DeepFRAP: Fast fluorescence recovery after photobleaching data analysis using deep neural networks
Artikel i vetenskaplig tidskrift, 2021

Conventional analysis of fluorescence recovery after photobleaching (FRAP) data for diffusion coefficient estimation typically involves fitting an analytical or numerical FRAP model to the recovery curve data using non-linear least squares. Depending on the model this can be time-consuming, especially for batch analysis of large numbers of data sets and if multiple initial guesses for the parameter vector are used to ensure convergence. In this work, we develop a completely new approach, DeepFRAP, utilizing machine learning for parameter estimation in FRAP. From a numerical FRAP model developed in previous work, we generate a very large set of simulated recovery curve data with realistic noise levels. The data is used for training different deep neural network regression models for prediction of several parameters, most importantly the diffusion coefficient. The neural networks are extremely fast and can estimate the parameters orders of magnitude faster than least squares. The performance of the neural network estimation framework is compared to conventional least squares estimation on simulated data, and found to be strikingly similar. Also, a simple experimental validation is performed, demonstrating excellent agreement between the two methods. We make the data and code used publicly available to facilitate further 34
development of machine learning-based estimation in FRAP.

37 machine learning

diffusion

confocal laser scanning microscopy

regression

deep learning

deep neural network

fluorescence recovery after photobleaching

Författare

Victor Wåhlstrand Skärström

RISE Research Institutes of Sweden

Annika Krona

RISE Research Institutes of Sweden

Niklas Lorén

RISE Research Institutes of Sweden

Chalmers, Fysik, Nano- och biofysik

Magnus Röding

RISE Research Institutes of Sweden

Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik

Göteborgs universitet

Journal of Microscopy

0022-2720 (ISSN) 1365-2818 (eISSN)

Vol. In press

Styrkeområden

Nanovetenskap och nanoteknik (SO 2010-2017, EI 2018-)

Livsvetenskaper och teknik (2010-2018)

Materialvetenskap

Ämneskategorier

Annan fysik

Sannolikhetsteori och statistik

Infrastruktur

Chalmers materialanalyslaboratorium

DOI

10.1111/jmi.12989

PubMed

33247838

Mer information

Senast uppdaterat

2021-01-25