| 1. |
- Althoff, Karin, 1974, et al.
(författare)
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Combined segmentation and tracking of neural stem-cells
- 2005
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Ingår i: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 1611-3349 .- 0302-9743. ; 3540, s. 282-291
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we analyze neural stem/progenitor cells in an time-lapse image sequence. By using information about the previous positions of the cells, we are able to make a. better selection of possible cells out of a collection of blob-like objects. As a blob detector we use Laplacian of Gaussian (LoG) filters at multiple scales, and the cell contours of the selected cells are segmented using dynamic programming. After the segmentation process the cells are tracked in the sequence using a. combined nearest-neighbor and correlation matching technique. An evaluation of the system show that 95% of the cells were correctly segmented and tracked between consecutive frames.
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| 2. |
- Andersson, J., et al.
(författare)
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Echogenecity of the carotid intima-media complex is related to cardiovascular risk factors, dyslipidemia, oxidative stress and inflammation The Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) study
- 2009
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Ingår i: Atherosclerosis. - : Elsevier BV. - 1879-1484 .- 0021-9150. ; 204:2, s. 612-618
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Tidskriftsartikel (refereegranskat)abstract
- Background: Increased carotid artery intima-media thickness (IMT), measured by ultrasound, is related to an increased risk of cardiovascular disease. Since presence of echolucent plaques increases the risk further, we investigated if echogenecity of the carotid intima-media complex is related to markers of cardiovascular risk. Our aim was therefore to investigate if intima-media echogenecity is related to cardiovascular risk factors, or to markers of inflammation and oxidation in an exploratory investigation. Methods: The PIVUS cohort study is an observational study of 1016 (509 women and 507 men) randomly chosen individuals aged 70 living in Uppsala, Sweden. Carotid artery ultrasound measurements were performed. IMT and the grey scale median (GSM) value were calculated in the intima-media complex (IM-GSM) in the far wall of the common carotid artery. Traditional risk factors were evaluated together with indices of oxidative stress and inflammation. Results: In the multiple regression analysis, HDL-cholesterol, body mass index, conjugated diens, glutathione, e-selectin and TNF alfa were significantly related to IM-GSM. IMT was independently related to blood pressure, smoking and body mass index. Conclusion: The echolucency of the carotid intima-media was related to several cardiovascular risk factors not related to IMT, such as dyslipidemia, oxidative stress and inflammation. Since the echogenecity of the carotid intima-media complex was related to different risk factors compared to carotid IMT, it is worthwhile to further explore the usefulness of this new marker of the vascular wall. (C) 2009 Published by Elsevier Ireland Ltd.
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| 3. |
- Andersson, J., et al.
(författare)
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The Carotid Artery Plaque Size and Echogenicity are Related to Different Cardiovascular Risk Factors in the Elderly
- 2009
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Ingår i: Lipids. - : Wiley. - 0024-4201 .- 1558-9307. ; 44:5, s. 397-403
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Tidskriftsartikel (refereegranskat)abstract
- Carotid plaques can be characterised by ultrasound by size and echogenicity. Both size and echogenicity are predictors of cardiovascular events. The aim of this study was to examine whether traditional risk factors and markers of inflammation and oxidation were associated with plaque size and echogenicity. Computerised analysis of carotid plaque size and echogenicity (grey scale median, GSM) were performed by ultrasound in a population-based health survey in 1,016 subjects aged 70 years (PIVUS study). Information on cardiovascular risk factors was collected, together with markers of inflammation and oxidation. Increased Framingham risk score, systolic blood pressure, higher BMI and decreased HDL, lower glutathione levels were related to echolucent plaques. Previous or present smoking was common with significantly more pack-years related to the echorich plaques. Plaque size was associated with increased Framingham risk score, systolic blood pressure, blood glucose levels, smoking, ApoB/A1 ratio, OxLDL, TNF alpha, HOMA insulin resistance, leucocyte count, decreased BCD-LDL and low levels of l-selectin. Low HDL, increased BMI and decreased glutathione levels were associated with the echolucency of carotid plaques, implying metabolic factors to play a role for plaque composition. Markers of inflammation were related to plaque size alone, implying inflammation to be predominantly associated with the amount of atherosclerosis. These results suggest that plaque size and echogenicity are influenced by different risk factors.
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| 4. |
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| 5. |
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| 6. |
- 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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| 7. |
- Hagmar, Jonas, 1974, et al.
(författare)
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Image analysis in non-linear microscopy
- 2008
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Ingår i: Journal of Optical Society of America. ; 25, s. 2195-2206
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Tidskriftsartikel (refereegranskat)abstract
- The ability to automatically extract quantitative data from non-linear microscopy images is here explored, taking their non-linear character into account. Objects of different degree of complexity were investigated: theoretical images of spherical objects, experimentally collected Coherent Anti-Stokes Raman Scattering images of polystyrene spheres in background generating agar, well-separated lipid droplets in living yeast cells and conglomerations of lipid droplets in living C. elegans nematodes. The in linear microscopy useful measure of Full-Width-at-Half-Maximum (FWHM) was shown to provide inadequate measures of object size due the non-linear density dependence of the signal. Instead, the capability of four state-of-the-art image analysis algorithms was evaluated. Among these Local thresholding was found to be the widest applicable segmentation algorithm.
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| 8. |
- Hagmar, Jonas, 1974, et al.
(författare)
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Image analysis of lipid deposits in living organisms visualized by CARS microscopy
- 2007
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Ingår i: Proc. Soc. Photo-Opt. Instrum. Eng. (SPIE). - 9780819466297 ; 6511:17
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Konferensbidrag (refereegranskat)abstract
- CARS microscopy is a novel technique for imaging bio-molecules in living cells using the molecular vibration as contrast mechanism. Global and local thresholding, state-of-the art image analysis techniques (watersheds, level sets) and a recent technique for anisotropic Gaussian fitting are used to segment lipid droplets in CARS microscopy images of, S. cerevisiae (yeast cells). The ability to extract quantitative information, such as vesicle size, is validated by means of images of polystyrene beads of well-defined size. Theoretical modeling of the CARS signal is performed, linking the physical object to its representation as a CARS microscopy image, as an attempt to take the non-linear relationship into account for refined image analysis. Theoretically modeled images of polystyrene beads correspond well to those experimentally obtained. Of the image analysis tools, it is found that global and local thresholding have limited use for segmentation of CARS microscopy images. Watershed and level set segmentation underestimate the size of a segmented object. Anisotropic Gaussian fitting overestimates the size of the object in the presence of non-resonant background. Reduced overestimation is achieved by background suppression. This emphasizes the importance of background removal in the CARS microscopy images, both experimentally as well as analytically. Automated image analysis of CARS microscopy images of S. cerevisiae is shown to be an excellent approach for in-depth studies of fat deposits in living organisms, with prospects for including human cells. Such a methodology will be of outmost importance for improved understanding of the mechanisms behind the development of obesity.
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| 9. |
- Holdfeldt, Peter, 1976, et al.
(författare)
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A Dynamic Programming Inspired Method for Boundary Detection in Ultrasound Image Sequences with Application to Brachial Artery Flow-Mediated Dilation (FMD) Studies
- 2009
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This paper describes a new method for boundary detection in ultrasound image sequences with specific application to brachial artery flow-mediated dilation (FMD) studies. The method represents an extension to conventional two-dimensional dynamic programming to be applied in a three-dimensional (spatio-temporal) context. A total of 42 digital image sequences, each of which contained 240 frames, were analyzed. The majority (34) of these sequences were analyzed successfully, and a few (8) partly successful. Following automated boundary detection, vessel diameter extrema (minima and maxima) could easily be computed and used for FMD calculations. It was concluded that the new method, although optimality when moving from two to three dimensions cannot be guaranteed, outperforms conventional dynamic programming.
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| 10. |
- Holdfeldt, Peter, 1976, et al.
(författare)
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A New Method Based on Dynamic Programming for Boundary Detection in Ultrasound Image Sequences
- 2008
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Ingår i: Engineering in Medicine and Biology Society, 2008. EMBS 2008. 30th Annual International Conference of the IEEE. EMBC 2008, August 20-24, Vancouver, Canada. - 9781424418145 ; , s. 3072-3074
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Konferensbidrag (refereegranskat)abstract
- Dynamic programming has previously been used when measuring Lumen Diameter (LD) and Intima-Media Thickness (IMT) in single frame ultrasound carotid artery images [1]. An extension to multiframe detection of that procedure is proposed in this paper. Our new method transforms a three dimensional problem into multiple two dimensional problems that can again be solved by dynamic programming. First, several “candidate boundaries” are detected in each image. Then, one boundary from each image in the sequence is selected in such a way that the sequence of boundaries is optimal among the considered possibilities. A model of the movements of the boundaries is used in the second step. Our proposed method shows promising performance on both synthetic and real ultrasound data.
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