Our understanding of the complexity of the brain is limited by the data we can collect and analyze. Because of experimental limitations and a desire for greater detail, most investigations focus on just one aspect of the brain. For example, brain function can be studied at many levels of abstraction including, but not limited to, gene expression, protein interactions, anatomical regions, neuronal connectivity, synaptic plasticity, and the electrical activity of neurons. By focusing on each of these levels, neuroscience has built up a detailed picture of how the brain works, but each level is understood mostly in isolation from the others. It is likely that interaction between all these levels is just as important. Therefore, a key hypothesis is that functional units spanning multiple levels of biological organization exist in the brain. This project attempted to combine neuronal circuitry analysis with functional proteomics and anatomical regions of the brain to explore this hypothesis, and took an evolutionary view of the results obtained. During the process we had to solve a number of technical challenges as the tools to undertake this type of research did not exist. Two informatics challenges for this research were to develop ways to analyze neurobiological data, such as brain protein expression patterns, to extract useful information, and how to share and present this data in a way that is fast and easy for anyone to access. This project contributes towards a more wholistic understanding of the fruit fly brain in three ways. Firstly, a screen was conducted to record the expression of proteins in the brain of the fruit fly, Drosophila melanogaster. Protein expression patterns in the fruit fly brain were recorded from 535 protein trap lines using confocal microscopy. A total of 884 3D images were annotated and made available on an easy to use website database, BrainTrap, available at fruitfly.inf.ed.ac.uk/braintrap. The website allows 3D images of the protein expression to be viewed interactively in the web browser, and an ontology-based search tool allows users to search for protein expression patterns in specific areas of interest. Different expression patterns mapped to a common template can be viewed simultaneously in multiple colours. This data bridges the gap between anatomical and biomolecular levels of understanding. Secondly, protein trap expression patterns were used to investigate the properties of the fruit fly brain. Thousands of protein-protein interactions have been recorded by methods such as yeast two-hybrid, however many of these protein pairs do not express in the same regions of the fruit fly brain. Using 535 protein expression patterns it was possible to rule out 149 protein-protein interactions. Also, protein expression patterns registered against a common template brain were used to produce new anatomical breakdowns of the fruit fly brain. Clustering techniques were able to naturally segment brain regions based only on the protein expression data. This is just one example of how, by combining proteomics with anatomy, we were able to learn more about both levels of understanding. Results are analysed further in combination with networks such as genetic homology networks, and connectivity networks. We show how the wealth of biological and neuroscience data now available in public databases can be combined with the Brain- Trap data to reveal similarities between areas of the fruit fly and mammalian brain. The BrainTrap data also informs us on the process of evolution and we show that genes found in fruit fly, yeast and mouse are more likely to be generally expressed throughout the brain, whereas genes found only in fruit fly and mouse, but not yeast, are more likely to have a specific expression pattern in the fruit fly brain. Thus, by combining data from multiple sources we can gain further insight into the complexity of the brain. Neural connectivity data is also analyzed and a new technique for enhanced motifs is developed for the combined analysis of connectivity data with other information such as neuron type data and potentially protein expression data. Thirdly, I investigated techniques for imaging the protein trap lines at higher resolution using electron microscopy (EM) and developed new informatics techniques for the automated analysis of neural connectivity data collected from serial section transmission electron microscopy (ssTEM). Measurement of the connectivity between neurons requires high resolution imaging techniques, such as electron microscopy, and images produced by this method are currently annotated manually to produce very detailed maps of cell morphology and connectivity. This is an extremely time consuming process and the volume of tissue and number of neurons that can be reconstructed is severely limited by the annotation step. I developed a set of computer vision algorithms to improve the alignment between consecutive images, and to perform partial annotation automatically by detecting membrane, synapses and mitochondria present in the images. Accuracy of the automatic annotation was evaluated on a small dataset and 96% of membrane could be identified at the cost of 13% false positives. This research demonstrates that informatics technology can help us to automatically analyze biological images and bring together genetic, anatomical, and connectivity data in a meaningful way. This combination of multiple data sources reveals more detail about each individual level of understanding, and gives us a more wholistic view of the fruit fly brain.

The important roles of fluid dynamics in immersion lithography (IL) and step-and-flash imprint lithography (S FIL) are analyzed experimentally and theoretically. In IL there are many challenges with managing a fluid droplet between the lens and the wafer, including preventing separation of the fluid droplet from the lens and deposition of small droplets behind the lens. Fluid management is also critical in S FIL because the imprint fluid creates capillary and lubrication forces, both of which are primarily responsible for the dynamics of the template and fluid motion. The fluid flow and shape of the wafer determine how uniform the gap height between the wafer and the template is, and they affect the resistance during the alignment phase. IL was investigated as a methodology to improve laser lithography for making photomasks. The fluid flow in IL was investigated by building a test apparatus to simulate the motion of the fluid droplet during microlithographic production, and using this apparatus to conduct experiments on various immersion fluids and wafer topcoats to determine what instabilities would occur. A theoretical model was used to predict the fluid separation instabilities. Finite element simulations were also used to model the fluid droplet, and these simulations accurately predict the fluid instabilities and quantitatively agreed with the model and experiments. It is shown that the process is viable: capillary forces are sufficient to keep the fluid droplet stable, heating effects due to the laser are negligible, and other concerns such as evaporation and dissolution are manageable. Euler beam theory and the lubrication equation were used to model the bending of an S FIL template and the flow of the fluid between the template and a non-flat wafer. The template filling time, conformance of the template to the wafer, and the alignment phase are investigated with an analytical model and finite element simulations. Analysis and simulations show that uniformity of the residual film thickness and ease of proper alignment depend greatly on the planarity of the wafer, the properties of the template, and the surface tension of the fluid. / text

The aim of this master’s thesis is to describe the Robotic Vision for Bin Picking usage and creating an application for the realization of this task. This application will be able to distinguish several objects based on data from a camera with deep perception and should find the location of object, recognize it and determine its location and orientation. Bin Picking is one of the biggest challenges in today's automation.

This thesis focuses on robotic 3D vision for application in Bin Picking. The new method based on Conformal Geometric Algebra (CGA) is proposed and tested for identification of spheres in Pointclouds created with 3D scanner. The speed, precision and scalability of this method is compared to traditional descriptors based method. It is proved that CGA maintains the same precision as the traditional method in much shorter time. The CGA based approach seems promising for the use in the future of robotic 3D vision for identification and localization of spheres.