OSA's Digital Library

Optics Express

Optics Express

  • Editor: Andrew M. Weiner
  • Vol. 21, Iss. 25 — Dec. 16, 2013
  • pp: 30755–30763

Locating particles accurately in microscope images requires image-processing kernels to be rotationally symmetric

Peter J. Lu, Maor Shutman, Eli Sloutskin, and Alexander V. Butenko  »View Author Affiliations


Optics Express, Vol. 21, Issue 25, pp. 30755-30763 (2013)
http://dx.doi.org/10.1364/OE.21.030755


View Full Text Article

Enhanced HTML    Acrobat PDF (1317 KB)





Browse Journals / Lookup Meetings

Browse by Journal and Year


   


Lookup Conference Papers

Close Browse Journals / Lookup Meetings

Article Tools

Share
Citations

Abstract

Computerized image-analysis routines deployed widely to locate and track the positions of particles in microscope images include several steps where images are convolved with kernels to remove noise. In many common implementations, some kernels are rotationally asymmetric. Here we show that the use of these asymmetric kernels creates significant artifacts, distorting apparent particle positions in a way that gives the artificial appearance of orientational crystalline order, even in such fully-disordered isotropic systems as simple fluids of hard-sphere-like colloids. We rectify this problem by replacing all asymmetric kernels with rotationally-symmetric kernels, which does not impact code performance. We show that these corrected codes locate particle positions properly, restoring measured isotropy to colloidal fluids. We also investigate rapidly-formed colloidal sediments, and with the corrected codes show that these sediments, often thought to be amorphous, may exhibit strong orientational correlations among bonds between neighboring colloidal particles.

© 2013 Optical Society of America

OCIS Codes
(100.2000) Image processing : Digital image processing
(100.2960) Image processing : Image analysis
(100.2980) Image processing : Image enhancement
(100.3010) Image processing : Image reconstruction techniques
(110.0180) Imaging systems : Microscopy
(180.1790) Microscopy : Confocal microscopy

ToC Category:
Image Processing

History
Original Manuscript: July 31, 2013
Revised Manuscript: October 27, 2013
Manuscript Accepted: November 1, 2013
Published: December 6, 2013

Virtual Issues
Vol. 9, Iss. 2 Virtual Journal for Biomedical Optics

Citation
Peter J. Lu, Maor Shutman, Eli Sloutskin, and Alexander V. Butenko, "Locating particles accurately in microscope images requires image-processing kernels to be rotationally symmetric," Opt. Express 21, 30755-30763 (2013)
http://www.opticsinfobase.org/oe/abstract.cfm?URI=oe-21-25-30755


Sort:  Author  |  Year  |  Journal  |  Reset  

References

  1. U. Gasser, E. R. Weeks, A. B. Schofield, P. N. Pusey, and D. A. Weitz, “Real-space imaging of nucleation and growth in colloidal crystallization,” Science292, 258–262 (2001). [CrossRef] [PubMed]
  2. A. van Blaaderen and P. Wiltzius, “Real-space structure of colloidal hard-sphere glasses,” Science270, 1177–1179 (1995). [CrossRef]
  3. E. R. Weeks, J. C. Crocker, A. C. Levitt, A. Schofield, and D. A. Weitz, “Three-dimensional direct imaging of structural relaxation near the colloidal glass transition,” Science287, 627–631 (2000). [CrossRef] [PubMed]
  4. Z. Zhang, N. Xu, D. T. N. Chen, P. Yunker, A. M. Alsayed, K. B. Aptowicz, P. Habdas, A. J. Liu, S. R. Nagel, and A. G. Yodh, “Thermal vestige of the zero-temperature jamming transition,” Nature459, 230–233 (2009). [CrossRef] [PubMed]
  5. Z. Zheng, F. Wang, and Y. Han, “Glass transitions in quasi-two-dimensional suspensions of colloidal ellipsoids,” Phys. Rev. Lett.107, 065702 (2011). [CrossRef] [PubMed]
  6. G. L. Hunter and E. R. Weeks, “The physics of the colloidal glass transition,” Rep. Prog. Phys.75, 066501 (2012). [CrossRef] [PubMed]
  7. P. J. Lu, E. Zaccarelli, F. Ciulla, A. B. Schofield, F. Sciortino, and D. A. Weitz, “Gelation of particles with short-range attraction,” Nature453, 499–503 (2008). [CrossRef] [PubMed]
  8. T. Aste, M. Saadatfar, and T. J. Senden, “Geometrical structure of disordered sphere packings,” Phys. Rev. E71, 061302 (2005). [CrossRef]
  9. M. Jerkins, M. Schröter, H. L. Swinney, T. J. Senden, M. Saadatfar, and T. Aste, “Onset of mechanical stability in random packings of frictional particles,” Phys. Rev. Lett.101, 018301 (2008). [CrossRef]
  10. S. R. Liber, S. Borohovich, A. V. Butenko, A. B. Schofield, and E. Sloutskin, “Dense colloidal fluids form denser amorphous sediments,” Proc. Nat. Acad. Sci. U. S. A.110, 5769–5773 (2013). [CrossRef]
  11. X. Cheng, J. H. McCoy, J. N. Israelachvili, and I. Cohen, “Imaging the microscopic structure of shear thinning and thickening colloidal suspensions,” Science333, 1276–1279 (2011). [CrossRef] [PubMed]
  12. U. Gasser, “Crystallization in three- and two-dimensional colloidal suspensions,” J. Phys. Condens. Mat.21, 203101 (2009). [CrossRef]
  13. J. C. Crocker and D. G. Grier, “Methods of digital video microscopy for colloidal studies,” J. Colloid Interface Sci.179, 298–310 (1996). [CrossRef]
  14. P. J. Lu, P. A. Sims, H. Oki, J. B. Macarthur, and D. A. Weitz, “Target-locking acquisition with real-time confocal (TARC) microscopy,” Opt. Express15, 8702–8712 (2007). [CrossRef] [PubMed]
  15. Y. Gao and M. L. Kilfoil, “Accurate detection and complete tracking of large populations of features in three dimensions,” Opt. Express17, 4685–4704 (2009). [CrossRef] [PubMed]
  16. http://tacaswell.github.io/tracking/html/
  17. http://github.com/peterlu/PLuTARC_centerfind2D
  18. S. W. Smith, The Scientist & Engineer’s Guide to Digital Signal Processing (California Technical, 1997).
  19. D. G. Grier and J. C. Crocker, personal communication.
  20. J.-P. Hansen and I. R. McDonald, Theory of Simple Liquids (Elsevier, 2006).
  21. D. Frenkel, R. J. Vos, C. G. de Kruif, and A. Vrij, “Structure factors of polydisperse systems of hard spheres: A comparison of Monte Carlo simulations and Percus-Yevick theory,” J. Chem. Phys.84, 4625–4630 (1986). [CrossRef]
  22. D. R. Wilkinson and S. F. Edwards, “The use of stereology to determine the partial two-body correlation functions for hard sphere ensembles,” J. Phys. D Appl. Phys.15, 551–562 (1982). [CrossRef]
  23. M. de Berg, O. Cheong, M. van Kreveld, and M. Overmars, Computational Geometry: Algorithms and Applications (Springer, 2008).
  24. C. P. Royall, M. E. Leunissen, A.-P. Hynninen, M. Dijkstra, and A. van Blaaderen, “Re-entrant melting and freezing in a model system of charged colloids,” J. Chem. Phys.124, 244706 (2006). [CrossRef] [PubMed]
  25. A. P. Cohen, E. Janai, E. Mogilko, A. B. Schofield, and E. Sloutskin, “Fluid suspensions of colloidal ellipsoids: Direct structural measurements,” Phys. Rev. Lett.107, 238301 (2011). [CrossRef] [PubMed]
  26. A. P. Cohen, E. Janai, D. C. Rapaport, A. B. Schofield, and E. Sloutskin, “Structure and interactions in fluids of prolate colloidal ellipsoids: Comparison between experiment, theory, and simulation,” J. Chem. Phys.137, 184505 (2012). [CrossRef] [PubMed]

Cited By

Alert me when this paper is cited

OSA is able to provide readers links to articles that cite this paper by participating in CrossRef's Cited-By Linking service. CrossRef includes content from more than 3000 publishers and societies. In addition to listing OSA journal articles that cite this paper, citing articles from other participating publishers will also be listed.

Figures

Fig. 1 Fig. 2 Fig. 3
 
Fig. 4
 

« Previous Article  |  Next Article »

OSA is a member of CrossRef.

CrossCheck Deposited