This document deals with devices which are used for the automatic Gram staining. The document starts by a research with the aim to discover existing devices and to compare them to the concept of the device developed by company Biovendor. There is theoretically and then practically dealed with the methods of the rotor imbalance detection and measurement of water-level. The Practical part of this document describes the development of the control unit with the microcontroller ARM Cortex-M3 which will be used for the prototype development of Biovendor’s device. The Last part describes measurement of imbalance of three different rotors with the aid of the control unit.

Med gymnasiereformen 1994 fick alla elever en gemensam första kurs i matematik, kurs A, och ett gemensamt nationellt prov på kursen. På de flesta yrkesförberedandeprogrammen är det över 40 procent av eleverna som inte får godkänt på detta kursprov och 30 procent av eleverna förväntas få ”Icke godkänt” i kursbetyg. En av de största anledningarna, till att eleverna lämnar gymnasieskolan utan fullständiga betyg, är bristen på motivation. Det finns därför ett stort behov av att se över vilka förändringar som kan utföras i de teoretiska ämnena för att öka elevernas motivation och självförtroende på de praktiska programmen. I denna rapport undersöks hur elevernas motivation, tron på den egna förmågan samt uppfattningen om behovet av matematikkunskaper i kommande yrkesliv, påverkas efter en termin med ämnesintegrerat arbetssätt. Undersökningen är utförd på eleverna i årskurs ett på en av byggföretaget Peabs gymnasieskolor och deras matematikundervisning under höstterminen 2009. Genom att utgå från moment i projektet ”Husbygge”, där matematik används naturligt i byggprocessen, kan eleverna uppnå kursmål i Matematik A genom att öva på verklighetsanknutna uppgifter både i bygghallen och under matematiklektionerna. Som kvalitativ metod valdes individuella intervjuer med åtta av eleverna före och efter det ämnesintegrerade projektet samt en enkätundersökning före och efter byggprojektet som utfördes på samtliga elever i årskurs ett. Resultatet av intervjuundersökningen visar att flertalet av eleverna har ökat motivationen för matematikämnet. Resultatet av både enkät- och intervjuundersökningen visar dessutom att majoriteten av eleverna har ökat självförtroendet i matematikämnet efter en termin med ämnesintegrerat arbetssätt. Vid den andra enkätundersökningen hade fler elever även insett hur ofta de faktiskt använder matematik i bygghallen och kommer använda matematik i kommande yrkesliv. / With the upper secondary school reform in 1994, all students´ got a first common course in matematic, course A, and a common national test in the course. More than 40 percent of the students on the most vocational programmes do not pass the national tests in the Mathematic A course and 30 percent of the students are expected not to pass the course. One of the biggest reasons the students leave upper secondary school without completed grades, is the lack of motivation. There is a great need to oversee what changes can be done in the theoretical subjects to increase the students’ motivation and belief in self-efficiency concerning the practical programmes. This report investigates how the students’ motivation, trust in their own ability as well as the understanding for the need of knowledge in mathematics for future occupations is affected after one semester with subject integrated studies. The investigation is performed on first grade students in one of the construction company Peab’s upper secondary schools and their mathematics teaching during the autumn term of 2009. By starting from elements in the project “House construction”, where mathematics is used naturally in the construction process, the students can achieve the criterions in Mathematics A by practising on reality-based tasks in the building area and in the classroom. As qualitative research method, eight students before and after the subject integrated project were chosen for interviews as well as a poll on the first grade students of the mandatory construction project. The results from the interviews indicate an increase for the majority of the students in motivation for mathematics. The result from both the poll and the interviews indicate an increase in self-efficiency beliefs for mathematics after one semester with subject integrated studies for the majority of the students. At the time for the second poll more students had realized how often they actually use mathematics in the building area and will continue to use it in future occupations.

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There are 5 distinct aspects to this study. (i) Two histological stains for collagen were compared against each other for the first time, namely Herovici's technique and picrosirius-polarization. (ii) Skin samples from embalmed cadaveric tissue from human cadavers were compared against samples taken from surgical patients. (iii) Skin samples were studied from different regions of the body to assess if dermal structure correlates with scarring potential. (iv) Skin samples were sectioned in a plane parallel to the epidermis to gain further insight into dermal structure. (v) A novel basement membrane stain was produced. Type I and type III collagen are important structural constituents of dermis and play a crucial role in wound healing. Only two traditional histological methods are thought to differentiate between them, so avoiding the need for antibodies. These were compared against each other for the first time in order to establish differences in image quality and discrimination between Type I and type III collagen. Neither technique requires antibodies, however picrosirius requires polarisation microscopy. to result in a clearer, consistently reproducible collagen staining pattern than the picrosirius method and more importantly did not require elaborate apparatus to analyze. Additionally other cellular elements were visible. Skin samples for research are often obtained from surgical excision. This clearly limits which tissues are available for comparative study to those areas operated on. Studying samples from embalmed medical school cadavers has the great advantage of studying areas of the body not routinely available from common surgical procedures. It was therefore desirable to assess whether embalmed cadaveric tissues exhibited different properties by virtue of their age and the embalming process compared to fresh surgical specimens, in order to give confidence that studies utilising the former would be equally valid. To test this, 58 skin samples from embalmed medical school cadavers were compared to skin samples from 38 fresh operative specimens. The levels of tissue preservation and processing artefacts were similar in both groups. Embalmed medical school cadavers clearly offer an opportunity to study tissue areas not routinely available during surgery. This is the first time such a comparison has been made. Many things will affect the final appearance of the scar, but the single most important determinant is the body region affected. The most common areas for unfavourable scarring, specifically keloid or hypertrophic scarring have been shown to be the ear, deltoid and sternal areas. To test the hypothesis that there is no difference in histological structure of skin that correlates to body region, comparative histology was undertaken exploring the regional variations of skin characteristics in 58 cadaveric samples. Closely comparable samples were taken from the deltoid (9), abdomen (13), sternum (10), post-auricular (5), earlobe (12) and eyelid (9). Epidermal thickness, epidermal appendage density and collagen fibre orientation were examined and qualitative structural differences were assessed for each region Skin samples were then grouped by both topographical location of the body and scarring potential. Skin samples exhibited qualitative and quantifiable regional variations in the characteristics studied. Epidermal thickness and appendage counts did not correlate with scarring potential. Both however were statistically significantly higher in skin sampled from the head compared to the trunk. Bundles of collagen fibres in the reticular dermis were grouped according to their orientation in relation to the coronal plane; either parallel, oblique or perpendicular. The ratio of oblique to parallel fibres was statistically significantly higher in body areas with poorer scarring prognosis. This corresponds to a more disorganised arrangement of collagen fibres in these areas. Further qualitative understanding of dermal collagen fibres came from perpendicular to conventional histological samples. This new method stained basement membranes purple, cytoplasm was stained greenish-brown and nuclei dark brown. Collagen fibres were either thin and blue or thick and green. This method was compared to PAS staining and although required more preparative steps allows greater identification of other cellular structures.

Sorting cells means manipulating them. This induces biological responses of the cells, resulting in functionalities not representing the previous state of the cells, but indicating effects of sorting procedures. Namely in cases that negative selection is not possible, isolated cells are distinct to their previous characteristics. This is true for bead-based sorting or flow cytometric cell separation and heavily skews functional markers of target cells. Of course, this is a limitation for any following investigation of these cells.

Label-free imaging modalities offer numerous advantages, such as the ability to avoid the time-consuming and potentially disruptive process of physical staining. However, one challenge that arises in label-free imaging is the limited ability to extract specific structural or molecular information from the acquired images. To overcome this limitation, a novel approach known as digital staining or digital labeling has emerged. Digital staining leverages the power of deep learning algorithms to virtually introduce labels or stains into label-free images, thereby enabling the extraction of detailed information that would typically require physical staining. The integration of digital staining with label-free imaging holds great promise in expanding the capabilities of imaging techniques, facilitating improved analysis, and advancing our understanding of biological systems at both the cellular and tissue level. In this thesis, I explore supervised and semi-supervised methodologies of digital staining and the applications in augmenting label-free imaging modalities, particularly in the context of cell imaging and brain imaging. In the first part of the thesis, I demonstrate the novel integration of multi-contrast dark-field reflectance microscopy and supervised deep learning to enable subcellular immunofluorescence labeling and cell cytometry from label-free imaging. By leveraging the rich structural information and sensitivity of reflectance microscopy, this method accurately predicts subcellular features without the need for physical staining. As a result of the use of a novel multi-contrast modality, the digital labeling approach demonstrates significant improvements over the state-of-the-art techniques, achieving up to 3× prediction accuracy. In addition to fluorescence prediction, the method successfully reproduces single-cell level structural phenotypes related to cell cycles. The multiplexed readouts obtained through digital labeling enable accurate multi-parametric single-cell profiling across a large cell population. In the second part, I investigated a novel digital staining optical coherence tomography (DS-OCT) modality combining advantages of serial sectioning OCT and semi-supervised deep learning and demonstrated several advantages for the application of 3D histological brain imaging. The DS model is trained using a semi-supervised learning framework that incorporates unpaired translation, a biophysical model, and cross-modality image registration, which manifests broad applicability to other weakly-paired bioimaging modalities. The DS model enables the translation of S-OCT images to Gallyas silver staining, providing consistent staining quality across different samples. I further show that DS enhances contrast across cortical layer boundaries and enables reliable cortical layer differentiation. Additionally, DS-OCT preserves 3D-geometry on centimeter-scale brain tissue blocks. My pilot study demonstrates promising results on other anatomical regions acquired from different S-OCT systems, highlighting its potential for generalization in various imaging contexts. Overall, I investigate the problems of augmenting label-free imaging modalities with deep learning generated digital stains. I explored both supervised and semi-supervised methods for building novel DS frameworks. My work showcased two important applications in the field of immunofluorescence cell imaging and 3D histological brain imaging. On the one hand, the integration of DS techniques with multi-contrast microscopy has the potential to enhance the throughput of single-cell imaging cytometry, and phenotyping. On the other hand, integrating DS techniques with S-OCT holds great potential for high-throughput human brain imaging, enabling comprehensive studies on the structure and function of the brain. Through the exploration, I aim to shed light on the impact of digital staining in the field of computational imaging and its implications for various scientific disciplines.

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This thesis examines stained glass windows in Indianapolis churches built between 1865 and 1915. It studies the trends in Indianapolis stained glass windows and compares them with the national trends in stained glass design. The evidence contained within this thesis indicates that a wide variety of styles popular at the time are represented in Indianapolis churches. The evidence also suggests that some national trends in stained glass did influence the design of the windows in Indianapolis. However, most of the windows in the surviving Indianapolis churches from the period are not typical of the high style trends in church stained glass found elsewhere in the United States. / Department of Architecture

<p dir="ltr">Generative Image-to-Image Translation (I2IT) involves transforming an input image from one domain to another. Typically, this transformation retains the content in the input image while adjusting the domain-dependent style elements. Generative I2IT finds utility in a wide range of applications, yet its effectiveness hinges on adaptations to the unique characteristics of the data at hand. This dissertation pushes the boundaries of I2IT by applying it to stain-related problems in computational pathology. Particularly, the main contributions span two major applications of stain translation: H&E-to-H&E and H&E-to-IHC, each with its unique requirements and challenges. More specifically, the first contribution addresses the generalization challenge posed by the high variability in H&E stain appearances to any task-specific machine learning models. To this end, the Generative Stain Augmentation Network (G-SAN) is introduced to augment the training images in any downstream task with random and diverse H&E stain appearances. Experimental results demonstrate G-SAN’s ability to enhance model generalization across stain variations in downstream tasks. The second key contribution in this dissertation focuses on H&E-to-IHC stain translation. The major challenge in learning accurate H&E-to-IHC stain translation is the frequent and sometimes severe inconsistencies in the groundtruth H&E-IHC image pairs. To make training more robust to these inconsistencies, a novel contrastive learning based loss, named the Adaptive Supervised PatchNCE (ASP) loss is presented. Experimental results suggest that the proposed ASP-based framework outperforms the state-of-the-art in H&E-to-IHC stain translation by significant margins. Additionally, a new dataset for H&E-to-IHC translation – the Multi-IHC Stain Translation (MIST) dataset, is released to the public, featuring paired images from H&E to four different IHC stains. For future directions of generative I2IT in stain translation problems, a proof-of-concept study of applying the latest diffusion model based I2IT methods to the problem of virtual H&E staining is presented.</p>

A goal in human embryonic stem cell (hESC) research is the faithful differentiation to given cell types such as neural lineages. During embryonic development, a basement membrane surrounds the neural plate that forms a tight, apico-basolaterally polarized epithelium before closing to form a neural tube with a single lumen. Here we show that the three-dimensional epithelial cyst culture of hESCs in Matrigel combined with neural induction results in a quantitative conversion into neuroepithelial cysts containing a single lumen. Cells attain a defined neuroepithelial identity by 5 days. The neuroepithelial cysts naturally generate retinal epithelium, in part due to IGF-1/insulin signaling. We demonstrate the utility of this epithelial culture approach by achieving a quantitative production of retinal pigment epithelial (RPE) cells from hESCs within 30 days. Direct transplantation of this RPE into a rat model of retinal degeneration without any selection or expansion of the cells results in the formation of a donor-derived RPE monolayer that rescues photoreceptor cells. The cyst method for neuroepithelial differentiation of pluripotent stem cells is not only of importance for RPE generation but will also be relevant to the production of other neuronal cell types and for reconstituting complex patterning events from three-dimensional neuroepithelia.