Three-dimensional quantification and visualization of vascular networks in engineered tissues

Three-dimensional textural and volumetric image analysis holds great potential in understanding the image data produced by multi-photon microscopy. In this thesis, a tool that provides quantitative textural and morphometric analyzes of vasculature in engineered tissues, alongside with a fast three-dimensional volume rendering is proposed. The investigated 3D artificial tissues consist of Human Umbilical Vein Endothelial Cells (HUVEC) embedded in collagen exposed to two regimes of ultrasound standing wave fields under different pressure conditions. Textural features were evaluated over the extracted connected region in our samples using the normalized Gray Level Co-occurrence Matrix (GLCM) combined with Gray-Level Run Length Matrix (GLRLM) analysis. To minimize the error resulting from any possible volumetric rotation and to provide a comprehensive textural analysis, an averaged version of nine GLCM and GLRLM orientations is used. To evaluate volumetric features, parameters such as volume run length and percentage volume were utilized. The z-projection versions of the samples were used to estimate the tortuosity of the vessels, as well as, to measure the length and the angle of the branches. We utilized a three-dimensional volume rendering technique named MATVTK (derived from MATLAB and VTK) and runs under MATLAB that shows a great improvement on the processing time to reconstruct our volumes compared to MATLAB built-in functions. Results show that our analysis is able to differentiate among the exposed samples, due to morphological changes induced by the ultrasound standing wave fields. Furthermore, we demonstrate that providing more textural parameters than what is currently being reported in the literature, enhances the quantitative understanding of the heterogeneity of artificial tissues

Deep Learning Methods for 3D Aerial and Satellite Data

Recent advances in digital electronics have led to an overabundance of observations from electro-optical (EO) imaging sensors spanning high spatial, spectral and temporal resolution. This unprecedented volume, variety, and velocity is overwhelming our capacity to manage and translate that data into actionable information. Although decades of image processing research have taken the human out of the loop for many important tasks, the human analyst is still an irreplaceable link in the image exploitation chain, especially for more complex tasks requiring contextual understanding, memory, discernment, and learning. If knowledge discovery is to keep pace with the growing availability of data, new processing paradigms are needed in order to automate the analysis of earth observation imagery and ease the burden of manual interpretation. To address this gap, this dissertation advances fundamental and applied research in deep learning for aerial and satellite imagery. We show how deep learning---a computational model inspired by the human brain---can be used for (1) tracking, (2) classifying, and (3) modeling from a variety of data sources including full-motion video (FMV), Light Detection and Ranging (LiDAR), and stereo photogrammetry. First we assess the ability of a bio-inspired tracking method to track small targets using aerial videos. The tracker uses three kinds of saliency maps: appearance, location, and motion. Our approach achieves the best overall performance, including being the only method capable of handling long-term occlusions. Second, we evaluate the classification accuracy of a multi-scale fully convolutional network to label individual points in LiDAR data. Our method uses only the 3D-coordinates and corresponding low-dimensional spectral features for each point. Evaluated using the ISPRS 3D Semantic Labeling Contest, our method scored second place with an overall accuracy of 81.6\%. Finally, we validate the prediction capability of our neighborhood-aware network to model the bare-earth surface of LiDAR and stereo photogrammetry point clouds. The network bypasses traditionally-used ground classifications and seamlessly integrate neighborhood features with point-wise and global features to predict a per point Digital Terrain Model (DTM). We compare our results with two widely used softwares for DTM extraction, ENVI and LAStools. Together, these efforts have the potential to alleviate the manual burden associated with some of the most challenging and time-consuming geospatial processing tasks, with implications for improving our response to issues of global security, emergency management, and disaster response

Uncertainty-aware Perception Models for Off-road Autonomous Unmanned Ground Vehicles

Off-road autonomous unmanned ground vehicles (UGVs) are being developed for military and commercial use to deliver crucial supplies in remote locations, help with mapping and surveillance, and to assist war-fighters in contested environments. Due to complexity of the off-road environments and variability in terrain, lighting conditions, diurnal and seasonal changes, the models used to perceive the environment must handle a lot of input variability. Current datasets used to train perception models for off-road autonomous navigation lack of diversity in seasons, locations, semantic classes, as well as time of day. We test the hypothesis that model trained on a single dataset may not generalize to other off-road navigation datasets and new locations due to the input distribution drift. Additionally, we investigate how to combine multiple datasets to train a semantic segmentation-based environment perception model and we show that training the model to capture uncertainty could improve the model performance by a significant margin. We extend the Masksembles approach for uncertainty quantification to the semantic segmentation task and compare it with Monte Carlo Dropout and standard baselines. Finally, we test the approach against data collected from a UGV platform in a new testing environment. We show that the developed perception model with uncertainty quantification can be feasibly deployed on an UGV to support online perception and navigation tasks