Resolving clustered worms via probabilistic shape models

Carolina Wählby; Tammy Riklin-Raviv; Vebjorn Ljosa; Annie L. Conery; Polina Golland; Frederick M. Ausubel; Anne E. Carpenter

doi:10.1109/ISBI.2010.5490286

Resolving clustered worms via probabilistic shape models

Carolina Wählby, Tammy Riklin-Raviv, Vebjorn Ljosa, Annie L. Conery, Polina Golland, Frederick M. Ausubel, Anne E. Carpenter

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

29 Scopus citations

Abstract

The roundworm Caenorhabditis elegans is an effective model system for biological processes such as immunity, behavior, and metabolism. Robotic sample preparation together with automated microscopy and image analysis has recently enabled high-throughput screening experiments using C. elegans. So far, such experiments have been limited to per-image measurements due to the tendency of the worms to cluster, which prevents extracting features from individual animals. We present a novel approach for the extraction of individual C. elegans from clusters of worms in high-throughput microscopy images. The key ideas are the construction of a low-dimensional shape-descriptor space and the definition of a probability measure on it. Promising segmentation results are shown.

Original language	English
Title of host publication	2010 7th IEEE International Symposium on Biomedical Imaging
Subtitle of host publication	From Nano to Macro, ISBI 2010 - Proceedings
Pages	552-555
Number of pages	4
DOIs	https://doi.org/10.1109/ISBI.2010.5490286
State	Published - 9 Aug 2010
Externally published	Yes
Event	7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Rotterdam, Netherlands Duration: 14 Apr 2010 → 17 Apr 2010

Publication series

Name	2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings

Conference

Conference	7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010
Country/Territory	Netherlands
City	Rotterdam
Period	14/04/10 → 17/04/10

Keywords

Active shape model
Caenorhabditis elegans
High-throughput screening
Image segmentation

ASJC Scopus subject areas

Biomedical Engineering
Radiology Nuclear Medicine and imaging

Access to Document

10.1109/ISBI.2010.5490286

Cite this

Wählby, C., Riklin-Raviv, T., Ljosa, V., Conery, A. L., Golland, P., Ausubel, F. M., & Carpenter, A. E. (2010). Resolving clustered worms via probabilistic shape models. In 2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings (pp. 552-555). Article 5490286 (2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings). https://doi.org/10.1109/ISBI.2010.5490286

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abstract = "The roundworm Caenorhabditis elegans is an effective model system for biological processes such as immunity, behavior, and metabolism. Robotic sample preparation together with automated microscopy and image analysis has recently enabled high-throughput screening experiments using C. elegans. So far, such experiments have been limited to per-image measurements due to the tendency of the worms to cluster, which prevents extracting features from individual animals. We present a novel approach for the extraction of individual C. elegans from clusters of worms in high-throughput microscopy images. The key ideas are the construction of a low-dimensional shape-descriptor space and the definition of a probability measure on it. Promising segmentation results are shown.",

keywords = "Active shape model, Caenorhabditis elegans, High-throughput screening, Image segmentation",

author = "Carolina W{\"a}hlby and Tammy Riklin-Raviv and Vebjorn Ljosa and Conery, {Annie L.} and Polina Golland and Ausubel, {Frederick M.} and Carpenter, {Anne E.}",

year = "2010",

month = aug,

day = "9",

doi = "10.1109/ISBI.2010.5490286",

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series = "2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings",

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Wählby, C, Riklin-Raviv, T, Ljosa, V, Conery, AL, Golland, P, Ausubel, FM & Carpenter, AE 2010, Resolving clustered worms via probabilistic shape models. in 2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings., 5490286, 2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings, pp. 552-555, 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010, Rotterdam, Netherlands, 14/04/10. https://doi.org/10.1109/ISBI.2010.5490286

Resolving clustered worms via probabilistic shape models. / Wählby, Carolina; Riklin-Raviv, Tammy; Ljosa, Vebjorn et al.
2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings. 2010. p. 552-555 5490286 (2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings).

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

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AU - Wählby, Carolina

AU - Riklin-Raviv, Tammy

AU - Ljosa, Vebjorn

AU - Conery, Annie L.

AU - Golland, Polina

AU - Ausubel, Frederick M.

AU - Carpenter, Anne E.

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Wählby C, Riklin-Raviv T, Ljosa V, Conery AL, Golland P, Ausubel FM et al. Resolving clustered worms via probabilistic shape models. In 2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings. 2010. p. 552-555. 5490286. (2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings). doi: 10.1109/ISBI.2010.5490286

Resolving clustered worms via probabilistic shape models

Abstract

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Keywords

ASJC Scopus subject areas

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