Introduction: The Third International Conference on Epigenetic Robotics

This paper summarizes the paper and poster contributions to the Third International Workshop on Epigenetic Robotics. The focus of this workshop is on the cross-disciplinary interaction of developmental psychology and robotics. Namely, the general goal in this area is to create robotic models of the psychological development of various behaviors. The term "epigenetic" is used in much the same sense as the term "developmental" and while we could call our topic "developmental robotics", developmental robotics can be seen as having a broader interdisciplinary emphasis. Our focus in this workshop is on the interaction of developmental psychology and robotics and we use the phrase "epigenetic robotics" to capture this focus

Foetal echocardiographic segmentation

Congenital heart disease affects just under one percentage of all live births [1]. Those defects that manifest themselves as changes to the cardiac chamber volumes are the motivation for the research presented in this thesis. Blood volume measurements in vivo require delineation of the cardiac chambers and manual tracing of foetal cardiac chambers is very time consuming and operator dependent. This thesis presents a multi region based level set snake deformable model applied in both 2D and 3D which can automatically adapt to some extent towards ultrasound noise such as attenuation, speckle and partial occlusion artefacts. The algorithm presented is named Mumford Shah Sarti Collision Detection (MSSCD). The level set methods presented in this thesis have an optional shape prior term for constraining the segmentation by a template registered to the image in the presence of shadowing and heavy noise. When applied to real data in the absence of the template the MSSCD algorithm is initialised from seed primitives placed at the centre of each cardiac chamber. The voxel statistics inside the chamber is determined before evolution. The MSSCD stops at open boundaries between two chambers as the two approaching level set fronts meet. This has significance when determining volumes for all cardiac compartments since cardiac indices assume that each chamber is treated in isolation. Comparison of the segmentation results from the implemented snakes including a previous level set method in the foetal cardiac literature show that in both 2D and 3D on both real and synthetic data, the MSSCD formulation is better suited to these types of data. All the algorithms tested in this thesis are within 2mm error to manually traced segmentation of the foetal cardiac datasets. This corresponds to less than 10% of the length of a foetal heart. In addition to comparison with manual tracings all the amorphous deformable model segmentations in this thesis are validated using a physical phantom. The volume estimation of the phantom by the MSSCD segmentation is to within 13% of the physically determined volume

Change blindness: eradication of gestalt strategies

Arrays of eight, texture-defined rectangles were used as stimuli in a one-shot change blindness (CB) task where there was a 50% chance that one rectangle would change orientation between two successive presentations separated by an interval. CB was eliminated by cueing the target rectangle in the first stimulus, reduced by cueing in the interval and unaffected by cueing in the second presentation. This supports the idea that a representation was formed that persisted through the interval before being 'overwritten' by the second presentation (Landman et al, 2003 Vision Research 43149–164]. Another possibility is that participants used some kind of grouping or Gestalt strategy. To test this we changed the spatial position of the rectangles in the second presentation by shifting them along imaginary spokes (by ±1 degree) emanating from the central fixation point. There was no significant difference seen in performance between this and the standard task [F(1,4)=2.565, p=0.185]. This may suggest two things: (i) Gestalt grouping is not used as a strategy in these tasks, and (ii) it gives further weight to the argument that objects may be stored and retrieved from a pre-attentional store during this task

Biomediation of Turbulence and Suspended Sediment Characteristics in Marsh Surface Flows - The Influence of Spartina anglica

Laboratory experimentation in a large aimular flume (radius 3 m, channel width and water depth 0.4 m) has been conducted using a geometrically and dynamically similar Spariina anglica mimic (canopy height 0.21 m, stem density 1000 stems m~^) to investigate the influence of submerged Spartina on hydrodynamics under unidirectional currents {Uh = 0.2 m s~*) and the impact upon the dynamics of suspended cohesive sediments near the bed within the canopy. The vertical distribution of canopy biomass strongly influences vertical profiles of time-averaged velocity and turbulent quantities. An inflected velocity profile is observed in the region 0.79 < z/h < 0.9 which generates shear, T K E and Reynolds Stress peaks within vicinity of the canopy top. In this region T K E peaks at 15 times the levels observed in un-vegetated experiments. Flows at the canopy top are strongly intermittent with extremely efficient downward momentum transfer, uf] and ufz (stream-wise and vertical zero-mean fluctuating velocity) skewness are 0.5 and -0.5 indicating the presence of intermittent downward penetrating gusts. Near the bed (0 < z/h < 0.3) mean flow velocities are reduced by 88 - 90% in comparison to un-vegetated flows but turbulence intensities are strongly augmented by wake shedding from vegetative elements. TKE in this region is approximately equal to that in un-vegetated flows. Novel field observations in a low energ>', estuarine fringing marsh site on the Tavy Estuary, UK, with a vertical array of synchronous velocimeters and optical backscatter sensors exhibit low velocities (<0.6 ra s"*) and suspension concentrations (<100 mg L"*) in agreement with laboratory simulations. While field observations of near bed flows exhibit similarity to those measured in the laboratory, magnitudes of time-averaged flow throughout the water column are so small that the velocity profile appears constant over depth. Superimposed upon the low field velocities are small wind generated waves ( < 0.05 m in height and with periods < 3 s) which have a considerable impact on flow energy and stress estimates, but crucially, cannot be replicated in the laboratory experiments. Dissipation rates within the laboratory canopy are 70-200x10"'* m~^s"^ giving reduced Kohnogorov length scales of 0.04 - 0.14 mm. Field values for dissipation are generally of similar magnitude but peak at up to 600 X10"** m~^s~^. Kolmogorov length scales are consequently 0.06 - 2.6 mm. Using natural intertidal mud, suspension concentrations of 100-200 mg L~* have been sheared through the mimic canopy. Observations from a vertical array of miniaturised OBS sensors suggests sediments are maintained in suspension twice as long, under constant unidirectional currents, compared to un-vegetated flows. In the field initial concentrations of 100 mg L~* quickly decay to background levels of <20 mg L"* indicating the rapid setthng of material from suspension. Use of a novel digital in-line holographic particle iinaging system and the development of a particle tracking methodology has enabled the high resolution observation of both sample size and settling velocities of suspended cohesive particles. Laboratory observations of sample averaged size (74.5 - 111.7 mm) and settling rates (0.35 - 1 mm s~*) are in agreement with published estimates and the limited observational data that exists for settling rates in marsh systems. Settling velocities estimated in the field at 0.1 - 0.8 mm s~^. Significantly larger and fast settling aggregates have been observed than previously recorded. In the narrow range of experimental suspension concentrations and shear stresses utilised in the present experiments, significant diff^erences in particle size and settling velocity between vegetated and un-vegetated flows cannot be identified. Contrasting flux estimates using sample averaged settling rates and concentrations with full spectral estimates derived from the holographic particle imager indicate an error in the former fluxes of, on average, 62%. The range of settling rates observed during the pr^ent study raises questions regarding the accurate representation of marsh surface settling fluxes in numerical simulations. Large magnitude flux errors may have significant implications for accurate accretion rates in numerical models of marsh sedimentation

Defining The Epichromatin Epitope

Epichromatin is identified by immunostaining fixed and permeabilized cells with particular bivalent anti-nucleosome antibodies (mAbs PL2-6 and 1H6). During interphase, epichromatin resides adjacent to the inner nuclear membrane; during mitosis, at the outer surface of mitotic chromosomes. By STED (stimulated emission depletion) microscopy, PL2-6 stained interphase epichromatin is ∼76 nm thick and quite uniform; mitotic epichromatin is more variable in thickness, exhibiting a “wrinkled” surface with an average thickness of ∼78 nm. Co-immunostaining with anti-Ki-67 demonstrates Ki-67 deposition between the PL2-6 “ridges” of mitotic epichromatin. Monovalent papain-derived Fab fragments of PL2-6 yield a strikingly different punctate “chromomeric” immunostaining pattern throughout interphase nuclei and along mitotic chromosome arms. Evidence from electrophoretic mobility shift assay (EMSA) and from analytical ultracentrifugation characterize the Fab/mononucleosome complex, supporting the concept that there are two binding sites per nucleosome. The peptide sequence of the Hv3 region (heavy chain variable region 3) of the PL2-6 antibody binding site strongly resembles other nucleosome acidic patch binding proteins (especially, LANA and CENPC), supporting that the nucleosome acidic patch is included within the epichromatin epitope. It is speculated that the interphase epichromatin epitope is “exposed” with favorable geometric arrangements for binding bivalent PL2-6 at the surface chromatin; whereas, the epitope is “hidden” within internal chromatin. Furthermore, it is suggested that the “exposed” nucleosome surface of mitotic epichromatin may play a role in post-mitotic nuclear envelope reformation

Improved 3D MR Image Acquisition and Processing in Congenital Heart Disease

Congenital heart disease (CHD) is the most common type of birth defect, affecting about 1% of the population. MRI is an essential tool in the assessment of CHD, including diagnosis, intervention planning and follow-up. Three-dimensional MRI can provide particularly rich visualization and information. However, it is often complicated by long scan times, cardiorespiratory motion, injection of contrast agents, and complex and time-consuming postprocessing. This thesis comprises four pieces of work that attempt to respond to some of these challenges. The first piece of work aims to enable fast acquisition of 3D time-resolved cardiac imaging during free breathing. Rapid imaging was achieved using an efficient spiral sequence and a sparse parallel imaging reconstruction. The feasibility of this approach was demonstrated on a population of 10 patients with CHD, and areas of improvement were identified. The second piece of work is an integrated software tool designed to simplify and accelerate the development of machine learning (ML) applications in MRI research. It also exploits the strengths of recently developed ML libraries for efficient MR image reconstruction and processing. The third piece of work aims to reduce contrast dose in contrast-enhanced MR angiography (MRA). This would reduce risks and costs associated with contrast agents. A deep learning-based contrast enhancement technique was developed and shown to improve image quality in real low-dose MRA in a population of 40 children and adults with CHD. The fourth and final piece of work aims to simplify the creation of computational models for hemodynamic assessment of the great arteries. A deep learning technique for 3D segmentation of the aorta and the pulmonary arteries was developed and shown to enable accurate calculation of clinically relevant biomarkers in a population of 10 patients with CHD

Development of polarization-resolved optical scanning microscopy imaging techniques to study biomolecular organizations

Light, as electromagnetic radiation, conveys energy through space and time via fluctuations in electric and magnetic fields. This thesis explores the interaction of light and biological structures through polarization-resolved imaging techniques. Light microscopy, and polarization analysis enable the examination of biological entities. Biological function often centers on chromatin, the genetic material composed of DNA wrapped around histone proteins within cell nuclei. This structure's chiral nature gives rise to interactions with polarized light. This research encompasses three main aspects. Firstly, an existing multimodal Circular Intensity Differential Scattering (CIDS) and fluorescence microscopy are upgraded into an open configuration to be integrated with other modalities. Secondly, a novel cell classification method employing CIDS and a phasor representation is introduced. Thirdly, polarization analysis of fluorescence emission is employed for pathological investigations. Accordingly, the thesis is organized into three chapters. Chapter 1 lays the theoretical foundation for light propagation and polarization, outlining the Jones and Stokes-Mueller formalisms. The interaction between light and optical elements, transmission, and reflection processes are discussed. Polarized light's ability to reveal image contrast in polarizing microscopes, linear and nonlinear polarization-resolved microscopy, and Mueller matrix microscopy as a comprehensive technique for studying biological structures are detailed. Chapter 2 focuses on CIDS, a label-free light scattering method, including a single point angular spectroscopy mode and scanning microscopy imaging. A significant upgrade of the setup is achieved, incorporating automation, calibration, and statistical analysis routines. An intuitive phasor approach is proposed, enabling image segmentation, cell discrimination, and enhanced interpretation of polarimetric contrast. As a result, image processing programs have been developed to provide automated measurements using polarization-resolved laser scanning microscopy imaging integrated with confocal fluorescence microscopy of cells and chromatin inside cell nuclei, including the use of new types of samples such as progeria cells. Chapter 3 applies a polarization-resolved two-photon excitation fluorescence (2PEF) microscopy to study multicellular cancerous cells. A homemade 2PEF microscope is developed for colon cancer cell analysis. The integration of polarization and fluorescence techniques leads to a comprehensive understanding of the molecular orientation within samples, particularly useful for cancer diagnosis. Overall, this thesis presents an exploration of polarization-resolved imaging techniques for studying biological structures, encompassing theory, experimental enhancements, innovative methodologies, and practical applications