Unsupervised Modeling of Cell Morphology Dynamics for Time-lapse Microscopy

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2012 May 29

PMID 22635062

Citations 32

Authors

Qing Zhong

Alberto Giovanni Busetto

Juan P Fededa

Joachim M Buhmann

Daniel W Gerlich

Affiliations

Soon will be listed here.

Abstract

Analysis of cellular phenotypes in large imaging data sets conventionally involves supervised statistical methods, which require user-annotated training data. This paper introduces an unsupervised learning method, based on temporally constrained combinatorial clustering, for automatic prediction of cell morphology classes in time-resolved images. We applied the unsupervised method to diverse fluorescent markers and screening data and validated accurate classification of human cell phenotypes, demonstrating fully objective data labeling in image-based systems biology.

Citing Articles

Exploring heterogeneous cell population dynamics in different microenvironments by novel analytical strategy based on images.

Huang Y, Zhou Z, Liu T, Tang S, Xin X NPJ Syst Biol Appl. 2024; 10(1):129.

PMID: 39505883 PMC: 11542073. DOI: 10.1038/s41540-024-00459-w.

Predicting cell cycle stage from 3D single-cell nuclear-stained images.

Li G, Nichols E, Browning V, Longhi N, Camplisson C, Beliveau B bioRxiv. 2024; .

PMID: 39257739 PMC: 11383680. DOI: 10.1101/2024.08.30.610553.

Automatic detection of cell-cycle stages using recurrent neural networks.

Jose A, Roy R, Moreno-Andres D, Stegmaier J PLoS One. 2024; 19(3):e0297356.

PMID: 38466708 PMC: 10927108. DOI: 10.1371/journal.pone.0297356.

Self-supervised machine learning for live cell imagery segmentation.

Robitaille M, Byers J, Christodoulides J, Raphael M Commun Biol. 2022; 5(1):1162.

PMID: 36323790 PMC: 9630527. DOI: 10.1038/s42003-022-04117-x.

Reconstructing data-driven governing equations for cell phenotypic transitions: integration of data science and systems biology.

Xing J Phys Biol. 2022; 19(6).

PMID: 35998617 PMC: 9585661. DOI: 10.1088/1478-3975/ac8c16.

References

Conrad C, Gerlich D . Automated microscopy for high-content RNAi screening. J Cell Biol. 2010; 188(4):453-61. PMC: 2828931. DOI: 10.1083/jcb.200910105. View

Schmitz M, Held M, Janssens V, Hutchins J, Hudecz O, Ivanova E . Live-cell imaging RNAi screen identifies PP2A-B55alpha and importin-beta1 as key mitotic exit regulators in human cells. Nat Cell Biol. 2010; 12(9):886-93. PMC: 3839080. DOI: 10.1038/ncb2092. View

Neumann B, Walter T, Heriche J, Bulkescher J, Erfle H, Conrad C . Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature. 2010; 464(7289):721-7. PMC: 3108885. DOI: 10.1038/nature08869. View

Thoma C, Toso A, Gutbrodt K, Reggi S, Frew I, Schraml P . VHL loss causes spindle misorientation and chromosome instability. Nat Cell Biol. 2009; 11(8):994-1001. DOI: 10.1038/ncb1912. View

Collinet C, Stoter M, Bradshaw C, Samusik N, Rink J, Kenski D . Systems survey of endocytosis by multiparametric image analysis. Nature. 2010; 464(7286):243-9. DOI: 10.1038/nature08779. View

Conrad C, Wunsche A, Tan T, Bulkescher J, Sieckmann F, Verissimo F . Micropilot: automation of fluorescence microscopy-based imaging for systems biology. Nat Methods. 2011; 8(3):246-9. PMC: 3086017. DOI: 10.1038/nmeth.1558. View

Wolthuis R, Clay-Farrace L, van Zon W, Yekezare M, Koop L, Ogink J . Cdc20 and Cks direct the spindle checkpoint-independent destruction of cyclin A. Mol Cell. 2008; 30(3):290-302. DOI: 10.1016/j.molcel.2008.02.027. View

Qi W, Tang Z, Yu H . Phosphorylation- and polo-box-dependent binding of Plk1 to Bub1 is required for the kinetochore localization of Plk1. Mol Biol Cell. 2006; 17(8):3705-16. PMC: 1525235. DOI: 10.1091/mbc.e06-03-0240. View

Goshima G, Wollman R, Goodwin S, Zhang N, Scholey J, Vale R . Genes required for mitotic spindle assembly in Drosophila S2 cells. Science. 2007; 316(5823):417-21. PMC: 2837481. DOI: 10.1126/science.1141314. View

10.

Meraldi P, Draviam V, Sorger P . Timing and checkpoints in the regulation of mitotic progression. Dev Cell. 2004; 7(1):45-60. DOI: 10.1016/j.devcel.2004.06.006. View

11.

Martin-Lluesma S, Stucke V, Nigg E . Role of Hec1 in spindle checkpoint signaling and kinetochore recruitment of Mad1/Mad2. Science. 2002; 297(5590):2267-70. DOI: 10.1126/science.1075596. View

12.

Schmitz M, Gerlich D . Automated live microscopy to study mitotic gene function in fluorescent reporter cell lines. Methods Mol Biol. 2009; 545:113-34. DOI: 10.1007/978-1-60327-993-2_7. View

13.

Held M, Schmitz M, Fischer B, Walter T, Neumann B, Olma M . CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging. Nat Methods. 2010; 7(9):747-54. DOI: 10.1038/nmeth.1486. View

14.

Waizenegger I, Gimenez-Abian J, Wernic D, Peters J . Regulation of human separase by securin binding and autocleavage. Curr Biol. 2002; 12(16):1368-78. DOI: 10.1016/s0960-9822(02)01073-4. View

15.

Loo L, Wu L, Altschuler S . Image-based multivariate profiling of drug responses from single cells. Nat Methods. 2007; 4(5):445-53. DOI: 10.1038/nmeth1032. View

16.

Jones T, Carpenter A, Lamprecht M, Moffat J, Silver S, Grenier J . Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. Proc Natl Acad Sci U S A. 2009; 106(6):1826-31. PMC: 2634799. DOI: 10.1073/pnas.0808843106. View

17.

Harder N, Mora-Bermudez F, Godinez W, Wunsche A, Eils R, Ellenberg J . Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time. Genome Res. 2009; 19(11):2113-24. PMC: 2775592. DOI: 10.1101/gr.092494.109. View

18.

Boland M, Murphy R . A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. Bioinformatics. 2001; 17(12):1213-23. DOI: 10.1093/bioinformatics/17.12.1213. View

19.

Neumann B, Held M, Liebel U, Erfle H, Rogers P, Pepperkok R . High-throughput RNAi screening by time-lapse imaging of live human cells. Nat Methods. 2006; 3(5):385-90. DOI: 10.1038/nmeth876. View

20.

Mackay A, Ainsztein A, Eckley D, Earnshaw W . A dominant mutant of inner centromere protein (INCENP), a chromosomal protein, disrupts prometaphase congression and cytokinesis. J Cell Biol. 1998; 140(5):991-1002. PMC: 2132686. DOI: 10.1083/jcb.140.5.991. View