Modeling of 2D diffusion processes based on microscopy data: Parameter estimation and practical identifiability analysis

Hock S, Hasenauer J, Theis FJ (2013)

Publication Type: Journal article

Publication year: 2013

Journal

BMC Bioinformatics BMC

Book Volume: 14

Article Number: S7

Journal Issue: SUPPL10

DOI: 10.1186/1471-2105-14-S10-S7

Abstract

Background: Diffusion is a key component of many biological processes such as chemotaxis, developmental differentiation and tissue morphogenesis. Since recently, the spatial gradients caused by diffusion can be assessed in-vitro and in-vivo using microscopy based imaging techniques. The resulting time-series of two dimensional, high-resolutions images in combination with mechanistic models enable the quantitative analysis of the underlying mechanisms. However, such a model-based analysis is still challenging due to measurement noise and sparse observations, which result in uncertainties of the model parameters.Methods: We introduce a likelihood function for image-based measurements with log-normal distributed noise. Based upon this likelihood function we formulate the maximum likelihood estimation problem, which is solved using PDE-constrained optimization methods. To assess the uncertainty and practical identifiability of the parameters we introduce profile likelihoods for diffusion processes.Results and conclusion: As proof of concept, we model certain aspects of the guidance of dendritic cells towards lymphatic vessels, an example for haptotaxis. Using a realistic set of artificial measurement data, we estimate the five kinetic parameters of this model and compute profile likelihoods. Our novel approach for the estimation of model parameters from image data as well as the proposed identifiability analysis approach is widely applicable to diffusion processes. The profile likelihood based method provides more rigorous uncertainty bounds in contrast to local approximation methods. © 2013 Hock et al; licensee BioMed Central Ltd.

Involved external institutions

Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU) / Helmholtz Munich DE Germany (DE)

How to cite

APA:

Hock, S., Hasenauer, J., & Theis, F.J. (2013). Modeling of 2D diffusion processes based on microscopy data: Parameter estimation and practical identifiability analysis. BMC Bioinformatics, 14(SUPPL10). https://doi.org/10.1186/1471-2105-14-S10-S7

MLA:

Hock, Sabrina, Jan Hasenauer, and Fabian J. Theis. "Modeling of 2D diffusion processes based on microscopy data: Parameter estimation and practical identifiability analysis." BMC Bioinformatics 14.SUPPL10 (2013).

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