Capturing natural-colour 3D models of insects for species discovery

Collections of biological specimens are fundamental to scientific understanding and characterization of natural diversity. This paper presents a system for liberating useful information from physical collections by bringing specimens into the digital domain so they can be more readily shared, analyzed, annotated and compared. It focuses on insects and is strongly motivated by the desire to accelerate and augment current practices in insect taxonomy which predominantly use text, 2D diagrams and images to describe and characterize species. While these traditional kinds of descriptions are informative and useful, they cannot cover insect specimens "from all angles" and precious specimens are still exchanged between researchers and collections for this reason. Furthermore, insects can be complex in structure and pose many challenges to computer vision systems. We present a new prototype for a practical, cost-effective system of off-the-shelf components to acquire natural-colour 3D models of insects from around 3mm to 30mm in length. Colour images are captured from different angles and focal depths using a digital single lens reflex (DSLR) camera rig and two-axis turntable. These 2D images are processed into 3D reconstructions using software based on a visual hull algorithm. The resulting models are compact (around 10 megabytes), afford excellent optical resolution, and can be readily embedded into documents and web pages, as well as viewed on mobile devices. The system is portable, safe, relatively affordable, and complements the sort of volumetric data that can be acquired by computed tomography. This system provides a new way to augment the description and documentation of insect species holotypes, reducing the need to handle or ship specimens. It opens up new opportunities to collect data for research, education, art, entertainment, biodiversity assessment and biosecurity control.Comment: 24 pages, 17 figures, PLOS ONE journa

Mesh-based 3D Textured Urban Mapping

In the era of autonomous driving, urban mapping represents a core step to let vehicles interact with the urban context. Successful mapping algorithms have been proposed in the last decade building the map leveraging on data from a single sensor. The focus of the system presented in this paper is twofold: the joint estimation of a 3D map from lidar data and images, based on a 3D mesh, and its texturing. Indeed, even if most surveying vehicles for mapping are endowed by cameras and lidar, existing mapping algorithms usually rely on either images or lidar data; moreover both image-based and lidar-based systems often represent the map as a point cloud, while a continuous textured mesh representation would be useful for visualization and navigation purposes. In the proposed framework, we join the accuracy of the 3D lidar data, and the dense information and appearance carried by the images, in estimating a visibility consistent map upon the lidar measurements, and refining it photometrically through the acquired images. We evaluate the proposed framework against the KITTI dataset and we show the performance improvement with respect to two state of the art urban mapping algorithms, and two widely used surface reconstruction algorithms in Computer Graphics.Comment: accepted at iros 201

Unsupervised Monocular Depth Estimation with Left-Right Consistency

Learning based methods have shown very promising results for the task of depth estimation in single images. However, most existing approaches treat depth prediction as a supervised regression problem and as a result, require vast quantities of corresponding ground truth depth data for training. Just recording quality depth data in a range of environments is a challenging problem. In this paper, we innovate beyond existing approaches, replacing the use of explicit depth data during training with easier-to-obtain binocular stereo footage. We propose a novel training objective that enables our convolutional neural network to learn to perform single image depth estimation, despite the absence of ground truth depth data. Exploiting epipolar geometry constraints, we generate disparity images by training our network with an image reconstruction loss. We show that solving for image reconstruction alone results in poor quality depth images. To overcome this problem, we propose a novel training loss that enforces consistency between the disparities produced relative to both the left and right images, leading to improved performance and robustness compared to existing approaches. Our method produces state of the art results for monocular depth estimation on the KITTI driving dataset, even outperforming supervised methods that have been trained with ground truth depth.Comment: CVPR 2017 ora

High-resolution ab initio three-dimensional X-ray diffraction microscopy

Coherent X-ray diffraction microscopy is a method of imaging non-periodic isolated objects at resolutions only limited, in principle, by the largest scattering angles recorded. We demonstrate X-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the 3D diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a non-periodic object. We also construct 2D images of thick objects with infinite depth of focus (without loss of transverse spatial resolution). These methods can be used to image biological and materials science samples at high resolution using X-ray undulator radiation, and establishes the techniques to be used in atomic-resolution ultrafast imaging at X-ray free-electron laser sources.Comment: 22 pages, 11 figures, submitte