uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
Seeded watersheds for combined segmentation and tracking
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis.
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis.
2005 (English)In: Image Analysis and Processing – ICIAP 2005, Springer Berlin / Heidelberg , 2005, Vol. 3617, 336-343 p.Chapter in book (Other academic)
Abstract [en]

Watersheds are very powerful for image segmentation, and seeded watersheds have shown to be useful for object detection in images of cells in vitro. This paper shows that if cells are imaged over time, segmentation results from a previous time frame can be used as seeds for watershed segmentation of the current time frame. The seeds from the previous frame are combined with morphological seeds from the current frame, and over-segmentation is reduced by rule-based merging, propagating labels from one time-frame to the next. Thus, watershed segmentation is used for segmentation as well as tracking of cells over time. The described algorithm was tested on neural stem/progenitor cells imaged using time-lapse microscopy. Tracking results agreed to 71% to manual tracking results. The results were also compared to tracking based on solving the assignment problem using a modified version of the auction algorithm.

Place, publisher, year, edition, pages
Springer Berlin / Heidelberg , 2005. Vol. 3617, 336-343 p.
, Lecture Notes in Computer Science, ISSN 0302-9743 ; 3617/2005
National Category
Computer and Information Science
URN: urn:nbn:se:uu:diva-98013DOI: 10.1007/11553595_41ISBN: 978-3-540-28869-5OAI: oai:DiVA.org:uu-98013DiVA: diva2:173169
Available from: 2009-02-05 Created: 2009-02-05 Last updated: 2010-06-07Bibliographically approved
In thesis
1. Digital Image Analysis of Cells: Applications in 2D, 3D and Time
Open this publication in new window or tab >>Digital Image Analysis of Cells: Applications in 2D, 3D and Time
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Light microscopes are essential research tools in biology and medicine. Cell and tissue staining methods have improved immensely over the years and microscopes are now equipped with digital image acquisition capabilities. The image data produced require development of specialized analysis methods. This thesis presents digital image analysis methods for cell image data in 2D, 3D and time sequences.

Stem cells have the capability to differentiate into specific cell types. The mechanism behind differentiation can be studied by tracking cells over time. This thesis presents a combined segmentation and tracking algorithm for time sequence images of neural stem cells.The method handles splitting and merging of cells and the results are similar to those achieved by manual tracking.

Methods for detecting and localizing signals from fluorescence stained biomolecules are essential when studying how they function and interact. A study of Smad proteins, that serve as transcription factors by forming complexes and enter the cell nucleus, is included in the thesis. Confocal microscopy images of cell nuclei are delineated using gradient information, and Smad complexes are localized using a novel method for 3D signal detection. Thus, the localization of Smad complexes in relation to the nuclear membrane can be analyzed. A detailed comparison between the proposed and previous methods for detection of point-source signals is presented, showing that the proposed method has better resolving power and is more robust to noise.

In this thesis, it is also shown how cell confluence can be measured by classification of wavelet based texture features. Monitoring cell confluence is valuable for optimization of cell culture parameters and cell harvest. The results obtained agree with visual observations and provide an efficient approach to monitor cell confluence and detect necrosis.

Quantitative measurements on cells are important in both cytology and histology. The color provided by Pap (Papanicolaou) staining increases the available image information. The thesis explores different color spaces of Pap smear images from thyroid nodules, with the aim of finding the representation that maximizes detection of malignancies using color information in addition to quantitative morphological parameters.

The presented methods provide useful tools for cell image analysis, but they can of course also be used for other image analysis applications.

Place, publisher, year, edition, pages
Uppsala: Universitetsbiblioteket, 2009. 57 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 596
Digital image analysis, microscopy, fluorescent staining, watershed segmentation, sub-cellular localization, point-like signals, wavelets, cell confluence, cytology, color spaces.
National Category
Computer Vision and Robotics (Autonomous Systems)
urn:nbn:se:uu:diva-9541 (URN)978-91-554-7398-3 (ISBN)
Public defence
2009-02-27, Siegbansalen, Ångstrom Laboratory, Polackbacken, Uppsala, 10:15
Available from: 2009-02-05 Created: 2009-02-05Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full text
By organisation
Computerized Image AnalysisCentre for Image Analysis
Computer and Information Science

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 261 hits
ReferencesLink to record
Permanent link

Direct link