PVR: Patch-to-Volume Reconstruction for Large Area Motion Correction of Fetal MRI

In this paper we present a novel method for the correction of motion artifacts that are present in fetal Magnetic Resonance Imaging (MRI) scans of the whole uterus. Contrary to current slice-to-volume registration (SVR) methods, requiring an inflexible anatomical enclosure of a single investigated organ, the proposed patch-to-volume reconstruction (PVR) approach is able to reconstruct a large field of view of non-rigidly deforming structures. It relaxes rigid motion assumptions by introducing a specific amount of redundant information that is exploited with parallelized patch-wise optimization, super-resolution, and automatic outlier rejection. We further describe and provide an efficient parallel implementation of PVR allowing its execution within reasonable time on commercially available graphics processing units (GPU), enabling its use in the clinical practice. We evaluate PVR's computational overhead compared to standard methods and observe improved reconstruction accuracy in presence of affine motion artifacts of approximately 30% compared to conventional SVR in synthetic experiments. Furthermore, we have evaluated our method qualitatively and quantitatively on real fetal MRI data subject to maternal breathing and sudden fetal movements. We evaluate peak-signal-to-noise ratio (PSNR), structural similarity index (SSIM), and cross correlation (CC) with respect to the originally acquired data and provide a method for visual inspection of reconstruction uncertainty. With these experiments we demonstrate successful application of PVR motion compensation to the whole uterus, the human fetus, and the human placenta.Comment: 10 pages, 13 figures, submitted to IEEE Transactions on Medical Imaging. v2: wadded funders acknowledgements to preprin

Fast, Dense Feature SDM on an iPhone

In this paper, we present our method for enabling dense SDM to run at over 90 FPS on a mobile device. Our contributions are two-fold. Drawing inspiration from the FFT, we propose a Sparse Compositional Regression (SCR) framework, which enables a significant speed up over classical dense regressors. Second, we propose a binary approximation to SIFT features. Binary Approximated SIFT (BASIFT) features, which are a computationally efficient approximation to SIFT, a commonly used feature with SDM. We demonstrate the performance of our algorithm on an iPhone 7, and show that we achieve similar accuracy to SDM

Sparse representations of image gradient orientations for visual recognition and tracking

Recent results [18] have shown that sparse linear representations of a query object with respect to an overcomplete basis formed by the entire gallery of objects of interest can result in powerful image-based object recognition schemes. In this paper, we propose a framework for visual recognition and tracking based on sparse representations of image gradient orientations. We show that minimal `1 solutions to problems formulated with gradient orientations can be used for fast and robust object recognition even for probe objects corrupted by outliers. These solutions are obtained without the need for solving the extended problem considered in [18]. We further show that low-dimensional embeddings generated from gradient orientations perform equally well even when probe objects are corrupted by outliers, which, in turn, results in huge computational savings. We demonstrate experimentally that, compared to the baseline method in [18], our formulation results in better recognition rates without the need for block processing and even with smaller number of training samples. Finally, based on our results, we also propose a robust and efficient `1-based “tracking by detection” algorithm. We show experimentally that our tracker outperforms a recently proposed `1-based tracking algorithm in terms of robustness, accuracy and speed

To Learn or Not to Learn Features for Deformable Registration?

Feature-based registration has been popular with a variety of features ranging from voxel intensity to Self-Similarity Context (SSC). In this paper, we examine the question on how features learnt using various Deep Learning (DL) frameworks can be used for deformable registration and whether this feature learning is necessary or not. We investigate the use of features learned by different DL methods in the current state-of-the-art discrete registration framework and analyze its performance on 2 publicly available datasets. We draw insights into the type of DL framework useful for feature learning and the impact, if any, of the complexity of different DL models and brain parcellation methods on the performance of discrete registration. Our results indicate that the registration performance with DL features and SSC are comparable and stable across datasets whereas this does not hold for low level features.Comment: 9 pages, 4 figure

Efficient Bayesian-based Multi-View Deconvolution

Light sheet fluorescence microscopy is able to image large specimen with high resolution by imaging the sam- ples from multiple angles. Multi-view deconvolution can significantly improve the resolution and contrast of the images, but its application has been limited due to the large size of the datasets. Here we present a Bayesian- based derivation of multi-view deconvolution that drastically improves the convergence time and provide a fast implementation utilizing graphics hardware.Comment: 48 pages, 20 figures, 1 table, under review at Nature Method