Abstract
The life of a cell is governed by highly dynamical microscopic processes. Two notable examples are the diffusion of membrane receptors and the kinetics of transcription factors governing the rates of gene expression. Different fluorescence imaging techniques have emerged to study molecular dynamics. Among them, fluorescence correlation spectroscopy (FCS) and single-particle tracking (SPT) have proven to be instrumental to our understanding of cell dynamics and function. The analysis of SPT and FCS is an ongoing effort, and despite decades of work, much progress remains to be done. In this paper, we give a quick overview of the existing techniques used to analyze anomalous diffusion in cells and propose a collaborative challenge to foster the development of state-of-the-art analysis algorithms. We propose to provide labelled (training) and unlabelled (evaluation) simulated data to competitors all over the world in an open and fair challenge. The goal is to offer unified data benchmarks based on biologically-relevant metrics in order to compare the diffusion analysis software available for the community.
Highlights
The life of a cell is governed by highly dynamical microscopic processes occurring at different space and time scales from single macromolecules up to organelles
Several factors have colluded to popularize these techniques in many biophysics and biology labs: (i) the development of highly sensitive detectors, (ii) the emergence of genetically encoded fluorescent protein labeling in the late 90s [5,6,7], and (iii) the advent in the years 2000–2010 of far-field super-resolution microscopy [8,9,10,11,12]
We will first focus on three classical models for anomalous subdiffusion and their common biological interpretation, namely the continuous-time random walk (CTRW) model, the fractional Brownian motion model, and random walks on fractal and disordered systems, we will briefly describe different models covering super-diffusion processes that can be encountered in cells, such as run and tumble model, Lévy flights and super-diffusive fBm
Summary
The life of a cell is governed by highly dynamical microscopic processes occurring at different space and time scales from single macromolecules up to organelles. Several factors have colluded to popularize these techniques in many biophysics and biology labs: (i) the development of highly sensitive detectors, (ii) the emergence of genetically encoded fluorescent protein labeling in the late 90s [5,6,7], and (iii) the advent in the years 2000–2010 of far-field super-resolution microscopy [8,9,10,11,12] All these technological efforts have granted us access to the monitoring of molecular motion in cells with unprecedented spatial (down to single molecule) and temporal resolution [13, 14]. The adoption of these techniques has been paramount in the advancement of the understanding of cell organization and dynamics [15,16,17]
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