Phase contrast time-lapse microscopy datasets with automated and manual cell tracking annotations

Dai Fei Elmer Ker; Sungeun Eom; Sho Sanami; Ryoma Bise; Corinne Pascale; Zhaozheng Yin; Seung Il Huh; Elvira Osuna-Highley; Silvina N. Junkers; Casey J. Helfrich; Peter Yongwen Liang; Jiyan Pan; Soojin Jeong; Steven S. Kang; Jinyu Liu; Ritchie Nicholson; Michael F. Sandbothe; Phu T. Van; Anan Liu; Mei Chen; Takeo Kanade; Lee E. Weiss; Phil G. Campbell

doi:10.1038/sdata.2018.237

Phase contrast time-lapse microscopy datasets with automated and manual cell tracking annotations

Dai Fei Elmer Ker
, Sungeun Eom
, Sho Sanami
, Ryoma Bise
, Corinne Pascale
, Zhaozheng Yin
, Seung Il Huh
, Elvira Osuna-Highley
, Silvina N. Junkers
, Casey J. Helfrich
, Peter Yongwen Liang
, Jiyan Pan
, Soojin Jeong
, Steven S. Kang
, Jinyu Liu
, Ritchie Nicholson
, Michael F. Sandbothe
, Phu T. Van
, Anan Liu
, Mei Chen

Takeo Kanade, Lee E. Weiss, Phil G. Campbell

Biomedical Informatics

Carnegie Mellon University
Chinese University of Hong Kong
Dai Nippon Printing Co., Ltd.
Kyushu University
Intel
Tianjin University
University at Albany

Research output: Contribution to journal › Article › peer-review

44 Scopus citations

Abstract

Phase contrast time-lapse microscopy is a non-destructive technique that generates large volumes of image-based information to quantify the behaviour of individual cells or cell populations. To guide the development of algorithms for computer-aided cell tracking and analysis, 48 time-lapse image sequences, each spanning approximately 3.5 days, were generated with accompanying ground truths for C2C12 myoblast cells cultured under 4 different media conditions, including with fibroblast growth factor 2 (FGF2), bone morphogenetic protein 2 (BMP2), FGF2 + BMP2, and control (no growth factor). The ground truths generated contain information for tracking at least 3 parent cells and their descendants within these datasets and were validated using a two-tier system of manual curation. This comprehensive, validated dataset will be useful in advancing the development of computer-aided cell tracking algorithms and function as a benchmark, providing an invaluable opportunity to deepen our understanding of individual and population-based cell dynamics for biomedical research.

Original language	English
Article number	180237
Journal	Scientific Data
Volume	5
DOIs	https://doi.org/10.1038/sdata.2018.237
State	Published - 2018

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Ker, D. F. E., Eom, S., Sanami, S., Bise, R., Pascale, C., Yin, Z., Huh, S. I., Osuna-Highley, E., Junkers, S. N., Helfrich, C. J., Liang, P. Y., Pan, J., Jeong, S., Kang, S. S., Liu, J., Nicholson, R., Sandbothe, M. F., Van, P. T., Liu, A., ... Campbell, P. G. (2018). Phase contrast time-lapse microscopy datasets with automated and manual cell tracking annotations. Scientific Data, 5, Article 180237. https://doi.org/10.1038/sdata.2018.237

@article{5fc3f9ee11f545b38f024397132be147,

title = "Phase contrast time-lapse microscopy datasets with automated and manual cell tracking annotations",

abstract = "Phase contrast time-lapse microscopy is a non-destructive technique that generates large volumes of image-based information to quantify the behaviour of individual cells or cell populations. To guide the development of algorithms for computer-aided cell tracking and analysis, 48 time-lapse image sequences, each spanning approximately 3.5 days, were generated with accompanying ground truths for C2C12 myoblast cells cultured under 4 different media conditions, including with fibroblast growth factor 2 (FGF2), bone morphogenetic protein 2 (BMP2), FGF2 + BMP2, and control (no growth factor). The ground truths generated contain information for tracking at least 3 parent cells and their descendants within these datasets and were validated using a two-tier system of manual curation. This comprehensive, validated dataset will be useful in advancing the development of computer-aided cell tracking algorithms and function as a benchmark, providing an invaluable opportunity to deepen our understanding of individual and population-based cell dynamics for biomedical research.",

author = "Ker, \{Dai Fei Elmer\} and Sungeun Eom and Sho Sanami and Ryoma Bise and Corinne Pascale and Zhaozheng Yin and Huh, \{Seung Il\} and Elvira Osuna-Highley and Junkers, \{Silvina N.\} and Helfrich, \{Casey J.\} and Liang, \{Peter Yongwen\} and Jiyan Pan and Soojin Jeong and Kang, \{Steven S.\} and Jinyu Liu and Ritchie Nicholson and Sandbothe, \{Michael F.\} and Van, \{Phu T.\} and Anan Liu and Mei Chen and Takeo Kanade and Weiss, \{Lee E.\} and Campbell, \{Phil G.\}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2018.",

year = "2018",

doi = "10.1038/sdata.2018.237",

language = "English",

volume = "5",

journal = "Scientific Data",

issn = "2052-4463",

}

Ker, DFE, Eom, S, Sanami, S, Bise, R, Pascale, C, Yin, Z, Huh, SI, Osuna-Highley, E, Junkers, SN, Helfrich, CJ, Liang, PY, Pan, J, Jeong, S, Kang, SS, Liu, J, Nicholson, R, Sandbothe, MF, Van, PT, Liu, A, Chen, M, Kanade, T, Weiss, LE & Campbell, PG 2018, 'Phase contrast time-lapse microscopy datasets with automated and manual cell tracking annotations', Scientific Data, vol. 5, 180237. https://doi.org/10.1038/sdata.2018.237

TY - JOUR

T1 - Phase contrast time-lapse microscopy datasets with automated and manual cell tracking annotations

AU - Ker, Dai Fei Elmer

AU - Eom, Sungeun

AU - Sanami, Sho

AU - Bise, Ryoma

AU - Pascale, Corinne

AU - Yin, Zhaozheng

AU - Huh, Seung Il

AU - Osuna-Highley, Elvira

AU - Junkers, Silvina N.

AU - Helfrich, Casey J.

AU - Liang, Peter Yongwen

AU - Pan, Jiyan

AU - Jeong, Soojin

AU - Kang, Steven S.

AU - Liu, Jinyu

AU - Nicholson, Ritchie

AU - Sandbothe, Michael F.

AU - Van, Phu T.

AU - Liu, Anan

AU - Chen, Mei

AU - Kanade, Takeo

AU - Weiss, Lee E.

AU - Campbell, Phil G.

PY - 2018

Y1 - 2018

N2 - Phase contrast time-lapse microscopy is a non-destructive technique that generates large volumes of image-based information to quantify the behaviour of individual cells or cell populations. To guide the development of algorithms for computer-aided cell tracking and analysis, 48 time-lapse image sequences, each spanning approximately 3.5 days, were generated with accompanying ground truths for C2C12 myoblast cells cultured under 4 different media conditions, including with fibroblast growth factor 2 (FGF2), bone morphogenetic protein 2 (BMP2), FGF2 + BMP2, and control (no growth factor). The ground truths generated contain information for tracking at least 3 parent cells and their descendants within these datasets and were validated using a two-tier system of manual curation. This comprehensive, validated dataset will be useful in advancing the development of computer-aided cell tracking algorithms and function as a benchmark, providing an invaluable opportunity to deepen our understanding of individual and population-based cell dynamics for biomedical research.

AB - Phase contrast time-lapse microscopy is a non-destructive technique that generates large volumes of image-based information to quantify the behaviour of individual cells or cell populations. To guide the development of algorithms for computer-aided cell tracking and analysis, 48 time-lapse image sequences, each spanning approximately 3.5 days, were generated with accompanying ground truths for C2C12 myoblast cells cultured under 4 different media conditions, including with fibroblast growth factor 2 (FGF2), bone morphogenetic protein 2 (BMP2), FGF2 + BMP2, and control (no growth factor). The ground truths generated contain information for tracking at least 3 parent cells and their descendants within these datasets and were validated using a two-tier system of manual curation. This comprehensive, validated dataset will be useful in advancing the development of computer-aided cell tracking algorithms and function as a benchmark, providing an invaluable opportunity to deepen our understanding of individual and population-based cell dynamics for biomedical research.

UR - https://www.scopus.com/pages/publications/85056339888

U2 - 10.1038/sdata.2018.237

DO - 10.1038/sdata.2018.237

M3 - Article

C2 - 30422120

AN - SCOPUS:85056339888

SN - 2052-4463

VL - 5

JO - Scientific Data

JF - Scientific Data

M1 - 180237

ER -

Phase contrast time-lapse microscopy datasets with automated and manual cell tracking annotations

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