Pipeline for Tracking Neural Progenitor Cells

Jacob Schack Vestergaard; Anders Lindbjerg Dahl; Peter Holm; Rasmus Larsen

doi:10.1007/978-3-642-36620-8_16

Pipeline for Tracking Neural Progenitor Cells

Jacob Schack Vestergaard, Anders Lindbjerg Dahl, Peter Holm, Rasmus Larsen

University of Copenhagen

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

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Abstract

Automated methods for neural stem cell lineage construction become increasingly important due to the large amount of data produced from time lapse imagery of in vitro cell growth experiments. Segmentation algorithms with the ability to adapt to the problem at hand and robust tracking methods play a key role in constructing these lineages. We present here a tracking pipeline based on learning a dictionary of discriminative image patches for segmentation and a graph formulation of the cell matching problem incorporating topology changes and acknowledging the fact that segmentation errors do occur. A matched filter for detection of mitotic candidates is constructed to ensure that cell division is only allowed in the model when relevant. Potentially the combination of these robust methods can simplify the initiation of cell lineage construction and extraction of statistics.

Original language	English
Title of host publication	Medical Computer Vision. Recognition Techniques and Applications in Medical Imaging : Second International MICCAI Workshop, MCV 2012, Nice, France, October 5, 2012, Revised Selected Papers
Publisher	Springer
Publication date	2012
Pages	155-164
ISBN (Print)	978-3-642-36619-2
ISBN (Electronic)	978-3-642-36620-8
DOIs	https://doi.org/10.1007/978-3-642-36620-8_16
Publication status	Published - 2012
Event	15th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2012) : Workshop on Medical Computer Vision (MCV) - Nice, France Duration: 5 Oct 2012 → … http://www.cir.meduniwien.ac.at/mcv2012/MCV2012/MCV2012.html

Workshop

Workshop	15th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2012) : Workshop on Medical Computer Vision (MCV)
Country/Territory	France
City	Nice
Period	05/10/2012 → …
Internet address	http://www.cir.meduniwien.ac.at/mcv2012/MCV2012/MCV2012.html

Series	Lecture Notes in Computer Science
Volume	7766
ISSN	0302-9743

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JSV MCV2012 paper29

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Vestergaard, J. S., Dahl, A. L., Holm, P., & Larsen, R. (2012). Pipeline for Tracking Neural Progenitor Cells. In Medical Computer Vision. Recognition Techniques and Applications in Medical Imaging: Second International MICCAI Workshop, MCV 2012, Nice, France, October 5, 2012, Revised Selected Papers (pp. 155-164). Springer. https://doi.org/10.1007/978-3-642-36620-8_16

Vestergaard, Jacob Schack ; Dahl, Anders Lindbjerg ; Holm, Peter et al. / Pipeline for Tracking Neural Progenitor Cells. Medical Computer Vision. Recognition Techniques and Applications in Medical Imaging: Second International MICCAI Workshop, MCV 2012, Nice, France, October 5, 2012, Revised Selected Papers. Springer, 2012. pp. 155-164 (Lecture Notes in Computer Science, Vol. 7766).

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abstract = "Automated methods for neural stem cell lineage construction become increasingly important due to the large amount of data produced from time lapse imagery of in vitro cell growth experiments. Segmentation algorithms with the ability to adapt to the problem at hand and robust tracking methods play a key role in constructing these lineages. We present here a tracking pipeline based on learning a dictionary of discriminative image patches for segmentation and a graph formulation of the cell matching problem incorporating topology changes and acknowledging the fact that segmentation errors do occur. A matched filter for detection of mitotic candidates is constructed to ensure that cell division is only allowed in the model when relevant. Potentially the combination of these robust methods can simplify the initiation of cell lineage construction and extraction of statistics.",

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note = "15th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2012) : Workshop on Medical Computer Vision (MCV) ; Conference date: 05-10-2012",

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Vestergaard, JS, Dahl, AL, Holm, P & Larsen, R 2012, Pipeline for Tracking Neural Progenitor Cells. in Medical Computer Vision. Recognition Techniques and Applications in Medical Imaging: Second International MICCAI Workshop, MCV 2012, Nice, France, October 5, 2012, Revised Selected Papers. Springer, Lecture Notes in Computer Science, vol. 7766, pp. 155-164, 15th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2012) : Workshop on Medical Computer Vision (MCV), Nice, France, 05/10/2012. https://doi.org/10.1007/978-3-642-36620-8_16

Pipeline for Tracking Neural Progenitor Cells. / Vestergaard, Jacob Schack; Dahl, Anders Lindbjerg; Holm, Peter et al.
Medical Computer Vision. Recognition Techniques and Applications in Medical Imaging: Second International MICCAI Workshop, MCV 2012, Nice, France, October 5, 2012, Revised Selected Papers. Springer, 2012. p. 155-164 (Lecture Notes in Computer Science, Vol. 7766).

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

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Vestergaard JS, Dahl AL, Holm P, Larsen R. Pipeline for Tracking Neural Progenitor Cells. In Medical Computer Vision. Recognition Techniques and Applications in Medical Imaging: Second International MICCAI Workshop, MCV 2012, Nice, France, October 5, 2012, Revised Selected Papers. Springer. 2012. p. 155-164. (Lecture Notes in Computer Science, Vol. 7766). doi: 10.1007/978-3-642-36620-8_16

Pipeline for Tracking Neural Progenitor Cells

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