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

Structured Light-Based 3D Reconstruction System for Plants.

Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance

Online Mutual Foreground Segmentation for Multispectral Stereo Videos

The segmentation of video sequences into foreground and background regions is a low-level process commonly used in video content analysis and smart surveillance applications. Using a multispectral camera setup can improve this process by providing more diverse data to help identify objects despite adverse imaging conditions. The registration of several data sources is however not trivial if the appearance of objects produced by each sensor differs substantially. This problem is further complicated when parallax effects cannot be ignored when using close-range stereo pairs. In this work, we present a new method to simultaneously tackle multispectral segmentation and stereo registration. Using an iterative procedure, we estimate the labeling result for one problem using the provisional result of the other. Our approach is based on the alternating minimization of two energy functions that are linked through the use of dynamic priors. We rely on the integration of shape and appearance cues to find proper multispectral correspondences, and to properly segment objects in low contrast regions. We also formulate our model as a frame processing pipeline using higher order terms to improve the temporal coherence of our results. Our method is evaluated under different configurations on multiple multispectral datasets, and our implementation is available online.Comment: Preprint accepted for publication in IJCV (December 2018

EchoFusion: Tracking and Reconstruction of Objects in 4D Freehand Ultrasound Imaging without External Trackers

Ultrasound (US) is the most widely used fetal imaging technique. However, US images have limited capture range, and suffer from view dependent artefacts such as acoustic shadows. Compounding of overlapping 3D US acquisitions into a high-resolution volume can extend the field of view and remove image artefacts, which is useful for retrospective analysis including population based studies. However, such volume reconstructions require information about relative transformations between probe positions from which the individual volumes were acquired. In prenatal US scans, the fetus can move independently from the mother, making external trackers such as electromagnetic or optical tracking unable to track the motion between probe position and the moving fetus. We provide a novel methodology for image-based tracking and volume reconstruction by combining recent advances in deep learning and simultaneous localisation and mapping (SLAM). Tracking semantics are established through the use of a Residual 3D U-Net and the output is fed to the SLAM algorithm. As a proof of concept, experiments are conducted on US volumes taken from a whole body fetal phantom, and from the heads of real fetuses. For the fetal head segmentation, we also introduce a novel weak annotation approach to minimise the required manual effort for ground truth annotation. We evaluate our method qualitatively, and quantitatively with respect to tissue discrimination accuracy and tracking robustness.Comment: MICCAI Workshop on Perinatal, Preterm and Paediatric Image analysis (PIPPI), 201

Fast Monte-Carlo Localization on Aerial Vehicles using Approximate Continuous Belief Representations

Size, weight, and power constrained platforms impose constraints on computational resources that introduce unique challenges in implementing localization algorithms. We present a framework to perform fast localization on such platforms enabled by the compressive capabilities of Gaussian Mixture Model representations of point cloud data. Given raw structural data from a depth sensor and pitch and roll estimates from an on-board attitude reference system, a multi-hypothesis particle filter localizes the vehicle by exploiting the likelihood of the data originating from the mixture model. We demonstrate analysis of this likelihood in the vicinity of the ground truth pose and detail its utilization in a particle filter-based vehicle localization strategy, and later present results of real-time implementations on a desktop system and an off-the-shelf embedded platform that outperform localization results from running a state-of-the-art algorithm on the same environment