Spherical fluorescent particle segmentation and tracking in 3D confocal microscopy

From LRDE

Abstract

Spherical fluorescent particle are micrometer-scale spherical beads used in various areas of physics, chemistry or biology as markers associated with local physical media. They are useful for example in fluid dynamics to characterize flows, diffusion coefficients, viscosity or temperature; they are used in cells dynamics to estimate mechanical strain and stress at the micrometer scale. In order to estimate these physical measurements, tracking these particles is necessary. Numerous approaches and existing packages, both open-source and proprietary are available to achieve tracking with a high degree of precision in 2D. However, little such software is available to achieve tracking in 3D. One major difficulty is that 3D confocal microscopy acquisition is not typically fast enough to assume that the beads are stationary during the whole 3D scan. As a result, beads may move between planar scans. Classical approaches to 3D segmentation may yield objects are not spherical. In this article, we propose a 3D bead segmentation that deals with this situation.


Bibtex (lrde.bib)

@InProceedings{	  puybareau.19.ismm,
  author	= {\'{E}lodie Puybareau and Edwin Carlinet and Alessandro
		  Benfenati and Hugues Talbot},
  title		= {Spherical fluorescent particle segmentation and tracking
		  in {3D} confocal microscopy},
  booktitle	= {Mathematical Morphology and Its Application to Signal and
		  Image Processing -- Proceedings of the 14th International
		  Symposium on Mathematical Morphology (ISMM)},
  year		= 2019,
  series	= {Lecture Notes in Computer Science Series},
  address	= {Saarbr\"ucken, Germany},
  publisher	= {Springer},
  pages		= {1--12},
  month		= jul,
  abstract	= {Spherical fluorescent particle are micrometer-scale
		  spherical beads used in various areas of physics, chemistry
		  or biology as markers associated with local physical media.
		  They are useful for example in fluid dynamics to
		  characterize flows, diffusion coefficients, viscosity or
		  temperature; they are used in cells dynamics to estimate
		  mechanical strain and stress at the micrometer scale. In
		  order to estimate these physical measurements, tracking
		  these particles is necessary. Numerous approaches and
		  existing packages, both open-source and proprietary are
		  available to achieve tracking with a high degree of
		  precision in 2D. However, little such software is available
		  to achieve tracking in 3D. One major difficulty is that 3D
		  confocal microscopy acquisition is not typically fast
		  enough to assume that the beads are stationary during the
		  whole 3D scan. As a result, beads may move between planar
		  scans. Classical approaches to 3D segmentation may yield
		  objects are not spherical. In this article, we propose a 3D
		  bead segmentation that deals with this situation.}
}