| 1. |
- Antonsson, Helena, et al.
(författare)
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Caregivers' reflections on their interactions with adult people with learning disabilities
- 2008
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 15:6, s. 484-91
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Tidskriftsartikel (refereegranskat)abstract
- People with learning disabilities and their professional carers often have difficulty interacting. The aim of this study was to illuminate carers' reflections on their interactions with adult people with learning disabilities. In a previous study, interactions between 16 carers and 11 residents with learning disabilities were recorded on video. In this study, stimulated recall interviews about the interactions were carried out with all the carers. The text was analysed using qualitative content analysis. The findings indicate that the carers reflected on both successful and unsuccessful interaction. Examples of successful interaction included understanding cues, satisfying needs, and managing challenging behaviours, and the carers reflected on the influences that successful interaction had on security, confidence, and satisfaction among the residents. Examples of unsuccessful interaction included failing to understand cues, failing to satisfy needs and failing to manage challenging behaviours, and the carers reflected on the consequences of such interaction, which included irritation, aggression and violence among the residents. Our findings have implications for interventions aimed at strengthening the competence of carers and developing strategies for managing challenging behaviour, in order to ensure high-quality care and a good working climate. © 2008 The Authors.
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| 2. |
- Degerman, Johan, 1976, et al.
(författare)
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An automatic system for in vitro cell migration studies
- 2009
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 233:1, s. 178-191
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Tidskriftsartikel (refereegranskat)abstract
- This paper describes a system for in vitro cell migration analysis. Adult neural stem/progenitor cells are studied using time-lapse bright-field microscopy and thereafter stained immunohistochemically to find and distinguish undifferentiated glial progenitor cells and cells having differentiated into type-1 or type-2 astrocytes. The cells are automatically segmented and tracked through the time-lapse sequence. An extension to the Chan-Vese Level Set segmentation algorithm, including two new terms for specialized growing and pruning, made it possible to resolve clustered cells, and reduced the tracking error by 65%. We used a custom-built manual correction module to form a ground truth used as a reference for tracked cells that could be identified from the fluorescence staining. On average, the tracks were correct 95% of the time, using our new segmentation. The tracking, or association of segmented cells, was performed using a 2-state Hidden Markov Model describing the random behaviour of the cells. By re-estimating the motion model to conform with the segmented data we managed to reduce the number of tracking parameters to essentially only one. Upon characterization of the cell migration by the HMM state occupation function, it was found that glial progenitor cells were moving randomly 2/3 of the time, while the type-2 astrocytes showed a directed movement 2/3 of the time. This finding indicates possibilities for cell-type specific identification and cell sorting of live cells based on specific movement patterns in individual cell populations, which would have valuable applications in neurobiological research.
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| 3. |
- Gustafsson, Anders
(författare)
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Cathodoluminescence studies of nanostructured semiconductors
- 2006
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 224:1, s. 72-78
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Tidskriftsartikel (refereegranskat)abstract
- Spatially and spectrally resolved cathodoluminescence in the scanning electron microscope is a very powerful technique for studying the optical properties of semiconductor structures, especially low-dimensional structures (structures with nanometre-sized features). The technique is generally nondestructive and can be combined with the normal imaging capabilities and analysis possibilities of the scanning electron microscope. This article gives an introduction to the technique and a number of examples of the possibilities of the technique.
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| 4. |
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| 5. |
- Jonasson, Jenny, 1976, et al.
(författare)
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A pixel-based likelihood framework for analysis of fluorescence recovery after photobleaching data
- 2008
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 232:2, s. 260-269
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Tidskriftsartikel (refereegranskat)abstract
- A new framework for the estimation of diffusion coefficients from data on fluorescence recovery after photobleaching (FRAP) with confocal laser scanning microscopy (CLSM) is presented. It is a pixel-based statistical methodology that efficiently utilizes all information about the diffusion process in the available set of images. The likelihood function for a series of images is maximized which gives both an estimate of the diffusion coefficient and a corresponding error. This framework opens up possibilities (1) to obtain localized diffusion coefficient estimates in both homogeneous and heterogeneous materials, (2) to account for time differences between the registrations at the pixels within each image, and (3) to plan experiments optimized with respect to the number of replications, the number of bleached regions for each replicate, pixel size, the number of pixels, the number of images in each series etc. To demonstrate the use of the new framework, we have applied it to a simple system with polyethylene glycol (PEG) and water where we find good agreement with diffusion coefficient estimates from NMR diffusometry. In this experiment, it is also shown that the effect of the point spread function is negligible, and we find fluorochrome-concentration levels that give a linear response function for the fluorescence intensity. © 2008 The Authors.
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| 6. |
- Jonasson, Jenny, 1976, et al.
(författare)
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Pixel-based analysis of FRAP data with a general initial bleaching profile
- 2010
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 239:2, s. 142-153
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Tidskriftsartikel (refereegranskat)abstract
- Jonasson et al. (2008), we presented a new pixel-based maximum likelihood framework for the estimation of diffusion coefficients from data on fluorescence recovery after photobleaching (FRAP) with confocal laser scanning microscopy (CLSM). The main method there, called the Gaussian profile method below, is based on the assumption that the initial intensity profile after photobleaching is approximately Gaussian. In the present paper, we introduce a method, called the Monotone profile method, where the maximum likelihood framework is extended to a general initial bleaching profile only assuming that the profile is a non-decreasing function of the distance to the bleaching centre. The statistical distribution of the image noise is further assumed to be Poisson instead of normal, which should be a more realistic description of the noise in the detector. The new Monotone profile method and the Gaussian profile method are applied to FRAP data on swelling of super absorbent polymers (SAP) in water with a Fluorescein probe. The initial bleaching profile is close to a step function at low degrees of swelling and close to a Gaussian profile at high degrees of swelling. The results obtained from the analysis of the FRAP data are corroborated with NMR diffusometry analysis of SAP with a polyethylene glycol probe having size similar to the Fluorescein. The comparison of the Gaussian and Monotone profile methods is also performed by use of simulated data. It is found that the new Monotone profile method is accurate for all types of initial profiles studied, but it suffers from being computationally slow. The fast Gaussian profile method is sufficiently accurate for most of the profiles studied, but underestimates the diffusion coefficient for profiles close to a step function. We also provide a diagnostic plot, which indicates whether the Gaussian profile method is acceptable or not.
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| 7. |
- Mölder, Anna, et al.
(författare)
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Non-invasive, label-free cell counting and quantitative analysis of adherent cells using digital holography
- 2008
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 232:2, s. 240-247
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Tidskriftsartikel (refereegranskat)abstract
- Manual cell counting is time consuming and requires a high degree of skill on behalf of the person performing the count. Here we use a technique that utilizes digital holography, allowing label-free and completely non-invasive cell counting directly in cell culture vessels with adherent viable cells. The images produced can provide both quantitative and qualitative phase information from a single hologram. The recently constructed microscope HolomonitorTM (Phase Holographic Imaging AB, Lund, Sweden) combines the commonly used phase contrast microscope with digital holography, the latter giving us the possibility of achieving quantitative information on cellular shape, area, confluence and optical thickness. This project aimed at determining the accuracy and repeatability of cell counting measurements using digital holography compared to the conventional manual cell counting method using a haemocytometer. The collected datawere also used to determine cell size and cellular optical thickness.Theresults showthat digital holography can be used for non-invasive automatic cell counting as precisely as conventional manual cell counting
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| 8. |
- Nygren, Håkan, 1952, et al.
(författare)
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Silver deposition on freeze-dried cells allows subcellular localization of cholesterol with imaging TOF-SIMS.
- 2004
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Ingår i: Journal of microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 215:Pt 2, s. 156-61
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Tidskriftsartikel (refereegranskat)abstract
- Imaging time-of-flight secondary ion mass spectrometry (TOF-SIMS) was used for characterization and subcellular localization of organic ions in leucocytes adhering to glass surfaces. The cells were fixed by freeze drying in 0.15 m ammonium formate buffer at pH 7.2-7.4. The freeze-dried cells were sputter-coated with silver, and the silver surface was analysed with imaging TOF-SIMS. TOF-SIMS spectra were recorded by scanning the primary ion beam over the analysis area and acquiring positive mass spectra of the ions leaving the surface. The relative brightness of each pixel within the analysis area reflects the signal intensity of a selected ion in that pixel. Data were collected separately at high mass resolution m/delta m > 7000 and at high lateral resolution (= 0.5 micro m). The images were analysed by principal component analysis (PCA). The glass-adhering cells showed a well defined attachment area with a diameter of up to 20 micro m, and an equally well defined cell body, containing the nucleus, with a diameter of 8-10 micro m. On the raw data images, the obtained cholesterol distributions were consistent with a higher cholesterol content of the cell membrane in the attachment area than in the cell body. Using PCA analysis, silver-cationized molecular cholesterol was found localized mainly in the attachment area of the cells. Cholesterol was also seen at higher concentration in circular spots of
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| 9. |
- Yao, Yiming, 1957, et al.
(författare)
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Cross sectional TEM investigation of Ni-catalysed carbon nanotube films grown by plasma enhanced CVD
- 2005
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 219, s. 69-75
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Nickel-catalysed multiwall carbon nanotubes synthesized by plasma-enhanced chemical vapour deposition on a silicon substrate with acetylene and ammonia at 700 °C have been characterized by high-resolution and analytical transmission electron microscopy. The nucleation of the carbon nanotubes occurs as a consequence of the carburization and dusting of supported preformed nickel- and silicon-rich particles. This process yields disintegrated silicon-containing nickel particles dispersed in dome-shaped carbon islands adherent to the substrate. The particles act as catalysts for tube growth, resulting in aligned multiwall carbon nanotubes with a bamboo-like structure anchored to the dome-shaped carbon islands. The bottom part of the carbon islands contains bundles of graphene sheets orientated parallel to the substrate. The nanotubes are capped with fcc nickel particles containing dissolved silicon. Most of these particles have a conical shape orientated with a <110> direction along the tube growth axis, and with {110} and {111} planes as exposed faces.
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| 10. |
- Spiecker, E., et al.
(författare)
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Advantages of aberration correction for HRTEM investigation of complex layer compounds
- 2010
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Ingår i: Journal of Microscopy. - : Wiley: 12 months. - 0022-2720 .- 1365-2818. ; 237:3, s. 341-346
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Tidskriftsartikel (refereegranskat)abstract
- Aberration-corrected high-resolution transmission electron microscopy (HRTEM) has been applied to resolve the atomic structure of a complex layered crystal, (PbS)(1.14)NbS(2), which comprises a high density of incommensurate interfaces. The strong suppression of image delocalization and the favourable contrast transfer under negative C(s) imaging (NCSI) conditions have been exploited for obtaining HRTEM images which directly reveal the projected crystal structure and allow to study lattice imperfections, like stacking disorder and layer undulations, with atomic scale resolution. The advantages of aberration-corrected HRTEM over conventional HRTEM are demonstrated by direct comparison of experimental images and computer simulations.
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| 11. |
- Stollberg, Heide, et al.
(författare)
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A vacuum-compatible wet-specimen chamber for compact x-ray microscopy
- 2007
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 226:1, s. 71-73
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Tidskriftsartikel (refereegranskat)abstract
- Soft X-ray microscopy is a powerful tool for investigations of, for example, polymers or soils in their natural liquid environment. This requires a wet-specimen chamber. Compact X-ray microscopy allows the horizontal mounting of such samples, thereby reducing the influence of gravitational forces. We have developed a wet-specimen chamber for such compact X-ray microscope. The chamber is vacuum compatible, which reduces the exposure time. The vacuum sealing is achieved by a combination of mechanical sealing and sealing by bio-compatible glue. With the wet-specimen chamber the specimens can be kept in an aqueous environment in a vacuum of 10(-4) mbar for several hours. Imaging of lipid droplets in water demonstrates the function of the wet-specimen chamber.
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| 12. |
- Stollberg, Heide, et al.
(författare)
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Wavelet-based image restoration for compact x-ray microscopy
- 2003
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 211:2, s. 154-160
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Tidskriftsartikel (refereegranskat)abstract
- Compact water-window X-ray microscopy with short exposure times will always be limited on photons owing to sources of limited power in combination with low-efficency X-ray optics. Thus, it is important to investigate methods for improving the signal-to-noise ratio in the images. We show that a wavelet-based denoising procedure significantly improves the quality and contrast in compact X-ray microscopy images. A non-decimated, discrete wavelet transform (DWT) is applied to original, noisy images. After applying a thresholding procedure to the finest scales of the DWT, by setting to zero all wavelet coefficients of magnitude below a prescribed value, the inverse DWT to the thresholded DWT produces denoised images. It is concluded that the denoising procedure has potential to reduce the exposure time by a factor of 2 without loss of relevant image information.
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| 13. |
- Stollberg, Heide, et al.
(författare)
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Size-selective colloidal-gold localization in transmission x-ray microscopy
- 2007
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 225:1, s. 80-87
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Tidskriftsartikel (refereegranskat)abstract
- Colloidal gold is a useful marker for functional-imaging experiments in transmission X-ray microscopy. Due to the low contrast of gold particles with small diameters it is necessary to develop a powerful algorithm to localize the single gold particles. The presented image-analysis algorithm for identifying colloidal gold particles is based on the combination of a threshold with respect to the local absorption and shape discrimination, realized by fitting a Gaussian profile to the identified regions of interest. The shape discrimination provides the possibility of size-selective identification and localization of single colloidal gold particles down to a diameter of 50 nm. The image-analysis algorithm, therefore, has potential for localization studies of several proteins simultaneously and for localization of fiducial markers in X-ray tomography.
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| 14. |
- Adler, Jeremy
(författare)
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The unitary scale bar : human and machine readable
- 2008
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 230:1, s. 163-166
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Tidskriftsartikel (refereegranskat)abstract
- A format is described for a scale bar that encodes the length represented within the structure of the bar itself, thereby removing the need for any supporting text. Although the 'unitary' scale bar has a conventional appearance it is also machine readable and therefore retains information about the scale even when the file format is changed. The format is based on the metre and is suitable for all terrestrial applications.
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| 15. |
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| 16. |
- Almqvist, Nils, et al.
(författare)
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Micromechanical and structural properties of a pennate diatom investigated by atomic force microscopy
- 2001
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 202:3, s. 518-532
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Tidskriftsartikel (refereegranskat)abstract
- The mechanisms behind natural nanofabrication of highly structured silicas are increasingly being investigated. We have explored the use of a standard Nanoscope III Multimode atomic force microscope (AFM) to study the silica shell of diatoms. The delicate structures of the shell surface of the diatom Navicula pelliculosa (Breb.) Hilse were imaged and the shell's micromechanical properties were measured semi-quantitatively with a resolution down to approximately 10 nm. The technique to measure elasticity and hardness with the AFM was demonstrated to be useable even on these hard glass-like surfaces, Different experimental configurations and evaluation methods were tested, They gave a consistent result of the shell micromechanical properties, The first results showed that the diatom shell's overall hardness and elasticity was similar to that of known silicas. However, regions with different mechanical proper ties were distinguished. The elastic modulus varied from 7 to 20 GPa, from 20 to 100 GPa and from 30 to hundreds of GPa depending on the location. In general, the hardness measurements showed similar spatial differences, The hardness values ranged from 1 to 12 GPa but one specific part of the shell was even harder. Hence, certain localized regions of the shell were significantly harder or more elastic. These regions coincide with known characteristic features and mechanisms appearing at the different stages of the shell's growth. These results show that this method serves as a complementary tool in the study of silica biomineralization, and can detect eventual crystalline phases.
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| 17. |
- Andersson, Viktor, et al.
(författare)
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Morphology of organic electronic materials imaged via electron tomography
- 2012
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 247:3, s. 277-287
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Tidskriftsartikel (refereegranskat)abstract
- Several organic materials and blends have been studied with the use of electron tomography. Tomography reconstructions of active layers of organic solar cells, where various preparation techniques have been used, have been analysed and compared to device behaviour. In addition, materials with predefined structures, including contrast enhancing features, have been studied and double tilt data collection has been employed to improve reconstructions. Small changes in preparation procedures may lead to large differences in morphology and device performance, and the results also indicate a complex relation between these.
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| 18. |
- Berglund, M., et al.
(författare)
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Compact water-window transmission X-ray microscopy
- 2000
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 197, s. 268-273
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate sub-100 nm resolution water-window soft X-ray full-field transmission microscopy with a compact system. The microscope operates at lambda = 3.37 nm and is based on a 100 Hz table-top regenerative debris-free droplet-target laser-plasma X-ray source in combination with normal-incidence multilayer condenser optics for sample illumination. High-spatial-resolution imaging is performed with a 7.3% efficiency nickel zone plate and a 1024 x 1024 pixel CCD detector. Images of dry test samples are recorded with exposure times of a few minutes and show features smaller than 60 nm.
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| 19. |
- Bongini, Lorenzo, et al.
(författare)
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Resolving the geometry of biomolecules imaged by cryo electron tomography
- 2007
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 228:2, s. 174-184
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we describe two methods for computerized analysis of cryo electron tomography reconstructions of biomolecules. Both methods aim at quantifying the degree of structural flexibility of macromolecules and eventually resolving the inner dynamics through automatized protocols. The first method performs a Brownian dynamics evolution of a simplified molecular model into a fictitious force field generated by the tomograms. This procedure enables us to dock the simplified model into the experimental profiles. The second uses a fuzzy framework to delineate the subparts of the proteins and subsequently determine their interdomain relations. The two methods are discussed and their complementarities highlighted with reference to the case of the immunoglobulin antibody. Both artificial maps, constructed from immunoglobulin G entries in the Protein Data Bank and real tomograms are analyzed. Robustness issues and agreement with previously reported measurements are discussed.
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| 20. |
- Carlsson, Kjell, et al.
(författare)
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Confocal pH imaging of microscopic specimens using fluorescence lifetimes and phase fluorometry : influence of parameter choice on system performance
- 2000
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 199, s. 106-114
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the performance of confocal pH imaging when using phase fluorometry and fluorophores with pH-dependent lifetimes. In these experiments, the specimen is illuminated by a laser beam, whose intensity is sinusoidally modulated. The lifetime-dependent phase shift in the fluorescent signal is detected by a lock-in amplifier, and converted into a pH value through a calibration procedure. A theoretical investigation is made of how the different system parameters will influence the results concerning sensitivity and noise. Experiments carried out with the fluorophore SNAFL-2 support these theoretical predictions. It is found that, under realistic experimental conditions, we can expect a pH change of 0.1 units to be easily detected in an 8-bit digital image. However, the pixel-to-pixel root mean square noise is often of the order of one pH unit. This comparatively high level of noise has its origin in photon quantum noise. pH measurements on living cells show a systematic deviation from expected values. This discrepancy appears to be the result of fluorophore interaction with various cell constituents, and is the subject of further investigation.
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| 21. |
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| 22. |
- Dahlström, Christina, et al.
(författare)
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New Method for Characterizing Paper Coating Structures Using Argon Ion Beam Milling and Field Emission Scanning Electron Microscopy
- 2011
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 241:2, s. 179-187
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a new method for characterizing microstructures of paper coating using argon ion beam milling technique and field emission scanning electron microscopy. The combination of these two techniques produces extremely high-quality images with very few artefacts, which are particularly suited for quantitative analyses of coating structures. A new evaluation method has been developed by using marker-controlled watershed segmentation technique of the secondary electron images. The high-quality secondary electron images with well-defined pores makes it possible to use this semi-automatic segmentation method. One advantage of using secondary electron images instead of backscattered electron images is being able to avoid possible overestimation of the porosity because of the signal depth. A comparison was made between the new method and the conventional method using greyscale histogram thresholding of backscattered electron images. The results showed that the conventional method overestimated the pore area by 20% and detected around 5% more pores than the new method. As examples of the application of the new method, we have investigated the distributions of coating binders, and the relationship between local coating porosity and base sheet structures. The technique revealed, for the first time with direct evidence, the long-suspected coating non-uniformity, i.e. binder migration, and the correlation between coating porosity versus base sheet mass density, in a straightforward way.
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| 23. |
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| 24. |
- Gavrilovic, Milan, 1981-, et al.
(författare)
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Quantification of colocalization and cross-talk based on spectral angles
- 2009
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Ingår i: Journal of Microscopy. - Oxford, UK : Blackwell Publishing. - 0022-2720 .- 1365-2818. ; 234:3, s. 311-324
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Tidskriftsartikel (refereegranskat)abstract
- Common methods for quantification of colocalization in fluorescence microscopy typically require cross-talk free images or images where cross-talk has been eliminated by image processing, as they are based on intensity thresholding. Quantification of colocalization includes not only calculating a global measure of the degree of colocalization within an image, but also a classification of each image pixel as showing colocalized signals or not. In this paper, we present a novel, automated method for quantification of colocalization and classification of image pixels. The method, referred to as SpecDec, is based on an algorithm for spectral decomposition of multispectral data borrowed from the field of remote sensing. Pixels are classified based on hue rather than intensity. The hue distribution is presented as a histogram created by a series of steps that compensate for the quantization noise always present in digital image data, and classification rules are thereafter based on the shape of the angle histogram. Detection of colocalized signals is thus only dependent on the hue, making it possible to classify also low-intensity objects, and decoupling image segmentation from detection of colocalization. Cross-talk will show up as shifts of the peaks of the histogram, and thus a shift of the classification rules, making the method essentially insensitive to cross-talk. The method can also be used to quantify and compensate for cross-talk, independent of the microscope hardware.
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| 25. |
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