From Calibration to Large-Scale Structure from Motion with Light Fields

Classic pinhole cameras project the multi-dimensional information of the light flowing through a scene onto a single 2D snapshot. This projection limits the information that can be reconstructed from the 2D acquisition. Plenoptic (or light field) cameras, on the other hand, capture a 4D slice of the plenoptic function, termed the “light field”. These cameras provide both spatial and angular information on the light flowing through a scene; multiple views are captured in a single photographic exposure facilitating various applications. This thesis is concerned with the modelling of light field (or plenoptic) cameras and the development of structure from motion pipelines using such cameras. Specifically, we develop a geometric model for a multi-focus plenoptic camera, followed by a complete pipeline for the calibration of the suggested model. Given a calibrated light field camera, we then remap the captured light field to a grid of pinhole images. We use these images to obtain metric 3D reconstruction through a novel framework for structure from motion with light fields. Finally, we suggest a linear and efficient approach for absolute pose estimation for light fields

Part-to-whole Registration of Histology and MRI using Shape Elements

Image registration between histology and magnetic resonance imaging (MRI) is a challenging task due to differences in structural content and contrast. Too thick and wide specimens cannot be processed all at once and must be cut into smaller pieces. This dramatically increases the complexity of the problem, since each piece should be individually and manually pre-aligned. To the best of our knowledge, no automatic method can reliably locate such piece of tissue within its respective whole in the MRI slice, and align it without any prior information. We propose here a novel automatic approach to the joint problem of multimodal registration between histology and MRI, when only a fraction of tissue is available from histology. The approach relies on the representation of images using their level lines so as to reach contrast invariance. Shape elements obtained via the extraction of bitangents are encoded in a projective-invariant manner, which permits the identification of common pieces of curves between two images. We evaluated the approach on human brain histology and compared resulting alignments against manually annotated ground truths. Considering the complexity of the brain folding patterns, preliminary results are promising and suggest the use of characteristic and meaningful shape elements for improved robustness and efficiency.Comment: Paper accepted at ICCV Workshop (Bio-Image Computing

Towards predicting Pedestrian Evacuation Time and Density from Floorplans using a Vision Transformer

Conventional pedestrian simulators are inevitable tools in the design process of a building, as they enable project engineers to prevent overcrowding situations and plan escape routes for evacuation. However, simulation runtime and the multiple cumbersome steps in generating simulation results are potential bottlenecks during the building design process. Data-driven approaches have demonstrated their capability to outperform conventional methods in speed while delivering similar or even better results across many disciplines. In this work, we present a deep learning-based approach based on a Vision Transformer to predict density heatmaps over time and total evacuation time from a given floorplan. Specifically, due to limited availability of public datasets, we implement a parametric data generation pipeline including a conventional simulator. This enables us to build a large synthetic dataset that we use to train our architecture. Furthermore, we seamlessly integrate our model into a BIM-authoring tool to generate simulation results instantly and automatically

A Linear Approach to Absolute Pose Estimation for Light Fields

This paper presents the first absolute pose estimation approach tailored to Light Field cameras. It builds on the observation that the ratio between the disparity arising in different sub-aperture images and their corresponding baseline is constant. Hence, we augment the 2D pixel coordinates with the corresponding normalised disparity to obtain the Light Field feature. This new representation reduces the effect of noise by aggregating multiple projections and allows for linear estimation of the absolute pose of a Light Field camera using the well-known Direct Linear Transformation algorithm. We evaluate the resulting absolute pose estimates with extensive simulations and experiments involving real Light Field datasets, demonstrating the competitive performance of our linear approach. Furthermore, we integrate our approach in a state-of-the-art Light Field Structure from Motion pipeline and demonstrate accurate multi-view 3D reconstruction

Corner-Based Geometric Calibration of Multi-focus Plenoptic Cameras

We propose a method for geometric calibration of multi-focus plenoptic cameras using raw images. Multi-focus plenoptic cameras feature several types of micro-lenses spatially aligned in front of the camera sensor to generate micro-images at different magnifications. This multi-lens arrangement provides computational-photography benefits but complicates calibration. Our methodology achieves the detection of the type of micro-lenses, the retrieval of their spatial arrangement, and the estimation of intrinsic and extrinsic camera parameters therefore fully characterising this specialised camera class. Motivated from classic pinhole camera calibration, our algorithm operates on a checker-board's corners, retrieved by a custom micro-image corner detector. This approach enables the introduction of a reprojection error that is used in a minimisation framework. Our algorithm compares favourably to the state-of-the-art, as demonstrated by controlled and freehand experiments, making it a first step towards accurate 3D reconstruction and Structure-from-Motion

Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing

Meagre (Argyrosomus regius), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax, traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production.info:eu-repo/semantics/publishedVersio

Substance deposition assessment in obstructed pulmonary system through numerical characterization of airflow and inhaled particles attributes

Background Chronic obstructive pulmonary disease (COPD) and asthma are considered as the two most widespread obstructive lung diseases, whereas they affect more than 500 million people worldwide. Unfortunately, the requirement for detailed geometric models of the lungs in combination with the increased computational resources needed for the simulation of the breathing did not allow great progress to be made in the past for the better understanding of inflammatory diseases of the airways through detailed modelling approaches. In this context, computational fluid dynamics (CFD) simulations accompanied by fluid particle tracing (FPT) analysis of the inhaled ambient particles are deemed critical for lung function assessment. Also they enable the understanding of particle depositions on the airways of patients, since these accumulations may affect or lead to inflammations. In this direction, the current study conducts an initial investigation for the better comprehension of particle deposition within the lungs. More specifically, accurate models of the airways obstructions that relate to pulmonary disease are developed and a thorough assessment of the airflow behavior together with identification of the effects of inhaled particle properties, such as size and density, is conducted. Our approach presents a first step towards an effective personalization of pulmonary treatment in regards to the geometric characteristics of the lungs and the in depth understanding of airflows within the airways. Methods A geometry processing technique involving contraction algorithms is established and used to employ the different respiratory arrangements associated with lung related diseases that exhibit airways obstructions. Apart from the normal lung case, two categories of obstructed cases are examined, i.e. models with obstructions in both lungs and models with narrowings in the right lung only. Precise assumptions regarding airflow and deposition fraction (DF) over various sections of the lungs are drawn by simulating these distinct incidents through the finite volume method (FVM) and particularly the CFD and FPT algorithms. Moreover, a detailed parametric analysis clarifies the effects of the particles size and density in terms of regional deposition upon several parts of the pulmonary system. In this manner, the deposition pattern of various substances can be assessed. Results For the specific case of the unobstructed lung model most particles are detected on the right lung (48.56% of total, when the air flowrate is 12.6 L/min), a fact that is also true when obstructions arise symmetrically in both lungs (51.45% of total, when the air flowrate is 6.06 L/min and obstructions occur after the second generation). In contrast, when narrowings are developed on the right lung only, most particles are pushed on the left section (68.22% of total, when the air flowrate is 11.2 L/min) indicating that inhaled medication is generally deposited away from the areas of inflammation. This observation is useful when designing medical treatment of lung diseases. Furthermore, particles with diameters from 1 μm to 10 μm are shown to be mainly deposited on the lower airways, whereas particles with diameters of 20 μm and 30 μm are mostly accumulated in the upper airways. As a result, the current analysis indicates increased DF levels in the upper airways when the particle diameter is enlarged. Additionally, when the particles density increases from 1000 Kg/m3 to 2000 Kg/m3, the DF is enhanced on every generation and for all cases investigated herein. The results obtained by our simulations provide an accurate and quantitative estimation of all important parameters involved in lung modeling. Conclusions The treatment of respiratory diseases with inhaled medical substances can be advanced by the clinical use of accurate CFD and FPT simulations and specifically by evaluating the deposition of inhaled particles in a regional oriented perspective in regards to different particle sizes and particle densities. Since a drug with specific characteristics (i.e. particle size and density) exhibits maximum deposition on particular lung areas, the current study provides initial indications to a qualified physician for proper selection of medication