Topology preserving stacs segmentation of protein subcellular location images

Lionel Coulot, Heather Kirschner, Amina Chebira, José M.F. Moura, Jelena Kovacevic, Elvira Garcia Osuna, Robert F. Murphy

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We present an algorithm for the segmentation of multicell fluorescence microscopy images. Such images abound and a segmentation algorithm robust to different experimental conditions as well as cell types is becoming a necessity. In cellular imaging, among the most often used segmentation algorithms is seeded watershed. One of its features is that it tends to oversegment, splitting the cells, as well as create segmented regions much larger than a true cell. This can be an advantage (the entire cell is within the region) as well as a disadvantage (a large amount of background noise is included). We present an algorithm which segments with tight contours by building upon an active contour algorithm - STAGS, by Pluempitiwiriyawej et al. We adapt the algorithm to suit the needs of our data and use another technique, topology preservation by Han et al., to build our topology preserving STACS (TPSTACS). Our algorithm significantly outperforms the seeded watershed both visually as well as by standard measures of segmentation quality: recall/precision, area similarity and area overlap.

Original languageEnglish (US)
Title of host publication2006 3rd IEEE International Symposium on Biomedical Imaging
Subtitle of host publicationFrom Nano to Macro - Proceedings
Pages566-569
Number of pages4
Volume2006
StatePublished - Nov 17 2006
Event2006 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Arlington, VA, United States
Duration: Apr 6 2006Apr 9 2006

Other

Other2006 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro
CountryUnited States
CityArlington, VA
Period4/6/064/9/06

Fingerprint

Topology
Proteins
Watersheds
Fluorescence microscopy
Imaging techniques

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Coulot, L., Kirschner, H., Chebira, A., Moura, J. M. F., Kovacevic, J., Osuna, E. G., & Murphy, R. F. (2006). Topology preserving stacs segmentation of protein subcellular location images. In 2006 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings (Vol. 2006, pp. 566-569). [1624979]

Topology preserving stacs segmentation of protein subcellular location images. / Coulot, Lionel; Kirschner, Heather; Chebira, Amina; Moura, José M.F.; Kovacevic, Jelena; Osuna, Elvira Garcia; Murphy, Robert F.

2006 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings. Vol. 2006 2006. p. 566-569 1624979.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Coulot, L, Kirschner, H, Chebira, A, Moura, JMF, Kovacevic, J, Osuna, EG & Murphy, RF 2006, Topology preserving stacs segmentation of protein subcellular location images. in 2006 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings. vol. 2006, 1624979, pp. 566-569, 2006 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Arlington, VA, United States, 4/6/06.
Coulot L, Kirschner H, Chebira A, Moura JMF, Kovacevic J, Osuna EG et al. Topology preserving stacs segmentation of protein subcellular location images. In 2006 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings. Vol. 2006. 2006. p. 566-569. 1624979
Coulot, Lionel ; Kirschner, Heather ; Chebira, Amina ; Moura, José M.F. ; Kovacevic, Jelena ; Osuna, Elvira Garcia ; Murphy, Robert F. / Topology preserving stacs segmentation of protein subcellular location images. 2006 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings. Vol. 2006 2006. pp. 566-569
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