Advertisement

Semi-Automatic Cell Correspondence Analysis Using Iterative Point Cloud Registration

  • Shuqing ChenEmail author
  • Simone Gehrer
  • Sara Kaliman
  • Nishant Ravikumar
  • Abdurrahman Becit
  • Maryam Aliee
  • Diana Dudziak
  • Rudolf Merkel
  • Ana-Sunćana Smith
  • Andreas Maier
Conference paper
Part of the Informatik aktuell book series (INFORMAT)

Zusammenfassung

In the field of biophysics, deformation of in-vitro model tissues is an experimental technique to explore the response of tissue to a mechanical stimulus. However, automated registration before and after deformation is an ongoing obstacle for measuring the tissue response on the cellular level. Here, we propose to use an iterative point cloud registration (IPCR) method, for this problem. We apply the registration method on point clouds representing the cellular centers of mass, which are evaluated with aWatershed based segmentation of phase-contrast images of living tissue, acquired before and after deformation. Preliminary evaluation of this method on three data sets shows high accuracy, with 82% - 92% correctly registered cells, which outperforms coherent point drift (CPD). Hence, we propose the application of the IPCR method on the problem of cell correspondence analysis.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Literatur

  1. 1.
    Mualla F, Schöll S, Sommerfeldt B, et al. Automatic cell detection in bright-field microscope images using SIFT, random forests, and hierarchical clustering. IEEE Trans Med Imaging. 2013; 32(12):2274-2286.CrossRefGoogle Scholar
  2. 2.
    Mualla F, Schöll S, Sommerfeldt B, et al. Unsupervised unstained cell detection by SIFT keypoint clustering and self-labeling algorithm. Med Image Comput Comput Assist Interv. 2014; p. 377-384.Google Scholar
  3. 3.
    De Vylder J, De Vos WH, Manders EM, et al. 2D mapping of strongly deformable cell nuclei-based on contour matching. Cytometry A. 2011;79A(7):580-588.CrossRefGoogle Scholar
  4. 4.
    Hand A, Sun T, Barber D, et al. Automated tracking of migrating cells in phase-contrast video microscopy sequences using image registration. J Microsc. 2009;234(1):62-79.MathSciNetCrossRefGoogle Scholar
  5. 5.
    Faust U, Hampe N, Rubner W, et al. Cyclic stress at mHz frequencies aligns fibroblasts in direction of zero strain. PLoS One. 2011;6(12):e28963.CrossRefGoogle Scholar
  6. 6.
    Gehrer S. Stress-strain relation in reconstituted tissue. Friedrich-Alexander-Universität Erlangen-Nürnberg; 2016.Google Scholar
  7. 7.
    Sternberg SR. Biomedical image processing. Comput. 1983;16:22 - 34.CrossRefGoogle Scholar
  8. 8.
    Preibisch S, Saalfeld S, Tomancak P. Globally optimal stitching of tiled 3D microscopic image acquisitions. Bioinform. 2009;25(11):1463.CrossRefGoogle Scholar
  9. 9.
    Kaliman S, Jayachandran C, Rehfeldt F, et al. Limits of applicability of the voronoi tessellation determined by centers of cell nuclei to epithelium morphology. Front Physiol. 2016;7.Google Scholar
  10. 10.
    Otsu N. A threshold selection method from gray-level histograms. IEEE Trans Syst Man Cybern. 1979;9(1):62-66.CrossRefGoogle Scholar
  11. 11.
    Meyer F. Topographic distance and watershed lines. Sign Process. 1994;38(1):113 - 125.CrossRefGoogle Scholar
  12. 12.
    Muja M, Lowe DG. Fast approximate nearest neighbors with automatic algorithm configuration. VISAPP. 2009; p. 331-340.Google Scholar
  13. 13.
    Hansen N. The CMA evolution strategy: a comparing review. Towards New Evol Comput. 2006; p. 75-102.Google Scholar
  14. 14.
    Myronenko A, Song X. Point set registration: coherent point drift. IEEE Trans Pattern Anal Mach Intell. 2010;32(12):2262-2275.CrossRefGoogle Scholar

Copyright information

© Springer Fachmedien Wiesbaden GmbH, ein Teil von Springer Nature 2019

Authors and Affiliations

  • Shuqing Chen
    • 1
    • 2
    Email author
  • Simone Gehrer
    • 2
  • Sara Kaliman
    • 2
  • Nishant Ravikumar
    • 1
    • 2
  • Abdurrahman Becit
    • 1
    • 2
  • Maryam Aliee
    • 2
  • Diana Dudziak
    • 3
  • Rudolf Merkel
    • 4
  • Ana-Sunćana Smith
    • 2
    • 5
  • Andreas Maier
    • 1
    • 2
  1. 1.Pattern Recognition LabFAU Erlangen-NürnbergErlangenDeutschland
  2. 2.PULS GroupTheo. Physics I, FAU Erlangen-NürnbergErlangenDeutschland
  3. 3.Department of DermatologyUniversity Hospital ErlangenErlangenDeutschland
  4. 4.ICS 7: BiomechanicsForschungszentrum Jülich GmbHJülichDeutschland
  5. 5.Division of Physical ChemestryInstitute Ruđer BoškovićZagrebCroatia

Personalised recommendations