A computational approach for detecting micro-domains and confinement domains in cells: a simulation study

Abstract

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Charles Kervrann. A computational approach for detecting microdomains and confinement domains in cells: a simulation study. Physical Biology, Institute of Physics: Hybrid Open Access, In press, pp.Abstract. In this paper, we aim at detecting trapping areas (equivalently microdomains or confinement areas) within cells, corresponding to regions where molecules are trapped and thereby undergo subdiffusion. We propose an original computational approach that takes as input a set of molecule trajectories estimated by appropriate tracking methods. The core of the algorithm is based on a combination of clustering algorithms with trajectory classification procedures able to distinguish subdiffusion, superdiffusion and Brownian motion. The idea is to automatically identify trapping areas where we observe a high concentration of subdiffusive particles. We evaluate our proof of concept on artificial sequences obtained with a biophysicsbased simulator (Fluosim), and we illustrate its potential on real TIRF microscopy data.

FluoSim: simulator of single molecule dynamics for fluorescence live-cell and super-resolution imaging of membrane proteins

“…The software can also be used to test the robustness and predictions of single molecule tracking algorithms that have been implemented those past years, e.g. SR-Tesseler and InferenceMap [48][49][50] . Compared to existing software such as PyFRAP, SuReSim, FERNET, or MCell [13][14][15] , FluoSim integrates many fluorescence modalities into a single program and achieves real-time display (Supplementary Table 1).…”

Detecting Transient Trapping from a Single Trajectory: A Structural Approach

“…The detection of trapping is challenging and has been the subject of investigation by several authors. A possible strategy, based on an ensemble of trajectories, consists of evaluating trapping domains from the evaluation of local confining force [4][5][6][7][8]. On the side of single trajectory analysis, techniques were based on the maximum square displacement [9][10][11], although they are generally too sensitive to noise and local fluctuations of trajectory dynamics.…”

Uncover Single Nanoparticle Dynamics on Live Cell Membrane with Data-Driven Historical Experience Analysis

“…Given the high spatiotemporal complexity of NP–cell interactions, the primary issue is to find an appropriate approach to differentiate and describe the particle movement. Considering the trajectories as a combination of subsequence with independent and discrete underlying states that can be inferred by local features or probabilistic estimation, a large number of methods based on moving windows or machine learning have been developed to assign each point in the trajectory with a specific predefined physical state. − However, these methods need handcrafted feature selection and generate training data set by specific physical models. The feature extraction process always involves fitting or averaging operations, which may neglect detailed dynamics information.…”