Solutions to common issues in widefield microscopy: vignetting, mosaicing and depth of focus

In this thesis we have developed solutions to common issues regarding widefield microscopes, facing the problem of the intensity inhomogeneity of an image and dealing with two strong limitations: the impossibility of acquiring either high detailed images representative of whole samples or deep 3D objects. First, we cope with the problem of the non-uniform distribution of the light signal inside a single image, named vignetting. In particular we proposed, for both light and fluorescent microscopy, non-parametric multi-image based methods, where the vignetting function is estimated directly from the sample without requiring any prior information. After getting flat-field corrected images, we studied how to fix the problem related to the limitation of the field of view of the camera, so to be able to acquire large areas at high magnification. To this purpose, we developed mosaicing techniques capable to work on-line. Starting from a set of overlapping images manually acquired, we validated a fast registration approach to accurately stitch together the images. Finally, we worked to virtually extend the field of view of the camera in the third dimension, with the purpose of reconstructing a single image completely in focus, stemming from objects having a relevant depth or being displaced in different focus planes. After studying the existing approaches for extending the depth of focus of the microscope, we proposed a general method that does not require any prior information. In order to compare the outcome of existing methods, different standard metrics are commonly used in literature. However, no metric is available to compare different methods in real cases. First, we validated a metric able to rank the methods as the Universal Quality Index does, but without needing any reference ground truth. Second, we proved that the approach we developed performs better in both synthetic and real cases.

Integrazione di elementi sintetici in scene reali mediante Photoshop 3d e Maya

Lo scopo di questa tesi è dimostrare che è possibile integrare elementi sintetici in scene reali, producendo rendering realistici, avvalendosi di software come Autodesk Maya e Adobe Photoshop. Il progetto, infatti, consiste nella realizzazione di cinque immagini ottenute assemblando in fotografie reali, oggetti 3D, generati usando il software di modellazione Maya, con l’obiettivo di produrre immagini finali altamente fotorealistiche, per cui l’osservatore non riesce a distinguere se l’immagine è reale o sintetica.

Design methods and geometric modelling of scaffolds for bone tissue engineering

Every year, thousand of surgical treatments are performed in order to fix up or completely substitute, where possible, organs or tissues affected by degenerative diseases. Patients with these kind of illnesses stay long times waiting for a donor that could replace, in a short time, the damaged organ or the tissue. The lack of biological alternates, related to conventional surgical treatments as autografts, allografts, e xenografts, led the researchers belonging to different areas to collaborate to find out innovative solutions. This research brought to a new discipline able to merge molecular biology, biomaterial, engineering, biomechanics and, recently, design and architecture knowledges. This discipline is named Tissue Engineering (TE) and it represents a step forward towards the substitutive or regenerative medicine. One of the major challenge of the TE is to design and develop, using a biomimetic approach, an artificial 3D anatomy scaffold, suitable for cells adhesion that are able to proliferate and differentiate themselves as consequence of the biological and biophysical stimulus offered by the specific tissue to be replaced. Nowadays, powerful instruments allow to perform analysis day by day more accurateand defined on patients that need more precise diagnosis and treatments.Starting from patient specific information provided by TC (Computed Tomography) microCT and MRI(Magnetic Resonance Imaging), an image-based approach can be performed in order to reconstruct the site to be replaced. With the aid of the recent Additive Manufacturing techniques that allow to print tridimensional objects with sub millimetric precision, it is now possible to practice an almost complete control of the parametrical characteristics of the scaffold: this is the way to achieve a correct cellular regeneration. In this work, we focalize the attention on a branch of TE known as Bone TE, whose the bone is main subject. Bone TE combines osteoconductive and morphological aspects of the scaffold, whose main properties are pore diameter, structure porosity and interconnectivity. The realization of the ideal values of these parameters represents the main goal of this work: here we'll a create simple and interactive biomimetic design process based on 3D CAD modeling and generative algorithmsthat provide a way to control the main properties and to create a structure morphologically similar to the cancellous bone. Two different typologies of scaffold will be compared: the first is based on Triply Periodic MinimalSurface (T.P.M.S.) whose basic crystalline geometries are nowadays used for Bone TE scaffolding; the second is based on using Voronoi's diagrams and they are more often used in the design of decorations and jewellery for their capacity to decompose and tasselate a volumetric space using an heterogeneous spatial distribution (often frequent in nature). In this work, we will show how to manipulate the main properties (pore diameter, structure porosity and interconnectivity) of the design TE oriented scaffolding using the implementation of generative algorithms: "bringing back the nature to the nature".

Is restricted femoral navigation sufficient for accuracy of total knee arthroplasty?

A total knee arthroplasty performed with navigation results in more accurate component positioning with fewer outliers. It is not known whether image-based or image-free-systems are preferable and if navigation for only one component leads to equal accuracy in leg alignment than navigation of both components. We evaluated the results of total knee arthroplasties performed with femoral navigation. We studied 90 knees in 88 patients who had conventional total knee arthroplasties, image-based total knee arthroplasties, or total knee arthroplasties with image-free navigation. We compared patients' perioperative times, component alignment accuracy, and short-term outcomes. The total surgical time was longer in the image-based total knee arthroplasty group (109 +/- 7 minutes) compared with the image-free (101 +/- 17 minutes) and conventional total knee arthroplasty groups (87 +/- 20 minutes). The mechanical axis of the leg was within 3 degrees of neutral alignment, although the conventional total knee arthroplasty group showed more (10.6 degrees ) variance than the navigated groups (5.8 degrees and 6.4 degrees , respectively). We found a positive correlation between femoral component malalignment and the total mechanical axis in the conventional group. Our results suggest image-based navigation is not necessary, and image-free femoral navigation may be sufficient for accurate component alignment.

Discrete element methods for asphalt concrete : development and application of user-defined microstructural models and a viscoelastic micromechanical model

As an important Civil Engineering material, asphalt concrete (AC) is commonly used to build road surfaces, airports, and parking lots. With traditional laboratory tests and theoretical equations, it is a challenge to fully understand such a random composite material. Based on the discrete element method (DEM), this research seeks to develop and implement computer models as research approaches for improving understandings of AC microstructure-based mechanics. In this research, three categories of approaches were developed or employed to simulate microstructures of AC materials, namely the randomly-generated models, the idealized models, and image-based models. The image-based models were recommended for accurately predicting AC performance, while the other models were recommended as research tools to obtain deep insight into the AC microstructure-based mechanics. A viscoelastic micromechanical model was developed to capture viscoelastic interactions within the AC microstructure. Four types of constitutive models were built to address the four categories of interactions within an AC specimen. Each of the constitutive models consists of three parts which represent three different interaction behaviors: a stiffness model (force-displace relation), a bonding model (shear and tensile strengths), and a slip model (frictional property). Three techniques were developed to reduce the computational time for AC viscoelastic simulations. It was found that the computational time was significantly reduced to days or hours from years or months for typical three-dimensional models. Dynamic modulus and creep stiffness tests were simulated and methodologies were developed to determine the viscoelastic parameters. It was found that the DE models could successfully predict dynamic modulus, phase angles, and creep stiffness in a wide range of frequencies, temperatures, and time spans. Mineral aggregate morphology characteristics (sphericity, orientation, and angularity) were studied to investigate their impacts on AC creep stiffness. It was found that aggregate characteristics significantly impact creep stiffness. Pavement responses and pavement-vehicle interactions were investigated by simulating pavement sections under a rolling wheel. It was found that wheel acceleration, steadily moving, and deceleration significantly impact contact forces. Additionally, summary and recommendations were provided in the last chapter and part of computer programming codes wree provided in the appendixes.

Interactive Ray Tracing for Virtual TV Studio Applications

In the last years, the well known ray tracing algorithm gained new popularity with the introduction of interactive ray tracing methods. The high modularity and the ability to produce highly realistic images make ray tracing an attractive alternative to raster graphics hardware. Interactive ray tracing also proved its potential in the field of Mixed Reality rendering and provides novel methods for seamless integration of real and virtual content. Actor insertion methods, a subdomain of Mixed Reality and closely related to virtual television studio techniques, can use ray tracing for achieving high output quality in conjunction with appropriate visual cues like shadows and reflections at interactive frame rates. In this paper, we show how interactive ray tracing techniques can provide new ways of implementing virtual studio applications.

Validation of targeting the ventrointermediate thalamic nucleus using Q-ball calculation in deep brain stimulation for tremor

Objective: Identification of the ventrointermediate thalamic nucleus (Vim) in modern 3T high-field MRI for image-based targeting in deep brain stimulation (DBS) is still challenging. To evaluate the usefulness and reliability of analyzing the connectivity with the cerebellum using Q-ball-calculation we performed a retrospective analysis. Method: 5 patients who underwent bilateral implantation of electrodes in the Vim for treatment of Essential Tremor between 2011 and 2012 received additional preoperative Q-ball imaging. Targeting was performed according to atlas coordinates and standard MRI. Additionally we performed a retrospective identification of the Vim by analyzing the connectivity of the thalamus with the dentate nucleus. The exact position of the active stimulation contact in the postoperative CT was correlated with the Vim as it was identified by Q-ball calculation. Results: Localization of the Vim by analysis of the connectivity between thalamus and cerebellum was successful in all 5 patients on both sides. The average position of the active contacts was 14.6 mm (SD 1.24) lateral, 5.37 mm (SD 0.094 posterior and 2.21 mm (SD 0.69) cranial of MC. The cranial portion of the dentato-rubro-thalamic tract was localized an average of 3.38 mm (SD 1.57) lateral and 1.5 mm (SD 1.22) posterior of the active contact. Conclusions: Connectivity analysis by Q-ball calculation provided direct visualization of the Vim in all cases. Our preliminary results suggest, that the target determined by connectivity analysis is valid and could possibly be used in addition to or even instead of atlas based targeting. Larger prospective calculations are needed to determine the robustness of this method in providing refined information useful for neurosurgical treatment of tremor.

Integrated Segmentation of Brain Tumor Images for Radiotherapy and Neurosurgery

Image-based modeling of tumor growth combines methods from cancer simulation and medical imaging. In this context, we present a novel approach to adapt a healthy brain atlas to MR images of tumor patients. In order to establish correspondence between a healthy atlas and a pathologic patient image, tumor growth modeling in combination with registration algorithms is employed. In a first step, the tumor is grown in the atlas based on a new multi-scale, multi-physics model including growth simulation from the cellular level up to the biomechanical level, accounting for cell proliferation and tissue deformations. Large-scale deformations are handled with an Eulerian approach for finite element computations, which can operate directly on the image voxel mesh. Subsequently, dense correspondence between the modified atlas and patient image is established using nonrigid registration. The method offers opportunities in atlasbased segmentation of tumor-bearing brain images as well as for improved patient-specific simulation and prognosis of tumor progression.

Summer temperature in the eastern part of southern South America: its variability in the twentieth century and a teleconnection with Oceania

The 1907–2001 summer-to-summer surface air temperature variability in the eastern part of southern South America (SSA, partly including Patagonia) is analysed. Based on records from instruments located next to the Atlantic Ocean (36°S–55°S), we define indices for the interannual and interdecadal timescales. The main interdecadal mode reflects the late-1970s cold-to-warm climate shift in the region and a warm-to-cold transition during early 1930s. Although it has been in phase with the Pacific Decadal Oscillation (PDO) index since the 1960s, they diverged in the preceding decades. The main interannual variability index exhibits high spectral power at ~3.4 years and is representative of temperature variability in a broad area in the southern half of the continent. Eleven-years running correlation coefficients between this index and December-to-February (DJF) Niño3.4 show significant decadal fluctuations, out-of-phase with the running correlation with a DJF index of the Southern Annular Mode. The main interannual variability index is associated with a barotropic wavetrain-like pattern extending over the South Pacific from Oceania to SSA. During warm (cold) summers in SSA, significant anticyclonic (cyclonic) anomalies tend to predominate over eastern Australia, to the north of the Ross Sea, and to the east of SSA, whereas anomalous cyclonic (anticyclonic) circulation is observed over New Zealand and west of SSA. This teleconnection links warm (cold) SSA anomalies with dry (wet) summers in eastern Australia. The covariability seems to be influenced by the characteristics of tropical forcing; indeed, a disruption has been observed since late 1970s, presumably due to the PDO warm phase.

Two-dimensional and three-dimensional oxygen mapping by 3He-MRI validation in a lung phantom

The aim of this study was to validate oxygen-sensitive 3He-MRI in noninvasive determination of the regional, two- and three-dimensional distribution of oxygen partial pressure. In a gas-filled elastic silicon ventilation bag used as a lung phantom, oxygen sensitive two- and three-dimensional 3He-MRI measurements were performed at different oxygen concentrations which had been equilibrated in a range of normal and pathologic values. The oxygen partial pressure distribution was determined from 3He-MRI using newly developed software allowing for mapping of oxygen partial pressure. The reference bulk oxygen partial pressure inside the phantom was measured by conventional respiratory gas analysis. In two-dimensional measurements, image-based and gas-analysis results correlated with r=0.98; in three-dimensional measurements the between-methods correlation coefficient was r=0.89. The signal-to-noise ratio of three-dimensional measurements was about half of that of two-dimensional measurements and became critical (below 3) in some data sets. Oxygen-sensitive 3He-MRI allows for noninvasive determination of the two- and three-dimensional distribution of oxygen partial pressure in gas-filled airspaces.

Is the acetabular cup orientation after total hip arthroplasty on a two dimension or three dimension model accurate?

Purpose Malposition of the acetabular component in total hip arthroplasty (THA) is a common surgical problem that can lead to hip dislocation, reduced range of motion and may result in early loosening. The aim of this study is to validate the accuracy and reproducibility of a single x-ray image based 2D/3D reconstruction technique in determining cup inclination and anteversion against two different computer tomography (CT)-based measurement techniques. Methods Cup anteversion and inclination of 20 patients after cementless primary THA was measured on standard anteroposterior (AP) radiographs with the help of the single x-ray 2D/3D reconstruction program and compared with two different 3D CT-based analyses [Ground Truth (GT) and MeVis (MV) reconstruction model]. Results The measurements from the single x-ray 2D/3D reconstruction technique were strongly correlated with both types of CT image-processing protocols for both cup inclination [R²=0.69 (GT); R²=0.59 (MV)] and anteversion [R²=0.89 (GT); R²=0.80 (MV)]. Conclusions The single x-ray image based 2D/3D reconstruction technique is a feasible method to assess cup position on postoperative x-rays. CTscans remain the golden standard for a more complex biomechanical evaluation when a lower tolerance limit (+/-2 degrees) is required.

PHENOTHIAZINES INDUCE ABORTIVE AUTOPHAGY LEADING TO CANCER CELL DEATH

Autophagy is an evolutionarily conserved process that functions to maintain homeostasis and provides energy during nutrient deprivation and environmental stresses for the survival of cells by delivering cytoplasmic contents to the lysosomes for recycling and energy generation. Dysregulation of this process has been linked to human diseases including immune disorders, neurodegenerative muscular diseases and cancer. Autophagy is a double edged sword in that it has both pro-survival and pro-death roles in cancer cells. Its cancer suppressive roles include the clearance of damaged organelles, which could otherwise lead to inflammation and therefore promote tumorigenesis. In its pro-survival role, autophagy allows cancer cells to overcome cytotoxic stresses generated the cancer environment or cancer treatments such as chemotherapy and evade cell death. A better understanding of how drugs that perturb autophagy affect cancer cell signaling is of critical importance toimprove the cancer treatment arsenal. In order to gain insights in the relationship between autophagy and drug treatments, we conducted a high-throughput drug screen to identify autophagy modulators. Our high-throughput screen utilized image based fluorescent microscopy for single cell analysis to identify chemical perturbants of the autophagic process. Phenothiazines emerged as the largest family of drugs that alter the autophagic process by increasing LC3-II punctae levels in different cancer cell lines. In addition, we observed multiple biological effects in cancer cells treated with phenothiazines. Those antitumorigenic effects include decreased cell migration, cell viability, and ATP production along with abortive autophagy. Our studies highlight the potential role of phenothiazines as agents for combinational therapy with other chemotherapeutic agents in the treatment of different cancers.

Global planktonic foraminifera seasonality

Shell fluxes of planktonic Foraminifera species vary intra-annually in a pattern that appears to follow the seasonal cycle. However, the variation in the timing and prominence of seasonal flux maxima in space and among species remains poorly constrained. Thus, although changing seasonality may result in a flux-weighted temperature offset of more than 5° C within a species, this effect is often ignored in the interpretation of Foraminifera-based paleoceanographic records. To address this issue we present an analysis of the intra-annual pattern of shell flux variability in 37 globally distributed time series. The existence of a seasonal component in flux variability was objectively characterised using periodic regression. This analysis yielded estimates of the number, timing and prominence of seasonal flux maxima. Over 80% of the flux series across all species showed a statistically significant periodic component, indicating that a considerable part of the intra-annual flux variability is predictable. Temperature appears to be a powerful predictor of flux seasonality, but its effect differs among species. Three different modes of seasonality are distinguishable. Tropical and subtropical species (Globigerinoides ruber (white and pink varieties), Neogloboquadrina dutertrei, Globigerinoides sacculifer, Orbulina universa, Globigerinella siphonifera, Pulleniatina obliquiloculata, Globorotalia menardii, Globoturborotalita rubescens, Globoturborotalita tenella and Globigerinoides conglobatus) appear to have a less predictable flux pattern, with random peak timing in warm waters. In colder waters, seasonality is more prevalent: peak fluxes occur shortly after summer temperature maxima and peak prominence increases. This tendency is stronger in species with a narrower temperature range, implying that warm-adapted species find it increasingly difficult to reproduce outside their optimum temperature range and that, with decreasing mean temperature, their flux is progressively more focussed in the warm season. The second group includes the temperate to cold-water species Globigerina bulloides, Globigerinita glutinata, Turborotalita quinqueloba, Neogloboquadrina incompta, Neogloboquadrina pachyderma, Globorotalia scitula, Globigerinella calida, Globigerina falconensis, Globorotalia theyeri and Globigerinita uvula. These species show a highly predictable seasonal pattern, with one to two peaks a year, which occur earlier in warmer waters. Peak prominence in this group is independent of temperature. The earlier-when-warmer pattern in this group is related to the timing of productivity maxima. Finally, the deep-dwelling Globorotalia truncatulinoides and Globorotalia inflata show a regular and pronounced peak in winter and spring. The remarkably low flux outside the main pulse may indicate a long reproductive cycle of these species. Overall, our analysis indicates that the seasonality of planktonic Foraminifera shell flux is predictable and reveals the existence of distinct modes of phenology among species. We evaluate the effect of changing seasonality on paleoceanographic reconstructions and find that, irrespective of the seasonality mode, the actual magnitude of environmental change will be underestimated. The observed constraints on flux seasonality can serve as the basis for predictive modelling of flux pattern. As long as the diversity of species seasonality is accounted for in such models, the results can be used to improve reconstructions of the magnitude of environmental change in paleoceanographic records.

High-resolution stratigraphic framework for Mediterranean sapropel S5

A high-resolution stratigraphic framework is presented for sapropel S5, which represents the low-mid latitude climate optimum of the previous interglacial period (Eemian). The framework is based on three sites along a transect from west to east through the eastern Mediterranean, and is further validated using a fourth site. This method allows expression of S5-based proxy records of Eemian climate variability along a standardised depth scale that offers unprecedented possibilities for assessment of spatial gradients and signal leads and lags in an interval where highresolution (radiocarbon-style) dating cannot be performed. Our lateral comparison of S5 sapropels suggests that the onset of S5 in ODP site 967C (Eratosthenes seamount) was 1-6 centuries delayed relative to the onsets in more westerly sites.

La puñalada de Amelia (o cómo se extinguió la discriminación de las mujeres casadas del servicio telefónico en la Argentina)

Esta comunicación ilumina las huellas de Amelia C. Su historia de vida como telefonista es relevante para comprender la discriminación de las mujeres en el mercado laboral en los comienzos del siglo XX. Este artículo se enfocará en el estado conyugal como pauta de exclusión femenina. La estrategia utilizada por Amelia contra dicha pauta, si bien individual e incluso desesperada, detonó una serie de revisiones de la legislación existente que fueron apoyadas por distintos grupos de la sociedad. El corpus está basado en expedientes de la compañía telefónica en la que Amelia se desempeñó como empleada durante varios años y en el impacto que sus estrategias tuvieron en la prensa local.