Journal Article
. 2016 Apr; 17(1):183.
doi: 10.1186/s12859-016-1030-9.

Detection and tracking of overlapping cell nuclei for large scale mitosis analyses

Yingbo Li 1 France Rose 1 Florencia di Pietro 2 Xavier Morin 2 Auguste Genovesio 3 
Affiliations
  • PMID: 27112769
  •     26 References
  •     3 citations

Abstract

Background: Cell culture on printed micropatterns slides combined with automated fluorescent microscopy allows for extraction of tens of thousands of videos of small isolated growing cell clusters. The analysis of such large dataset in space and time is of great interest to the community in order to identify factors involved in cell growth, cell division or tissue formation by testing multiples conditions. However, cells growing on a micropattern tend to be tightly packed and to overlap with each other. Consequently, image analysis of those large dynamic datasets with no possible human intervention has proven impossible using state of the art automated cell detection methods.

Results: Here, we propose a fully automated image analysis approach to estimate the number, the location and the shape of each cell nucleus, in clusters at high throughput. The method is based on a robust fit of Gaussian mixture models with two and three components on each frame followed by an analysis over time of the fitting residual and two other relevant features. We use it to identify with high precision the very first frame containing three cells. This allows in our case to measure a cell division angle on each video and to construct division angle distributions for each tested condition. We demonstrate the accuracy of our method by validating it against manual annotation on about 4000 videos of cell clusters.

Conclusions: The proposed approach enables the high throughput analysis of video sequences of isolated cell clusters obtained using micropatterns. It relies only on two parameters that can be set robustly as they reduce to the average cell size and intensity.

Keywords: Cell detection; Gaussian mixture; High throughput; Image analysis; Mitosis; Time-lapse microscopy.

Adaptive image contrast enhancement using generalizations of histogram equalization.
J A Stark.
IEEE Trans Image Process, 2008 Feb 08; 9(5). PMID: 18255459
Image segmentation and analysis via multiscale gradient watershed hierarchies.
J M Gauch.
IEEE Trans Image Process, 2008 Feb 12; 8(1). PMID: 18262866
Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition.
B Mathew, A Schmitz, +4 authors, S C Fischer.
BMC Bioinformatics, 2015 Jun 08; 16. PMID: 26049713    Free PMC article.
The extracellular matrix guides the orientation of the cell division axis.
Manuel Théry, Victor Racine, +4 authors, Michel Bornens.
Nat Cell Biol, 2005 Sep 24; 7(10). PMID: 16179950
Highly Cited.
Cytoplasmic intermediate filaments mediate actin-driven positioning of the nucleus.
Isabelle Dupin, Yasuhisa Sakamoto, Sandrine Etienne-Manneville.
J Cell Sci, 2011 Mar 08; 124(Pt 6). PMID: 21378307
Spatial organization of the extracellular matrix regulates cell-cell junction positioning.
Qingzong Tseng, Eve Duchemin-Pelletier, +4 authors, Manuel Théry.
Proc Natl Acad Sci U S A, 2012 Feb 07; 109(5). PMID: 22307605    Free PMC article.
Highly Cited.
Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data.
Fernando Amat, William Lemon, +5 authors, Philipp J Keller.
Nat Methods, 2014 Jul 22; 11(9). PMID: 25042785
Highly Cited.
Asymmetric cell divisions promote Notch-dependent epidermal differentiation.
Scott E Williams, Slobodan Beronja, H Amalia Pasolli, Elaine Fuchs.
Nature, 2011 Feb 19; 470(7334). PMID: 21331036    Free PMC article.
Highly Cited.
Experimental and theoretical study of mitotic spindle orientation.
Manuel Théry, Andrea Jiménez-Dalmaroni, +2 authors, Frank Jülicher.
Nature, 2007 May 15; 447(7143). PMID: 17495931
Highly Cited.
Automatic fluorescent tag detection in 3D with super-resolution: application to the analysis of chromosome movement.
D Thomann, D R Rines, P K Sorger, G Danuser.
J Microsc, 2002 Oct 09; 208(Pt 1). PMID: 12366597
Improved visualization and quantitative analysis of drug effects using micropatterned cells.
Sébastien Degot, Muriel Auzan, +7 authors, Alexandra Fuchs.
J Vis Exp, 2010 Dec 30; (46). PMID: 21189468    Free PMC article.
Planar spindle orientation and asymmetric cytokinesis in the mouse small intestine.
Elizabeth S Fleming, Mark Zajac, +4 authors, Jennifer S Tirnauer.
J Histochem Cytochem, 2007 Aug 23; 55(11). PMID: 17712178    Free PMC article.
Spindle orientation bias in gut epithelial stem cell compartments is lost in precancerous tissue.
Aaron J Quyn, Paul L Appleton, +6 authors, Inke S Näthke.
Cell Stem Cell, 2010 Feb 11; 6(2). PMID: 20144789
Highly Cited.
Mitotic spindle orientation in asymmetric and symmetric cell divisions during animal development.
Xavier Morin, Yohanns Bellaïche.
Dev Cell, 2011 Jul 19; 21(1). PMID: 21763612
Highly Cited. Review.
A method to recapitulate early embryonic spatial patterning in human embryonic stem cells.
Aryeh Warmflash, Benoit Sorre, +2 authors, Ali H Brivanlou.
Nat Methods, 2014 Jun 30; 11(8). PMID: 24973948    Free PMC article.
Highly Cited.
Image analysis for automatic segmentation of cytoplasms and classification of Rac1 activation.
Joakim Lindblad, Carolina Wählby, Ewert Bengtsson, Alla Zaltsman.
Cytometry A, 2003 Dec 31; 57(1). PMID: 14699602
Mitotic spindle (DIS)orientation and DISease: cause or consequence?
Anna Noatynska, Monica Gotta, Patrick Meraldi.
J Cell Biol, 2012 Dec 26; 199(7). PMID: 23266953    Free PMC article.
Review.
Closed-form density-based framework for automatic detection of cellular morphology changes.
Tarn Duong, Bruno Goud, Kristine Schauer.
Proc Natl Acad Sci U S A, 2012 May 16; 109(22). PMID: 22586080    Free PMC article.
Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software.
Lee Kamentsky, Thouis R Jones, +7 authors, Anne E Carpenter.
Bioinformatics, 2011 Feb 26; 27(8). PMID: 21349861    Free PMC article.
Highly Cited.
Mitotic spindle misorientation in cancer--out of alignment and into the fire.
Jillian C Pease, Jennifer S Tirnauer.
J Cell Sci, 2011 Mar 16; 124(Pt 7). PMID: 21402874
Topology adaptive deformable surfaces for medical image volume segmentation.
T McInerney, D Terzopoulos.
IEEE Trans Med Imaging, 2000 Jan 11; 18(10). PMID: 10628944
Cell segmentation, tracking, and mitosis detection using temporal context.
Fuxing Yang, Michael A Mackey, +2 authors, Milan Sonka.
Med Image Comput Comput Assist Interv, 2006 May 12; 8(Pt 1). PMID: 16685859
Coupled parametric active contours.
Christophe Zimmer, J C Olivo-Marin.
IEEE Trans Pattern Anal Mach Intell, 2005 Nov 16; 27(11). PMID: 16285382
Algorithms for cytoplasm segmentation of fluorescence labelled cells.
Carolina Wählby, Joakim Lindblad, +2 authors, Lennart Björkesten.
Anal Cell Pathol, 2002 Nov 26; 24(2-3). PMID: 12446959    Free PMC article.
Dlg1 controls planar spindle orientation in the neuroepithelium through direct interaction with LGN.
Mehdi Saadaoui, Mickaël Machicoane, +3 authors, Xavier Morin.
J Cell Biol, 2014 Sep 10; 206(6). PMID: 25202028    Free PMC article.
A gamma-gaussian mixture model for detection of mitotic cells in breast cancer histopathology images.
Adnan Mujahid Khan, Hesham Eldaly, Nasir M Rajpoot.
J Pathol Inform, 2013 Jul 17; 4. PMID: 23858386    Free PMC article.
Theranostic application of miR-429 in HER2+ breast cancer.
Claudia Cava, Chiara Novello, +7 authors, Isabella Castiglioni.
Theranostics, 2020 Jan 07; 10(1). PMID: 31903105    Free PMC article.
Separating Touching Cells Using Pixel Replicated Elliptical Shape Models.
Mark Winter, Walter Mankowski, +3 authors, Andrew R Cohen.
IEEE Trans Med Imaging, 2018 Oct 09; 38(4). PMID: 30296216    Free PMC article.
Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images.
Błażej Ruszczycki, Katarzyna Karolina Pels, +12 authors, Grzegorz Marek Wilczyński.
Front Neuroanat, 2019 Sep 05; 13. PMID: 31481881    Free PMC article.