Efficient Position Estimation of 3D Fluorescent Spherical Beads in Confocal Microscopy via Poisson Denoising
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Efficient Position Estimation of 3D Fluorescent Spherical Beads in Confocal Microscopy via Poisson Denoising Alessandro Benfenati1
· Francesco Bonacci2 · Tarik Bourouina3 · Hugues Talbot4
Received: 2 October 2019 / Accepted: 28 September 2020 © The Author(s) 2020
Abstract Particle estimation is a classical problem arising in many science fields, such as biophysics, fluid mechanics and biomedical imaging. Many interesting applications in these areas involve 3D imaging data: This work presents a technique to estimate the 3D coordinates of the center of spherical particles. This procedure has its core in the processing of the images of the scanned volume: It firstly applies denoising techniques to each frame of the scanned volume and then provides an estimation of both the center and the profile of the 2D intersections of the particles with the frames, by coupling the usage of Total Variation functional and of a regularized weighted Least Squares fit. Then, the 2D information is used to retrieve the 3D coordinates using geometrical properties. The experiments provide evidence that image denoising has a large impact on the performance of the particle tracking procedures, since they strongly depend on the quality of the initial acquisition. This work shows that the choice of tailored image denoising technique for Poisson noise leads to a better estimation of the particle positions. Keywords Particle estimation · Particle tracking · 3D data · Brownian motion
1 Introduction Particle tracking techniques are widely employed in several science fields for identifying particular structures or Funding for this project was provided in part by LABEX MMCD and ANR CoMeDIC. Alessandro Benfenati: Member of the INdAM Research Group GNCS.
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Alessandro Benfenati [email protected] Francesco Bonacci [email protected] Tarik Bourouina [email protected] Hugues Talbot [email protected]
1
Dipartimento di Scienze e Politiche Ambientali, Via Celoria 2, 20133 Milan, Italy
2
IFSTTAR, ENPC, Université Paris-Est, 14-20 Boulevard Newton, 77420 Champs sur Marne, France
3
ESYCOM, ESIEE, ENPC, Université Paris-Est, 5 Boulevard Descartes, 77420 Champs-sur-Marne, France
4
CVN, Inria, CentraleSupélec, Université Paris-Saclay, 9 Rue Joliot Curie, 91190 Gif-sur-Yvette, France
processes of interest. Some important examples include biophysics, where these techniques are involved in the observation of molecular level motion of kinesin in microtubules and of motion of myosin on actin [52], in the study of the infection path of a virus [49] or in the investigation of cytoskeletal filaments [1]; another topic involving particles tracking problem regards the observation of protein motion in cell membranes [37] or intracellular transport [32]. Other interesting areas of application include statistical mechanics [5,6], fluid dynamics and mechanics, in particular rheology [34], where the thermal motion of Brownian particles has been tracked to study local rheological properties [20], complex fluids [2,47] and
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