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Wadströmer, Niclas
Publications (6 of 6) Show all publications
Larsson, J.-Å., Wadströmer, N., Hermanson, O., Lendahl, U. & Forchheimer, R. (2011). Modelling cell lineage using a meta-Boolean tree model with a relation to gene regulatory networks. Journal of Theoretical Biology, 268(1), 62-76
Open this publication in new window or tab >>Modelling cell lineage using a meta-Boolean tree model with a relation to gene regulatory networks
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2011 (English)In: Journal of Theoretical Biology, ISSN 0022-5193, Vol. 268, no 1, p. 62-76Article in journal (Refereed) Published
Abstract [en]

A cell lineage is the ancestral relationship between a group of cells that originate from a single founder cell. For example, in the embryo of the nematode Caenorhabditis elegans an invariant cell lineage has been traced, and with this information at hand it is possible to theoretically model the emergence of different cell types in the lineage, starting from the single fertilized egg. In this report we outline a modelling technique for cell lineage trees, which can be used for the C. elegans embryonic cell lineage but also extended to other lineages. The model takes into account both cell-intrinsic (transcription factor-based) and -extrinsic (extracellular) factors as well as synergies within and between these two types of factors. The model can faithfully recapitulate the entire C. elegans cell lineage, but is also general, i.e., it can be applied to describe any cell lineage. We show that synergy between factors, as well as the use of extrinsic factors, drastically reduce the number of regulatory factors needed for recapitulating the lineage. The model gives indications regarding co-variation of factors, number of involved genes and where in the cell lineage tree that asymmetry might be controlled by external influence. Furthermore, the model is able to emulate other (Boolean, discrete and differential-equation-based) models. As an example, we show that the model can be translated to the language of a previous linear sigmoid-limited concentration-based model (Geard and Wiles, 2005). This means that this latter model also can exhibit synergy effects, and also that the cumbersome iterative technique for parameter estimation previously used is no longer needed. In conclusion, the proposed model is general and simple to use, can be mapped onto other models to extend and simplify their use, and can also be used to indicate where synergy and external influence would reduce the complexity of the regulatory process.

Place, publisher, year, edition, pages
Amsterdam: Elsevier, 2011
Keywords
Differentiation, Transcription factor, Asymmetric cell division
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-63386 (URN)10.1016/j.jtbi.2010.10.003 (DOI)000284918100007 ()
Available from: 2010-12-17 Created: 2010-12-17 Last updated: 2019-08-15Bibliographically approved
Wadströmer, N., Ahlberg, J. & Svensson, T. (2010). A new hyperspectral dataset and some challenges. In: Sylvia S. Shen; Paul E. Lewis (Ed.), Proc. SPIE 7695, Algorithms and Technologies for Multispectral, Hyperspectral, and Ultraspectral Imagery XVI: . Paper presented at Algorithms and Technologies for Multispectral, Hyperspectral, and Ultraspectral Imagery XVI, Orlando, Florida, USA, 5–8 April 2010 (pp. Art.nr. 7695-22). SPIE - International Society for Optical Engineering
Open this publication in new window or tab >>A new hyperspectral dataset and some challenges
2010 (English)In: Proc. SPIE 7695, Algorithms and Technologies for Multispectral, Hyperspectral, and Ultraspectral Imagery XVI / [ed] Sylvia S. Shen; Paul E. Lewis, SPIE - International Society for Optical Engineering, 2010, p. Art.nr. 7695-22-Conference paper, Published paper (Refereed)
Abstract [en]

We present a new hyperspectral data set that FOI will keep publicly available. The hyperspectral data set was collected in an airborne measurement over the countryside. The spectral resolution was about 10 nm which allowed registrations in 60 spectral bands in the visual and near infrared range (390-960 nm). Objects with various signature properties were placed in three areas: the edge of a wood, an open field and a rough open terrain. Several overflights were performed over the areas. Between the overflights some of the objects were moved, representing different scenarios. Our interest is primarily in anomaly detection of man-made objects placed in nature where no such objects are expected. The objects in the trial were military and civilian vehicles, boards of different size and a camouflage net. The size of the boards range from multipixel to subpixel size. Due to wind and cloud conditions the stability and the flight height of the airplane vary between the overflights, which makes the analysis extra challenging. 

Place, publisher, year, edition, pages
SPIE - International Society for Optical Engineering, 2010
Series
Proceedings of SPIE, ISSN 0277-786X ; 7695
Keywords
hyperspectral data, ROC, mutual information
National Category
Remote Sensing
Identifiers
urn:nbn:se:liu:diva-120527 (URN)10.1117/12.851325 (DOI)
Conference
Algorithms and Technologies for Multispectral, Hyperspectral, and Ultraspectral Imagery XVI, Orlando, Florida, USA, 5–8 April 2010
Available from: 2015-08-13 Created: 2015-08-13 Last updated: 2015-09-21Bibliographically approved
Ahlberg, J., Renhorn, I. G. & Wadströmer, N. (2010). An information measure of sensor performance and its relation to the ROC curve. In: Sylvia S. Shen; Paul E. Lewis (Ed.), Proc. SPIE 7695, Algorithms and Technologies for Multispectral, Hyperspectral, and Ultraspectral Imagery XVI: . Paper presented at Algorithms and Technologies for Multispectral, Hyperspectral, and Ultraspectral Imagery XVI, Orlando, Florida, USA, 5–8 April 2010 (pp. Art.nr. 7695-72). SPIE - International Society for Optical Engineering
Open this publication in new window or tab >>An information measure of sensor performance and its relation to the ROC curve
2010 (English)In: Proc. SPIE 7695, Algorithms and Technologies for Multispectral, Hyperspectral, and Ultraspectral Imagery XVI / [ed] Sylvia S. Shen; Paul E. Lewis, SPIE - International Society for Optical Engineering, 2010, p. Art.nr. 7695-72-Conference paper, Published paper (Refereed)
Abstract [en]

The ROC curve is the most frequently used performance measure for detection methods and the underlying sensor configuration. Common problems are that the ROC curve does not present a single number that can be compared to other systems and that no discrimination between sensor performance and algorithm performance is done. To address the first problem, a number of measures are used in practice, like detection rate at a specific false alarm rate, or area-under-curve. For the second problem, we proposed in a previous paper1 an information theoretic method for measuring sensor performance. We now relate the method to the ROC curve, show that it is equivalent to selecting a certain point on the ROC curve, and that this point is easily determined. Our scope is hyperspectral data, studying discrimination between single pixels.

Place, publisher, year, edition, pages
SPIE - International Society for Optical Engineering, 2010
Series
Proceedings of SPIE ; 7695
Keywords
ROC, information theory, target detection, hyperspectral, sensor performance
National Category
Computer Vision and Robotics (Autonomous Systems)
Identifiers
urn:nbn:se:liu:diva-120554 (URN)10.1117/12.851322 (DOI)
Conference
Algorithms and Technologies for Multispectral, Hyperspectral, and Ultraspectral Imagery XVI, Orlando, Florida, USA, 5–8 April 2010
Available from: 2015-08-14 Created: 2015-08-14 Last updated: 2018-01-11Bibliographically approved
Ringaby, E., Ahlberg, J., Wadströmer, N. & Forssén, P.-E. (2010). Co-aligning Aerial Hyperspectral Push-broom Strips for Change Detection. In: Gary W. Kamerman; Ove Steinvall; Keith L. Lewis; Richard C. Hollins; Thomas J. Merlet; Gary J. Bishop; John D. Gonglewski (Ed.), Proc. SPIE 7835, Electro-Optical Remote Sensing, Photonic Technologies, and Applications IV: . Paper presented at Electro-Optical Remote Sensing, Photonic Technologies, and Applications IV, 20-23 September, Toulouse, France (pp. Art.nr. 7835B-36). SPIE - International Society for Optical Engineering
Open this publication in new window or tab >>Co-aligning Aerial Hyperspectral Push-broom Strips for Change Detection
2010 (English)In: Proc. SPIE 7835, Electro-Optical Remote Sensing, Photonic Technologies, and Applications IV / [ed] Gary W. Kamerman; Ove Steinvall; Keith L. Lewis; Richard C. Hollins; Thomas J. Merlet; Gary J. Bishop; John D. Gonglewski, SPIE - International Society for Optical Engineering, 2010, p. Art.nr. 7835B-36-Conference paper, Published paper (Refereed)
Abstract [en]

We have performed a field trial with an airborne push-broom hyperspectral sensor, making several flights over the same area and with known changes (e.g., moved vehicles) between the flights. Each flight results in a sequence of scan lines forming an image strip, and in order to detect changes between two flights, the two resulting image strips must be geometrically aligned and radiometrically corrected. The focus of this paper is the geometrical alignment, and we propose an image- and gyro-based method for geometric co-alignment (registration) of two image strips. The method is particularly useful when the sensor is not stabilized, thus reducing the need for expensive mechanical stabilization. The method works in several steps, including gyro-based rectification, global alignment using SIFT matching, and a local alignment using KLT tracking. Experimental results are shown but not quantified, as ground truth is, by the nature of the trial, lacking.

Place, publisher, year, edition, pages
SPIE - International Society for Optical Engineering, 2010
Series
Proceedings Spie, ISSN 0277-786X ; 7835
National Category
Computer Vision and Robotics (Autonomous Systems)
Identifiers
urn:nbn:se:liu:diva-70464 (URN)10.1117/12.865034 (DOI)978-0-8194-8353-9 (ISBN)
Conference
Electro-Optical Remote Sensing, Photonic Technologies, and Applications IV, 20-23 September, Toulouse, France
Available from: 2011-09-13 Created: 2011-09-09 Last updated: 2018-01-12Bibliographically approved
Ringaby, E., Ahlberg, J., Forssén, P.-E. & Wadströmer, N. (2010). Co-alignmnent of Aerial Push-broom Strips using Trajectory Smoothness Constraints. In: : . Paper presented at SSBA10, Symposium on Image Analysis 11-12 March, Uppsala (pp. 63-66). Swedish Society for automated image analysis
Open this publication in new window or tab >>Co-alignmnent of Aerial Push-broom Strips using Trajectory Smoothness Constraints
2010 (English)Conference paper, Published paper (Other academic)
Abstract [en]

We study the problem of registering a sequence of scan lines (a strip) from an airborne push-broom imager to another sequence partly covering the same area. Such a registration has to compensate for deformations caused by attitude and speed changes in the aircraft. The registration is challenging, as both strips contain such deformations. Our algorithm estimates the 3D rotation of the camera for each scan line, by parametrising it as a linear spline with a number of knots evenly distributed in one of the strips. The rotations are estimated from correspondences between strips of the same area. Once the rotations are known, they can be compensated for, and each line of pixels can be transformed such that ground trace of the two strips are registered with respect to each other.

Place, publisher, year, edition, pages
Swedish Society for automated image analysis, 2010
National Category
Computer Vision and Robotics (Autonomous Systems)
Identifiers
urn:nbn:se:liu:diva-70706 (URN)
Conference
SSBA10, Symposium on Image Analysis 11-12 March, Uppsala
Available from: 2011-09-15 Created: 2011-09-15 Last updated: 2018-01-12Bibliographically approved
Lundmark, A., Wadströmer, N. & Li, H. (2001). Hierarchical subsampling giving fractal regions. IEEE Transactions on Image Processing, 10(1), 167-173
Open this publication in new window or tab >>Hierarchical subsampling giving fractal regions
2001 (English)In: IEEE Transactions on Image Processing, ISSN 1057-7149, E-ISSN 1941-0042, Vol. 10, no 1, p. 167-173Article in journal (Refereed) Published
Abstract [en]

Recursive image subsampling which yields support areas approaching fractals is described and analyzed using iterated function systems. The subsampling scheme is suitable in, e.g., hierarchical image processing and image coding schemes. For hexagonally sampled images a hierarchical subsampling structure is given which yields hexagon-like regions with fractal borders.

National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-47498 (URN)10.1109/83.892454 (DOI)
Available from: 2009-10-11 Created: 2009-10-11 Last updated: 2017-12-13
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