the overall classification. Our approach is similar to state-of-the-art energy minimisation techniques which use a global energy. However, we deal with the scaling factor (as the number of models increases) of the original combinatorial problem by relaxing the solution. This relaxation brings two advantages: first, by operating in the continuous domain we can parallelize the calculations. Second, it allows for the use of different metrics which results in a more general formulation. We demonstrate the versatility of our technique on two different problems of estimating structure from images: plane extraction from RGB-D data and homography estimation from pairs of images. In both cases, we report accurate results on publicly available datasets, in most of the cases outperforming the state-of-the-art

DeepCut: Object Segmentation from Bounding Box Annotations using Convolutional Neural Networks

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 fetal magnetic resonance dataset and obtain encouraging results in terms of accuracy

R3^3SGM: Real-time Raster-Respecting Semi-Global Matching for Power-Constrained Systems

Stereo depth estimation is used for many computer vision applications. Though many popular methods strive solely for depth quality, for real-time mobile applications (e.g. prosthetic glasses or micro-UAVs), speed and power efficiency are equally, if not more, important. Many real-world systems rely on Semi-Global Matching (SGM) to achieve a good accuracy vs. speed balance, but power efficiency is hard to achieve with conventional hardware, making the use of embedded devices such as FPGAs attractive for low-power applications. However, the full SGM algorithm is ill-suited to deployment on FPGAs, and so most FPGA variants of it are partial, at the expense of accuracy. In a non-FPGA context, the accuracy of SGM has been improved by More Global Matching (MGM), which also helps tackle the streaking artifacts that afflict SGM. In this paper, we propose a novel, resource-efficient method that is inspired by MGM's techniques for improving depth quality, but which can be implemented to run in real time on a low-power FPGA. Through evaluation on multiple datasets (KITTI and Middlebury), we show that in comparison to other real-time capable stereo approaches, we can achieve a state-of-the-art balance between accuracy, power efficiency and speed, making our approach highly desirable for use in real-time systems with limited power.Comment: Accepted in FPT 2018 as Oral presentation, 8 pages, 6 figures, 4 table

Inference by Learning: Speeding-up Graphical Model Optimization via a Coarse-to-Fine Cascade of Pruning Classifiers

We propose a general and versatile framework that significantly speeds-up graphical model optimization while maintaining an excellent solution accuracy. The proposed approach, refereed as Inference by Learning or in short as IbyL, relies on a multi-scale pruning scheme that progressively reduces the solution space by use of a coarse-to-fine cascade of learnt classifiers. We thoroughly experiment with classic computer vision related MRF problems, where our novel framework constantly yields a significant time speed-up (with respect to the most efficient inference methods) and obtains a more accurate solution than directly optimizing the MRF. We make our code available on-line [4]

Three-dimensional X-ray imaging and analysis of fungi on and in wood

As wood is prone to fungal degradation, fundamental research is necessary to increase our knowledge aiming at product improvement. Several imaging modalities are capable of visualizing fungi, but the X-ray equipment presented in this paper can envisage fungal mycelium in wood non-destructively in three dimensions with sub-micron resolution. Four types of wood subjected to the action of the white rot fungus Coriolus versicolor (Linnaeus) Quélet (CTB 863 A) were scanned using an X-ray based approach. Comparison of wood volumes before and after fungal exposure, segmented manually or semi-automatically, showed the presence of the fungal mass on and in the wood samples and therefore demonstrated the usefulness of computed X-ray tomography for mycological and wood research. Further improvements to the experimental set-up are necessary in order to resolve individual hyphae and enhance segmentation