An important step in data processing from terrestrial laser scanning (TLS) is georeferencing, i.e. transformation of the scanner data (point clouds) into a real world coordinate system, which is important for their integration with other geospatial data. An efficient approach for this is direct georeferencing, whereby the position and orientation of the scanner can be determined in the field, similarly to the working routine of total stations. Thus the efficiency of the survey can be increased, and the project time and costs reduced. An important factor that affects the results of TLS surveys, especially those with direct georeferencing, is scanner calibration. In the recent years, the method of self-calibration used in photogrammetry has become popular for the recovery of systematic errors in laser scanners. This thesis has two main aims. The first one is to develop an approach for self-calibration of terrestrial laser scanners, which can be made available to users, and apply it to the calibration of a number of pulsed laser scanners in order to get a better insight into the systematic instrumental errors present in these instruments. The second aim is to investigate the possibilities for direct georeferencing in TLS in static applications, with the focus on the use of GPS for this purpose, and to develop a survey system based on the combination of TLS and GPS. An additional aim of the thesis is to make a systematic description of the error sources in TLS surveys, where direct georeferencing is employed. A good understanding of these error sources is necessary to secure the data accuracy. We subdivide these errors into four groups: instrumental, object-related, environmental and georeferencing. We have developed a unified approach for self-calibration of terrestrial laser scanners, where one can introduce stochastic information about all the estimated parameters, which helps in reducing their correlations. In part, it is possible to use direct georeferencing to determine the exterior orientation parameters of the scanner. We applied this approach to the self-calibration of the pulsed scanners Callidus CP 3200, Leica HDS 3000 and Leica Scan Station. The initial assumption was that the scanner systematic instrumental errors, or calibration parameters, were similar to those in a total station. However, other errors not explained by the “a priori” total station error model can be present in the scanners. We revealed two such errors – the scale errors in the vertical angles and horizontal directions in the scanners Callidus CP 3200 and Leica HDS 3000, respectively. Most systematic errors were estimated with relatively high precision and low correlations with other system parameters. We have developed a prototype combined survey system, which allows the user to use GPS for direct georeferencing of the scanner parallel to the scanning. In the current implementation, the system consists of the scanning system Leica Scan Station 2, 2 GPS receivers and antennas from Leica and a number of necessary accessories. The scanner position can be determined from RTK (or possibly Network-RTK) measurements with the accuracy of better than 1 cm, both in plane and height. The position of the backsight target can be determined from post-processing of static GPS measurements with similar accuracy. In order to estimate the accuracy of the combined system and its efficiency in a typical TLS survey, we carried out several test measurements. The results have shown that it is possible to achieve the coordinate accuracy of better than 1 cm at the object distance of up to 50 m. This is comparable to the accuracy of conventional direct georeferencing, i.e. when the scanner is centred over a known point. The time expenses for the test survey of a building located at KTH campus, starting from the planning and finishing with the georeferenced point cloud, were about 1.5 workdays. The time expenses could be reduced further if the system was installed on a moving platform during the fieldwork. Hence, the combined system can be successfully used for the surveys of built environments, e.g. engineering constructions and historical monuments, which can be carried out fast and with high accuracy. / QC 20100806 / 3D laser scanning of engineering constructions and historical monuments

Intravital microscopy such as in vivo imaging of brain dynamics is often performed with custom-built microscope setups controlled by custom-written software to meet specific requirements. Continuous technological advancement in the field has created a need for new control software that is flexible enough to support the biological researcher with innovative imaging techniques and provide the developer with a solid platform for quickly and easily implementing new extensions. Here, we introduce HelioScan, a software package written in LabVIEW, as a platform serving this dual role. HelioScan is designed as a collection of components that can be flexibly assembled into microscope control software tailored to the particular hardware and functionality requirements. Moreover, HelioScan provides a software framework, within which new functionality can be implemented in a quick and structured manner. A specific HelioScan application assembles at run-time from individual software components, based on user-definable configuration files. Due to its component-based architecture, HelioScan can exploit synergies of multiple developers working in parallel on different components in a community effort. We exemplify the capabilities and versatility of HelioScan by demonstrating several in vivo brain imaging modes, including camera-based intrinsic optical signal imaging for functional mapping of cortical areas, standard two-photon laser-scanning microscopy using galvanometric mirrors, and high-speed in vivo two-photon calcium imaging using either acousto-optic deflectors or a resonant scanner. We recommend HelioScan as a convenient software framework for the in vivo imaging community. / <p>Paid Open Access</p>

Transcription elongation regulator 1 (TCERG1) is a nuclear protein involved in transcriptional elongation and splicing events, suggesting these two activities may be connected. Moreover, TCERG1 was recently identified as a novel interactor and co-repressor of CCAAT/Enhancer Binding Protein &alpha; (C/EBP&alpha;) transcriptional activity, suggesting TCERG1 has additional biological roles. Interestingly, TCERG1 also inhibits the growth arrest activity of C/EBP&alpha;. Additionally, the original clone found to interact with C/EBP&alpha; consisted of only the amino-terminal domain of TCERG1 and functional analysis of this clone indicated that it retained the ability to repress both C/EBP&alpha; mediated growth arrest and transcriptional activity. Furthermore, a TCERG1 mutant whose amino-terminal region was deleted was unable to interact with or repress the transcriptional and growth arrest activities of C/EBP&alpha;, suggesting the functional domain(s) lie elsewhere. In this study, domains of TCERG1 were examined for the ability to inhibit C/EBP&alpha;-mediated growth arrest and the mechanism whereby this effect occurs. By exploiting fluorescent properties of expressed proteins fused with green fluorescent protein, the extent to which each TCERG1 mutant was able to reverse C/EBP&alpha;-mediated growth arrest of cultured cells was assessed. Our analyses suggest that the inhibitory activity of TCERG1 lies within the amino-terminal region and may involve WWI and WWII domains within this region. Additionally, laser scanning confocal microscopy (LCSM) was used to visualize the subnuclear localization of fluorescent proteins fused to TCERG1 and C/EBP&alpha;. When expressed alone, TCERG1 localized to splicing factor-rich nuclear speckles while C/EBP&alpha; was found to reside in discrete punctate foci, both localization patterns being distinct and different from each other. Results from co-localization studies after co-expressing both proteins indicate an alteration in the subnuclear distribution of TCERG1. Furthermore, TCERG1 co-localizes with C/EBP&alpha;, suggesting a possible mechanism whereby TCERG1 inhibits the growth arrest and transcriptional activities mediated by C/EBP&alpha;.

This study aims to present and evaluate a new method for measuring the distribution of snow within built-up environments by differencing elevations collected by an Airborne Laser Scanner (ALS) before, and during peak snow accumulation. Few efforts have been made to study the distribution of snow within built-up environments due to the false assumption that high-intensity rainfall is the main contributor to peak yearly runoff rates. Traditional techniques for measuring snow are often difficult to replicate in built-up environments due to incompatibility of methods and barriers such as buildings, roads and private property. Light Detection and Ranging (LiDAR) technology, specifically ALSs, have previously been used to characterize the distribution of snow under forest canopy, and in remote mountain environments. This study investigates and assesses the utility of high resolution, non-intrusive ALS data for estimating the depth and distribution of snow within the town of Uxbridge, Ontario. ALS flights for this study were completed before the onset of snow accumulation, as well as near peak snow accumulation for the winters of 2010 and 2011. Pre and post snow accumulation ALS measured elevations were differenced to estimate the depth of the snowpack across the entire study area at a resolution of 0.5 m. Ground measurements of snow depth were also completed within 24 hours of each of the winter flights. The LiDAR-estimated and ground-measured snow depths were compared using Spearman's rank correlation coefficient as well as Mean Absolute Error (MAE) and Root Mean Squared Error (RMSE). Results from this thesis show that: 1) Snow depths estimated by differencing elevations from two ALS flights show a MAE of 3 cm and an RMSE of 10 cm when compared to ground-measured snow depths. (2) There is a strong, statistically significant relationship (ρ = 0:82, p < 0:001) between LiDAR-estimated and ground-measured snow depths. (3) An average bias of -3 cm was found for the entire dataset showing an underestimation in the LiDAR-estimated snow depths most likely caused by the effects of low lying vegetation on the fall ALS measurements. The results presented in this study demonstrate that ALSs are capable of providing high spatial resolution snow depth estimates within built-up environments. Furthermore, snow depth measurements made using an ALS can be used to increase the current body of knowledge on the distribution and re-distribution of snow within built-up environments. Snow distributions measured by an ALS could also be used for future development and verification of urban hydrological models.

Purpose: To locate protein sorption on the surface and inside the matrix of soft contact lens materials and intraocular lenses (IOL). Methods: The proteins albumin and lysozyme were investigated as they are highly abundant in blood serum and tears, respectively. Proteins were conjugated with organic fluorescent probes and using confocal laser scanning microscopy (CLSM) the sorption profile to contact lenses and IOL could be determined. Radiolabeled protein was used for quantification purposes. • Albumin sorption to etafilcon A and lotrafilcon B was determined (Chapter 3) • Different fluorescent probes were used for conjugation and the impact on albumin sorption behaviour was investigated (Chapter 4) • Lysozyme sorption to nine different pHEMA-based and silicone hydrogel contact lenses was determined using two fluorescent probes (Chapter 5) • The efficiency of protein removal from contact lenses using contact lens care regimens was investigated (Chapter 6) • Albumin sorption to IOL materials was quantified and imaged using a modified CLSM technique (Chapter 7) Results: Albumin and lysozyme sorption profiles differed between materials, and were influenced by the fluorescent probes used for conjugation. After one day of incubation, both proteins could be located within all contact lens materials, except for lotrafilcon A and lotrafilcon B, which primarily allowed deposition on the lens surface. An increase in protein accumulation was found for most materials over the maximum investigated period of 14 days, using CLSM and radiolabel techniques. The efficiency of contact lens care regimens to remove lysozyme and albumin depended on the lens material, care regimen and protein type investigated. PMMA and silicone IOLs showed protein exclusively on the surface, while a hydrophilic acrylic IOL allowed penetration into the lens matrix over time. Despite the albumin penetration depth into hydrophilic acrylic, the highest albumin levels were determined for the silicone IOL. Conclusions: CLSM provides detailed information that can describe the protein distribution in transparent biomaterials, with scanning depths up to a few hundred microns. However, the CLSM data are primarily of qualitative value, which necessitates a quantitative technique (e.g. radiolabeling) to determine the total protein content.

Orientering är en sport som går ut på att besöka ett antal förutbestämda kontrollpunkter med hjälp av en karta. Orienteringskartan redovisar olika objekt som finns i verkligheten så som stenar, gropar, höjder och branter. Att tillverka en orienteringskarta är dyrt och tidskrävande. Omkring 120 000–150 000 kr och mellan 20–30 h/km2 fältarbete läggs ner på varje karta som skapas. Eftersom orienteringskartorna framställs av ideella föreningar är alla sätt som gör kartframställningen billigare välkomna.   I detta examensarbete har en funktion skapats i ett befintligt program vid namn OL Laser. Funktionens syfte är att automatiskt identifiera branter i laserdata för användning som grundmaterial vid framställning av orienteringskartor. För att räknas som en orienteringsbrant krävs det att tre stycken kriterier uppfylls, nämligen minst 1 m höjdskillnad, minst 1 m utbredning och en lutning större än 85°. Dessa kriterier bestämdes genom att komplettera de befintliga avgränsningarna som anges i Internationella Orienteringsförbundets regleringar för orienteringskartor med egna mätningar i tre stycken olika referensområden kring Gävle. Därefter programmerades funktionen så att genom att klicka på en knapp startas en sökning i ett höjdraster. Steg för steg söks höjdrastret igenom efter pixlar som uppfyller de givna parametrarna för höjdskillnad, utbredning och lutning. Värdet på parametrarna för lutning, höjdskillnad och utbredning bestämdes genom att kalibrera funktionen mot referensområdena. Kalibrering gjordes för att det skulle vara möjligt att automatiskt identifiera branter. De inställningar på parametrarna som användes i funktionen efter kalibrering var 42,5° lutning, 0,6 m höjdskillnad och en utbredning över minst två sammanhängande pixlar. Resultatet utgörs av de pixlar som funktionen identifierar som en brant.   Resultatet visar att funktionen klarar av att hitta branter automatiskt, även i områden som den inte kalibrerats mot. För att använda branterna till en orienteringskarta krävs det att en kartritare verifierar resultat av funktionen ute i fält. Med hjälp av funktionen sparas både tid och pengar i framställningen av orienteringskartor. / Orienteering is a sport where the purpose is to visit a number of predefined control points using a map. The orienteering map shows various objects such as rocks, pits, knolls and cliffs. It is expensive and time consuming to produce an orienteering map. Approximately 120.000-150.000 SEK and 20–30 h/km2 field work is invested in every map produced. Considering orienteering maps are financed by non-profit orienteering organizations every time and money saving process is welcome.   In this degree project a function has been created in a software called OL Laser. The aim of the function is to automatically identify cliffs in laser data for the usage as base maps in the production of orienteering maps. First the definition for cliffs in orienteering was defined. To be classified as a cliff three requirements had to be fulfilled, namely at least 1 m in height difference, at least 1 meter wide and a gradient greater than 85°. These requirements were determined by supplementing the existing restrictions specified in the regulations for orienteering maps with own measurements in three different reference areas around Gävle. The function was programmed so that a search in a height raster was started. Step by step the raster was scanned for pixels that meet the given parameters of the height difference, the width and gradient. The values of the parameters were determined by calibrating the function in the reference areas. The calibration was made to make it possible to automatically identify cliffs. The settings of the parameters used in the function after the calibration were 42.5° gradient, 0.6 m height difference and a propagation of at least two consecutive pixels. The pixels that the function identified as a cliff is the result.   The result shows that the function is able to automatically find the cliffs, even in areas which it is not calibrated against. To be able to use the cliffs on an orienteering map, the cartographer has to verify the result of the function in the field. Both time and money is saved by using the function when producing orienteering maps.

The myocardial infarction (MI) is one of the leading causes of death in the world today. Accumulated atherosclerotic plaque occluding cardiac blood vessels results in a lack of oxygen supply to parts of the heart, and consequentially the death cardiomyocytes. The damaged area is replaced by scar tissue because of the heart’s insufficient regenerative capability, and the contraction property of the post-MI heart is therefore compromised. The recent findings of an endogenous cardiac progenitor cell (CPC) population gives hope for the establishment of new methods for medical treatments of the post-MI heart. Compared to other stem/progenitor cell sources, the CPCs are committed to a cardiac fate which places them in the forefront of interesting cell sources for regenerative treatments. In this thesis, the distribution of stem cell antigen 1 (Sca-1) positive CPCs in the healthy mouse myocardium, as well as the healthy and post-MI rat left ventricle was determined and compared to the total amount of nuclei. An immunohistochemistry protocol for the detection of Sca-1+ cells was established, and the number of Sca-1+ cells and the total number of nuclei in the different mouse and rat tissue samples were counted using laser scanning cytometry (LSC). The results could conclude a significantly higher distribution of Sca-1+ cells in the mouse atrium compared to the mouse ventricle, and a significantly higher distribution of Sca-1+ cells in the 8 days post-MI rat left ventricle compared to the healthy rat left ventricle. Furthermore, a heterogeneous distribution within the 8 days post-MI rat left ventricle was observed.

Accurate 3D models of natural environments are important for many modelling and simulation applications, for both civilian and military purposes. When building 3D models from high resolution data acquired by an airborne laser scanner it is de-sirable to separate and classify the data to be able to process it further. For example, to build a polygon model of a building the samples belonging to the building must be found. In this thesis we have developed, implemented (in IDL and ENVI), and evaluated algorithms for classification of buildings, vegetation, power lines, posts, and roads. The data is gridded and interpolated and a ground surface is estimated before the classification. For the building classification an object based approach was used unlike most classification algorithms which are pixel based. The building classifica-tion has been tested and compared with two existing classification algorithms. The developed algorithm classified 99.6 % of the building pixels correctly, while the two other algorithms classified 92.2 % respective 80.5 % of the pixels correctly. The algorithms developed for the other classes were tested with thefollowing result (correctly classified pixels): vegetation, 98.8 %; power lines, 98.2 %; posts, 42.3 %; roads, 96.2 %.

Purpose: To locate protein sorption on the surface and inside the matrix of soft contact lens materials and intraocular lenses (IOL). Methods: The proteins albumin and lysozyme were investigated as they are highly abundant in blood serum and tears, respectively. Proteins were conjugated with organic fluorescent probes and using confocal laser scanning microscopy (CLSM) the sorption profile to contact lenses and IOL could be determined. Radiolabeled protein was used for quantification purposes. • Albumin sorption to etafilcon A and lotrafilcon B was determined (Chapter 3) • Different fluorescent probes were used for conjugation and the impact on albumin sorption behaviour was investigated (Chapter 4) • Lysozyme sorption to nine different pHEMA-based and silicone hydrogel contact lenses was determined using two fluorescent probes (Chapter 5) • The efficiency of protein removal from contact lenses using contact lens care regimens was investigated (Chapter 6) • Albumin sorption to IOL materials was quantified and imaged using a modified CLSM technique (Chapter 7) Results: Albumin and lysozyme sorption profiles differed between materials, and were influenced by the fluorescent probes used for conjugation. After one day of incubation, both proteins could be located within all contact lens materials, except for lotrafilcon A and lotrafilcon B, which primarily allowed deposition on the lens surface. An increase in protein accumulation was found for most materials over the maximum investigated period of 14 days, using CLSM and radiolabel techniques. The efficiency of contact lens care regimens to remove lysozyme and albumin depended on the lens material, care regimen and protein type investigated. PMMA and silicone IOLs showed protein exclusively on the surface, while a hydrophilic acrylic IOL allowed penetration into the lens matrix over time. Despite the albumin penetration depth into hydrophilic acrylic, the highest albumin levels were determined for the silicone IOL. Conclusions: CLSM provides detailed information that can describe the protein distribution in transparent biomaterials, with scanning depths up to a few hundred microns. However, the CLSM data are primarily of qualitative value, which necessitates a quantitative technique (e.g. radiolabeling) to determine the total protein content.

Transcription elongation regulator 1 (TCERG1) is a nuclear protein involved in transcriptional elongation and splicing events, suggesting these two activities may be connected. Moreover, TCERG1 was recently identified as a novel interactor and co-repressor of CCAAT/Enhancer Binding Protein &alpha; (C/EBP&alpha;) transcriptional activity, suggesting TCERG1 has additional biological roles. Interestingly, TCERG1 also inhibits the growth arrest activity of C/EBP&alpha;. Additionally, the original clone found to interact with C/EBP&alpha; consisted of only the amino-terminal domain of TCERG1 and functional analysis of this clone indicated that it retained the ability to repress both C/EBP&alpha; mediated growth arrest and transcriptional activity. Furthermore, a TCERG1 mutant whose amino-terminal region was deleted was unable to interact with or repress the transcriptional and growth arrest activities of C/EBP&alpha;, suggesting the functional domain(s) lie elsewhere. In this study, domains of TCERG1 were examined for the ability to inhibit C/EBP&alpha;-mediated growth arrest and the mechanism whereby this effect occurs. By exploiting fluorescent properties of expressed proteins fused with green fluorescent protein, the extent to which each TCERG1 mutant was able to reverse C/EBP&alpha;-mediated growth arrest of cultured cells was assessed. Our analyses suggest that the inhibitory activity of TCERG1 lies within the amino-terminal region and may involve WWI and WWII domains within this region. Additionally, laser scanning confocal microscopy (LCSM) was used to visualize the subnuclear localization of fluorescent proteins fused to TCERG1 and C/EBP&alpha;. When expressed alone, TCERG1 localized to splicing factor-rich nuclear speckles while C/EBP&alpha; was found to reside in discrete punctate foci, both localization patterns being distinct and different from each other. Results from co-localization studies after co-expressing both proteins indicate an alteration in the subnuclear distribution of TCERG1. Furthermore, TCERG1 co-localizes with C/EBP&alpha;, suggesting a possible mechanism whereby TCERG1 inhibits the growth arrest and transcriptional activities mediated by C/EBP&alpha;.