Image registration and visualization of in situ gene expression images.

In the age of high-throughput molecular biology techniques, scientists have incorporated the methodology of in-situ hybridization to map spatial patterns of gene expression. In order to compare expression patterns within a common tissue structure, these images need to be registered or organized into a common coordinate system for alignment to a reference or atlas images. We use three different image registration methodologies (manual; correlation based; mutual information based) to determine the common coordinate system for the reference and in-situ hybridization images. All three methodologies are incorporated into a Matlab tool to visualize the results in a user friendly way and save them for future work. Our results suggest that the user-defined landmark method is best when considering images from different modalities; automated landmark detection is best when the images are expected to have a high degree of consistency; and the mutual information methodology is useful when the images are from the same modality

An Evolutionary Approach to Adaptive Image Analysis for Retrieving and Long-term Monitoring Historical Land Use from Spatiotemporally Heterogeneous Map Sources

Land use changes have become a major contributor to the anthropogenic global change. The ongoing dispersion and concentration of the human species, being at their orders unprecedented, have indisputably altered Earth’s surface and atmosphere. The effects are so salient and irreversible that a new geological epoch, following the interglacial Holocene, has been announced: the Anthropocene. While its onset is by some scholars dated back to the Neolithic revolution, it is commonly referred to the late 18th century. The rapid development since the industrial revolution and its implications gave rise to an increasing awareness of the extensive anthropogenic land change and led to an urgent need for sustainable strategies for land use and land management. By preserving of landscape and settlement patterns at discrete points in time, archival geospatial data sources such as remote sensing imagery and historical geotopographic maps, in particular, could give evidence of the dynamic land use change during this crucial period. In this context, this thesis set out to explore the potentials of retrospective geoinformation for monitoring, communicating, modeling and eventually understanding the complex and gradually evolving processes of land cover and land use change. Currently, large amounts of geospatial data sources such as archival maps are being worldwide made online accessible by libraries and national mapping agencies. Despite their abundance and relevance, the usage of historical land use and land cover information in research is still often hindered by the laborious visual interpretation, limiting the temporal and spatial coverage of studies. Thus, the core of the thesis is dedicated to the computational acquisition of geoinformation from archival map sources by means of digital image analysis. Based on a comprehensive review of literature as well as the data and proposed algorithms, two major challenges for long-term retrospective information acquisition and change detection were identified: first, the diversity of geographical entity representations over space and time, and second, the uncertainty inherent to both the data source itself and its utilization for land change detection. To address the former challenge, image segmentation is considered a global non-linear optimization problem. The segmentation methods and parameters are adjusted using a metaheuristic, evolutionary approach. For preserving adaptability in high level image analysis, a hybrid model- and data-driven strategy, combining a knowledge-based and a neural net classifier, is recommended. To address the second challenge, a probabilistic object- and field-based change detection approach for modeling the positional, thematic, and temporal uncertainty adherent to both data and processing, is developed. Experimental results indicate the suitability of the methodology in support of land change monitoring. In conclusion, potentials of application and directions for further research are given

Going Deep in Medical Image Analysis: Concepts, Methods, Challenges and Future Directions

Medical Image Analysis is currently experiencing a paradigm shift due to Deep Learning. This technology has recently attracted so much interest of the Medical Imaging community that it led to a specialized conference in `Medical Imaging with Deep Learning' in the year 2018. This article surveys the recent developments in this direction, and provides a critical review of the related major aspects. We organize the reviewed literature according to the underlying Pattern Recognition tasks, and further sub-categorize it following a taxonomy based on human anatomy. This article does not assume prior knowledge of Deep Learning and makes a significant contribution in explaining the core Deep Learning concepts to the non-experts in the Medical community. Unique to this study is the Computer Vision/Machine Learning perspective taken on the advances of Deep Learning in Medical Imaging. This enables us to single out `lack of appropriately annotated large-scale datasets' as the core challenge (among other challenges) in this research direction. We draw on the insights from the sister research fields of Computer Vision, Pattern Recognition and Machine Learning etc.; where the techniques of dealing with such challenges have already matured, to provide promising directions for the Medical Imaging community to fully harness Deep Learning in the future

Brave New GES World:A Systematic Literature Review of Gestures and Referents in Gesture Elicitation Studies

How to determine highly effective and intuitive gesture sets for interactive systems tailored to end users’ preferences? A substantial body of knowledge is available on this topic, among which gesture elicitation studies stand out distinctively. In these studies, end users are invited to propose gestures for specific referents, which are the functions to control for an interactive system. The vast majority of gesture elicitation studies conclude with a consensus gesture set identified following a process of consensus or agreement analysis. However, the information about specific gesture sets determined for specific applications is scattered across a wide landscape of disconnected scientific publications, which poses challenges to researchers and practitioners to effectively harness this body of knowledge. To address this challenge, we conducted a systematic literature review and examined a corpus of N=267 studies encompassing a total of 187, 265 gestures elicited from 6, 659 participants for 4, 106 referents. To understand similarities in users’ gesture preferences within this extensive dataset, we analyzed a sample of 2, 304 gestures extracted from the studies identified in our literature review. Our approach consisted of (i) identifying the context of use represented by end users, devices, platforms, and gesture sensing technology, (ii) categorizing the referents, (iii) classifying the gestures elicited for those referents, and (iv) cataloging the gestures based on their representation and implementation modalities. Drawing from the findings of this review, we propose guidelines for conducting future end-user gesture elicitation studies

Uses and Challenges of Collecting LiDAR Data from a Growing Autonomous Vehicle Fleet: Implications for Infrastructure Planning and Inspection Practices

Autonomous vehicles (AVs) that utilize LiDAR (Light Detection and Ranging) and other sensing technologies are becoming an inevitable part of transportation industry. Concurrently, transportation agencies are increasingly challenged with the management and tracking of large-scale highway asset inventory. LiDAR has become popular among transportation agencies for highway asset management given its advantage over traditional surveying methods. The affordability of LiDAR technology is increasing day by day. Given this, there will be substantial challenges and opportunities for the utilization of big data resulting from the growth of AVs with LiDAR. A proper understanding of the data size generated from this technology will help agencies in making decisions regarding storage, management, and transmission of the data. The original raw data generated from the sensor shrinks a lot after filtering and processing following the Cache county Road Manual and storing into ASPRS recommended (.las) file format. In this pilot study, it is found that while considering the road centerline as the vehicle trajectory larger portion of the data fall into the right of way section compared to the actual vehicle trajectory in Cache County, UT. And there is a positive relation between the data size and vehicle speed in terms of the travel lanes section given the nature of the selected highway environment