Abstract
This paper describes an image-processing pipeline for the automatic segmentation of the nuclear envelope of HeLa cells observed through Electron Microscopy. The pipeline was applied to a 3D stack of 300 images. The intermediate results of neighbouring slices are further combined to improve the final results. Comparison with a hand-segmented ground truth reported Jaccard similarity values between 94–98% on the central slices with a decrease towards the edges of the cell where the structure was considerably more complex. The processing is unsupervised and each 2D slice is processed in about 5–10 s running on a MacBook Pro. No systematic attempt to make the code faster was made. These encouraging results could be further used to provide data for more complex segmentation techniques like Deep Learning, which require a considerable amount of data to train architectures like Convolutional Neural Networks. The code is freely available from https://github.com/reyesaldasoro/HeLa-Cell-Segmentation.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Ellinger, I., Ellinger, A.: Smallest unit of life: cell biology. In: Jensen-Jarolim, E. (ed.) Comparative Medicine: Anatomy and Physiology, pp. 19–33. Springer, Vienna (2014). https://doi.org/10.1007/978-3-7091-1559-6_2
Alberts, B., et al.: Essential Cell Biology: An Introduction to the Molecular Biology of the Cell, 1st edn. Garland Publishing Inc., New York (1998)
Hanahan, D., Weinberg, R.A.: The hallmarks of cancer. Cell 100, 57–70 (2000)
Malumbres, M., Barbacid, M.: Cell cycle, CDKs and cancer: a changing paradigm. Nature 9(24), 153–166 (2009)
Hanahan, D., Weinberg, R.A.: Hallmarks of cancer: the next generation. Cell 144(5), 646674 (2011). pMID: 21376230
Verma, R.P., Hansch, C.: Chemical toxicity on HeLa cells. Curr. Med. Chem. 13(4), 423–448 (2006)
Masters, J.R.: HeLa cells 50 years on: the good, the bad and the ugly. Nat. Rev. Cancer 2, 315–319 (2002)
Lucey, B.P., Nelson-Rees, W.A., Hutchins, G.M.: Henrietta Lacks, HeLa cells and cell culture contamination. Arch. Pathol. Lab. Med. 133, 1463–1467 (2009)
Lacroix, M.: Persistent use of “false” cell lines. Int. J. Cancer 122, 1–4 (2008)
Reyes-Aldasoro, C.C.: The proportion of cancer-related entries in PubMed has increased considerably; is cancer truly the emperor of all maladies? PLoS One 12(3), e0173671 (2017)
Lozano, R., et al.: Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the global burden of disease study 2010. Lancet (Lond. Engl.) 380(9859), 2095–2128 (2012). pMID: 23245604
NHS, UK. https://www.nhs.uk/conditions/cervical-cancer/. Accessed 17 Jan 2018
Lu, L., Ladinsky, M.S., Kirchhausen, T.: Formation of the postmitotic nuclear envelope from extended ER cisternae precedes nuclear pore assembly. J. Cell Biol. 194(3), 425–440 (2011). pMID: 21825076 PMCID: PMC3153650
Mahamid, J., et al.: Visualizing the molecular sociology at the HeLa cell nuclear periphery. Science (N.Y., NY) 351(6276), 969–972 (2016). pMID: 26917770
Haguenau, F., Hawkes, P.W., Hutchison, J.L., Satiat-Jeunemaitre, B., Simon, G.T.: Key events in the history of electron microscopy. Microsc. Microanal. 9(4), 96–138 (2003)
Masters, B.R.: History of the Electron Microscope in Cell Biology, Encyclopedia of Life Sciences. Wiley, New York (2009)
Wang, Z., Li, H.: Generalizing cell segmentation and quantification. BMC Bioinform. 18(1), 189 (2017). pMID: 28335722 PMCID: PMC5364575
Cloppet, F., Boucher, A.: Segmentation of overlapping/aggregating nuclei cells in biological images. In: Proceedings IEEE International Conference Pattern Recognition, pp. 1–4 (2008)
Solis-Lemus, J.A., Stramer, B., Slabaugh, G., Reyes-Aldasoro, C.C.: Segmentation and shape analysis of macrophages using anglegram analysis. J. Imaging 4(2), 1–20 (2017)
Zhou, X., Li, F., Yan, J., Wong, S.T.C.: A novel cell segmentation method and cell phase identification using Markov model. IEEE Trans. Inf. Technol. Biomed. 13(2), 152–157 (2009)
Jung, C., Kim, C., Chae, S.W., Oh, S.: Unsupervised segmentation of overlapped nuclei using Bayesian classification. IEEE Trans. Biomed. Eng. 57(12), 2825–2832 (2010)
Cheng, J., Rajapakse, J.C.: Segmentation of clustered nuclei with shape markers and marking function. IEEE Trans. Biomed. Eng. 56(3), 741–748 (2009)
Yang, X., Li, H., Zhou, X.: Nuclei segmentation using marker-controlled watershed, tracking using mean-shift, and Kalman filter in time-lapse microscopy. IEEE Trans. Circu. Syst. I: Regul. Pap. 53(11), 2405–2414 (2006)
Kaya, B., et al.: Automated fluorescent miscroscopic image analysis of PTBP1 expression in glioma. PLoS One 12(3), e0170991 (2017)
Goceri, E., Goksel, B., Elder, J.B., Puduvalli, V.K., Otero, J.J.: Quantitative validation of anti-PTBP1 antibody for diagnostic neuropathology use: image analysis approach. J. Numer. Methods Biomed. Eng. 33, e2862 (2017)
Lu, L., Ladinsky, M.S., Kirchhausen, T.: Formation of the postmitotic nuclear envelope from extended ER cisternae precedes nuclear pore assembly. J. Cell Biol. 194(3), 425–440 (2011)
Walter, J., Schermelleh, L., Cremer, M., Tashiro, S., Cremer, T.: Chromosome order in HeLa cells changes during mitosis and early G1, but is stably maintained during subsequent interphase stages. J. Cell Biol. 160(5), 685–697 (2003)
Mahamid, J., et al.: Visualizing the molecular sociology at the HeLa cell nuclear periphery. Science 351(6276), 969–972 (2016)
Robinson, C.V., Sali, A., Baumeister, W.: The molecular sociology of the cell. Nature 450, 973–982 (2007)
Peddie, C.J., Collinson, L.M.: Exploring the third dimension: volume electron microscopy comes of age. Micron 61, 919 (2014)
Bajcsy, P., et al.: Survey statistics of automated segmentations applied to optical imaging of mammalian cells. BMC Bioinform. 16(330), 1–28 (2015)
Coelho, L.P., Shariff, A., Murphy, R.F.: Nuclear segmentation in microscope cell images: a hand-segmented dataset and comparison of algorithms. In: Proceeding IEEE International Symposium Biomedical Imaging, pp. 518–521 (2009)
Belevich, I., Joensuu, M., Kumar, D., Vihinen, H., Jokitalo, E.: Microscopy image browser: a platform for segmentation and analysis of multidimensional datasets. PLoS Biol. 14(1), e1002340 (2016)
Schnoor, J.L.: Citizen science. Environ. Sci. Technol. 41(17), 5923 (2007)
Etch a Cell. https://www.zooniverse.org/projects/h-spiers/etch-a-cell. Accessed 17 Jan 2018
Deerinck, T.J., Bushong, E., Thor, A., Ellisman, M.H.: NCMIR - national center for microscopy and imaging research. NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Block-Face SEM Microscopy (2010). https://ncmir.ucsd.edu/sbem-protocol. Accessed 09 Feb 2018
Canny, J.: A computational approach to edge detection. IEEE Trans. Pattern Anal. Mach. Intell. 8(6), 679–698 (1986)
Jaccard, P.: Étude comparative de la distribution florale dans une portion des Alpes et des Jura. Bull. del la Société Vaudoise des Sci. Nat. 37, 547–579 (1901)
Acknowledgements
This work was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001999), the UK Medical Research Council (FC001999), and the Wellcome Trust (FC001999).
The authors acknowledge the support of the Alan Turing Institute through the Data Study Groups organised by Dr Sebastian Vollmer where initial study of this data was made.
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Nature Switzerland AG
About this paper
Cite this paper
Karabağ, C., Jones, M.L., Peddie, C.J., Weston, A.E., Collinson, L.M., Reyes-Aldasoro, C.C. (2018). Automated Segmentation of HeLa Nuclear Envelope from Electron Microscopy Images. In: Nixon, M., Mahmoodi, S., Zwiggelaar, R. (eds) Medical Image Understanding and Analysis. MIUA 2018. Communications in Computer and Information Science, vol 894. Springer, Cham. https://doi.org/10.1007/978-3-319-95921-4_23
Download citation
DOI: https://doi.org/10.1007/978-3-319-95921-4_23
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-95920-7
Online ISBN: 978-3-319-95921-4
eBook Packages: Computer ScienceComputer Science (R0)