Acquisition and Mining of the Whole Mouse Brain Microstructure

Charting out the complete brain microstructure of a mammalian species is a grand challenge. Recent advances in serial sectioning microscopy such as the Knife- Edge Scanning Microscopy (KESM), a high-throughput and high-resolution physical sectioning technique, have the potential to finally address this challenge. Nevertheless, there still are several obstacles remaining to be overcome. First, many of these serial sectioning microscopy methods are still experimental and are not fully automated. Second, even when the full raw data have been obtained, morphological reconstruction, visualization/editing, statistics gathering, connectivity inference, and network analysis remain tough problems due to the unprecedented amounts of data. I designed a general data acquisition and analysis framework to overcome these challenges with a focus on data from the C57BL/6 mouse brain. Since there has been no such complete microstructure data from any mammalian species, the sheer amount of data can overwhelm researchers. To address the problems, I constructed a general software framework for automated data acquisition and computational analysis of the KESM data, and conducted two scientific case studies to discuss how the mouse brain microstructure from the KESM can be utilized. I expect the data, tools, and studies resulting from this dissertation research to greatly contribute to computational neuroanatomy and computational neuroscience

Proceedings, MSVSCC 2013

Proceedings of the 7th Annual Modeling, Simulation & Visualization Student Capstone Conference held on April 11, 2013 at VMASC in Suffolk, Virginia

Sparse Volumetric Deformation

Volume rendering is becoming increasingly popular as applications require realistic solid shape representations with seamless texture mapping and accurate filtering. However rendering sparse volumetric data is difficult because of the limited memory and processing capabilities of current hardware. To address these limitations, the volumetric information can be stored at progressive resolutions in the hierarchical branches of a tree structure, and sampled according to the region of interest. This means that only a partial region of the full dataset is processed, and therefore massive volumetric scenes can be rendered efficiently. The problem with this approach is that it currently only supports static scenes. This is because it is difficult to accurately deform massive amounts of volume elements and reconstruct the scene hierarchy in real-time. Another problem is that deformation operations distort the shape where more than one volume element tries to occupy the same location, and similarly gaps occur where deformation stretches the elements further than one discrete location. It is also challenging to efficiently support sophisticated deformations at hierarchical resolutions, such as character skinning or physically based animation. These types of deformation are expensive and require a control structure (for example a cage or skeleton) that maps to a set of features to accelerate the deformation process. The problems with this technique are that the varying volume hierarchy reflects different feature sizes, and manipulating the features at the original resolution is too expensive; therefore the control structure must also hierarchically capture features according to the varying volumetric resolution. This thesis investigates the area of deforming and rendering massive amounts of dynamic volumetric content. The proposed approach efficiently deforms hierarchical volume elements without introducing artifacts and supports both ray casting and rasterization renderers. This enables light transport to be modeled both accurately and efficiently with applications in the fields of real-time rendering and computer animation. Sophisticated volumetric deformation, including character animation, is also supported in real-time. This is achieved by automatically generating a control skeleton which is mapped to the varying feature resolution of the volume hierarchy. The output deformations are demonstrated in massive dynamic volumetric scenes

Dynamic Modeling of a Cubical Robot Balancing on Its Corner

Aiming at the problem of self-balancing control of a cubical robot, this paper makes a research on the dynamic modeling of the cubical robot balancing on its corner. Using the prototype of cubical robot we built as the research object, the dynamic model is derived with Lagrangian method on foundation of analysis of coordinate transformation relation of cubical robot. The correctness of the model is verified in theory by numerical simulation. The controller, designed based on reaction torque characteristic of inertia wheels, is used in balance control of the cubical robot. The effectiveness of the controller is verified again with the obtained expect effect. The dynamic model developed and controller can provide a base for further study of balance control of a cubical robot

Dynamic Modeling of a Cubical Robot Balancing on Its Corner

Aiming at the problem of self-balancing control of a cubical robot, this paper makes a research on the dynamic modeling of the cubical robot balancing on its corner. Using the prototype of cubical robot we built as the research object, the dynamic model is derived with Lagrangian method on foundation of analysis of coordinate transformation relation of cubical robot. The correctness of the model is verified in theory by numerical simulation. The controller, designed based on reaction torque characteristic of inertia wheels, is used in balance control of the cubical robot. The effectiveness of the controller is verified again with the obtained expect effect. The dynamic model developed and controller can provide a base for further study of balance control of a cubical robot

Computing multi-scale organizations built through assembly

The ability to generate and control assembling structures built over many orders of magnitude is an unsolved challenge of engineering and science. Many of the presumed transformational benefits of nanotechnology and robotics are based directly on this capability. There are still significant theoretical difficulties associated with building such systems, though technology is rapidly ensuring that the tools needed are becoming available in chemical, electronic, and robotic domains. In this thesis a simulated, general-purpose computational prototype is developed which is capable of unlimited assembly and controlled by external input, as well as an additional prototype which, in structures, can emulate any other computing device. These devices are entirely finite-state and distributed in operation. Because of these properties and the unique ability to form unlimited size structures of unlimited computational power, the prototypes represent a novel and useful blueprint on which to base scalable assembly in other domains. A new assembling model of Computational Organization and Regulation over Assembly Levels (CORAL) is also introduced, providing the necessary framework for this investigation. The strict constraints of the CORAL model allow only an assembling unit of a single type, distributed control, and ensure that units cannot be reprogrammed - all reprogramming is done via assembly. Multiple units are instead structured into aggregate computational devices using a procedural or developmental approach. Well-defined comparison of computational power between levels of organization is ensured by the structure of the model. By eliminating ambiguity, the CORAL model provides a pragmatic answer to open questions regarding a framework for hierarchical organization. Finally, a comparison between the designed prototypes and units evolved using evolutionary algorithms is presented as a platform for further research into novel scalable assembly. Evolved units are capable of recursive pairing ability under the control of a signal, a primitive form of unlimited assembly, and do so via symmetry-breaking operations at each step. Heuristic evidence for a required minimal threshold of complexity is provided by the results, and challenges and limitations of the approach are identified for future evolutionary studies

Reachability-based Trajectory Design

Autonomous mobile robots have the potential to increase the availability and accessibility of goods and services throughout society. However, to enable public trust in such systems, it is critical to certify that they are safe. This requires formally specifying safety, and designing motion planning methods that can guarantee safe operation (note, this work is only concerned with planning, not perception). The typical paradigm to attempt to ensure safety is receding-horizon planning, wherein a robot creates a short plan, then executes it while creating its next short plan in an iterative fashion, allowing a robot to incorporate new sensor information over time. However, this requires a robot to plan in real time. Therefore, the key challenge in making safety guarantees lies in balancing performance (how quickly a robot can plan) and conservatism (how cautiously a robot behaves). Existing methods suffer from a tradeoff between performance and conservatism, which is rooted in the choice of model used describe a robot; accuracy typically comes at the price of computation speed. To address this challenge, this dissertation proposes Reachability-based Trajectory Design (RTD), which performs real-time, receding-horizon planning with a simplified planning model, and ensures safety by describing the model error using a reachable set of the robot. RTD begins with the offline design of a continuum of parameterized trajectories for the plan- ning model; each trajectory ends with a fail-safe maneuver such as braking to a stop. RTD then computes the robot’s Forward Reachable Set (FRS), which contains all points in workspace reach- able by the robot for each parameterized trajectory. Importantly, the FRS also contains the error model, since a robot can typically never track planned trajectories perfectly. Online (at runtime), the robot intersects the FRS with sensed obstacles to provably determine which trajectory plans could cause collisions. Then, the robot performs trajectory optimization over the remaining safe trajectories. If no new safe plan can be found, the robot can execute its previously-found fail-safe maneuver, enabling perpetual safety. This dissertation begins by presenting RTD as a theoretical framework, then presents three representations of a robot’s FRS, using (1) sums-of-squares (SOS) polynomial programming, (2) zonotopes (a special type of convex polytope), and (3) rotatotopes (a generalization of zonotopes that enable representing a robot’s swept volume). To enable real-time planning, this work also de- velops an obstacle representation that enables provable safety while treating obstacles as discrete, finite sets of points. The practicality of RTD is demonstrated on four different wheeled robots (using the SOS FRS), two quadrotor aerial robots (using the zonotope FRS), and one manipulator robot (using the rotatotope FRS). Over thousands of simulations and dozens of hardware trials, RTD performs safe, real-time planning in arbitrary and challenging environments. In summary, this dissertation proposes RTD as a general purpose, practical framework for provably safe, real-time robot motion planning.PHDMechanical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/162884/1/skousik_1.pd

Werkzeugauslegung, Analyse und Simulation des In-Mold-Labeling-Spritzgießens

Years ago, the production of packaging with the injection-IML has been established. This procedure concept ranks nowadays among the most modern technologies in the area of the plastic packaging. With this manufacturing technique, label and packaging, both are of the same polymer materials, become inseparably connected during the injection molding process. Since thermal conductivity of the polymeric label material is clearly smaller than that of the metal mold wall, thermal induced warpage of injected IML part or part surface deformation could be occurred. The objective of this work is to analyze and simulate the filling, holding, and cooling phases of the injection IML process by means of the simulation program Moldex3D® and to study the effect of inserted label on the warpage behavior and modulus of elasticity of injected parts. For this study, the injection mold for injection IML equipped with vacuum ports for holding the label was designed and constructed. For the automation of the injection IML process, a linear pneumatic robot was employed. As a preliminary examination, the experimental study and numerical simulation of the melt front advancement, course of the pressure and melt temperature profile during the injection molding of double-plated parts with non-uniform part thickness were done in order to acquire better understanding of the simulation program Moldex3D® prior to its application later on to the injection IML simulation calculations. The molded part composes of two thin plates joined together with a cold runner. One fan gate is connected to the thick side of the first plate and the other connected to the thin side of the second plate. Comparisons between the experiment and simulation performed with the same molding parameters were carried out. From the results, 2.5D simulation was verified to be more reliable than 3D simulation particularly in terms of predicting the melt front advancement as well as the melt pressure development during the molding. Owing to the complex flow and unbalance of the pressure within two cavities of the part, 3D simulation based on non-isothermal computation failed to predict course of the pressure and hence the melt front advancement within both cavities. However, with the 3D isothermal computation, improvement in accuracy was achieved. This phenomenon resulted from the instability of the 3D simulation program. By molding the double-plated part separately, both 2.5D and 3D simulation results agreed well with those from the experiments. After the preliminary examination has been done, analysis and 3D simulation on filling, holding, and cooling phases of the injection IML process and warpage behavior of injected IML parts were investigated, since the presence of label can significantly affect the molding process. From the study, good agreement of the mold filling, holding, and cooling results between 3D simulation and experiment was acquired. Structure and warpage behavior of IML parts were also investigated. In order to cope with part warpage problem, variations in mold temperature on the stationary and moving mold halves were carried out. With the higher mold temperature setting on the label side, part warpage was reduced. Furthermore, study of the effect of the mold temperature combination settings on the modulus of elasticity of the IML part was conducted. The results revealed that despite a slight reduction in the modulus of elasticity of the IML part owing to the different mold temperature settings on two mold halves, modulus of elasticity of the IML part was still found to be satisfactory.Seit geraumer Zeit, hat sich die Herstellung von Verpackungskomponenten nach dem In-Mold-Labeling-Spritzgießverfahren (IML) etabliert. Bei dieser Technologie werden das Etikett und die Verpackung, die i.a. aus demselben Material bestehen, im Zuge des Formgebungsschrittes unlösbar miteinander verbunden. Beim Einspritzvorgang des Plastifikats in die mit dem Etikett bestückte Kavität kann es dazu kommen, dass das Etikett aus seiner Ursprungslage verschoben oder gefaltet wird. Außerdem ist die Wärmeleitfähigkeit des Label-Materials deutlich niedriger als die der metallischen Werkzeugwandung, so dass es zu Strukturfehlern auf der Formteiloberfläche und/oder zu einem Verzug des Spritzgießteils kommen kann. Im Rahmen dieser Arbeit werden deshalb die Formfüll- und Bauteil-Abkühlvorgänge beim IML-Spritzgießen analysiert, wobei das Simulationsprogramm Moldex3D® zum Einsatz kommt. Die dabei gewonnenen Ergebnisse werden mit denen des realen Prozesses verglichen. Des Weiteren werden die generierten Produkte im Bezug auf ihren Verzug und ihren E-Modul bewertet. Für diese Studie wurde ein spezielles Spritzgießwerkzeug, welches mit Vakuumanschlüssen für die Positionierung und Fixierung des In-Mold-Etiketts ausgerüstet ist, konstruiert und gebaut. Für die Automatisierung des IML-Spritzgießprozesses wurde ein linearer, pneumatisch betätigter Roboter eingesetzt. Um ein besseres Verständnis für das Simulationsprogramm bezüglich seiner Funktionsweise vor der Anwendung auf das In-Mold-Labeling-Spritzgießen zu erwerben, wurden vorab simulative und experimentelle Voruntersuchungen bezüglich der Fließfrontenverläufe, der Druckverläufe und der Temperaturprofile beim Spritzgießen von Doppelplatten mit Dickensprung durchgeführt. Dieses Formteil besteht aus zwei plattenförmigen Kavitäten, die jeweils über einen Filmanschnitt an der dicken und der dünnen Seite der Kavität angespritzt werden. Ein Vergleich von Versuchs- und Simulationsergebnissen wurde durchgeführt. Dabei zeigte sich, dass eine 2.5D-Simulation hinsichtlich der Voraussagen der Fließfrontenverläufe in den Kavitäten sowie der Schmelzedruckverteilungen während des Spritzgießens zu einer zufrieden stellenden Übereinstimmung führte. Infolge des komplexen Füllvorgangs und der "Druckumkehr" innerhalb der beiden Kavitäten konnte die nicht-isotherme 3D-Simulation den Druck und somit die Fließfrontenverläufe nicht richtig wiedergeben. Mit der isothermen 3D-Simulation konnte hingegen eine deutliche Verbesserung in der Genauigkeit erzielt werden. Des Weiteren wurde die Doppelplatte in zwei Einzelplatten zerlegt, die separat gespritzt werden. Mit diesen Platten konnten sowohl 2.5D- als auch 3D- Füllbildsimulationen erfolgreich durchgeführt und die Fließfrontenverläufe in der Kavität richtig beschrieben werden. Da das Etikett auf den Formteil-Herstellungsprozess zurückwirken kann, wurden nach diesen Voruntersuchungen die Einflüsse des Etiketts unter Durchführung von 3D-Simulationen bezüglich der Füll-, Nachdruck-, und Kühlphase sowie hinsichtlich des Verzugsverhaltens beim In-Mold-Labeling-Spritzgießen studiert. Dabei wurde eine gute Übereinstimmung von Versuchs- und Simulationsergebnissen festgestellt. Weiterführend wurden die Struktur und das Verzugsverhalten des IML-Formteils analysiert. Um den Verzug des IML-Formteils zu reduzieren wurden die Spritzgießversuche mit verschiedenen Werkzeugtemperatur-Kombinationen durchgeführt. Dabei zeigte sich, dass mit einer höheren Werkzeugtemperatur auf der Labelseite der Verzug verringert werden kann. Zusätzlich wurde der Einfluss der Werkzeugtemperatur-Kombination auf die Steifigkeit des IML-Formteils untersucht. Es zeigte sich, dass trotz einer geringfügigen Verringerung des Elastizitätsmoduls des IML-Formteils infolge der unterschiedlichen Werkzeugtemperaturen der beiden Werkzeughälften der Elastizitätsmodul des IML-Formteils noch in einem akzeptablen Bereich bleibt