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Cited by 49Advanced Fluorescence Microscopy TechniquesDiffusion Coefficients in LiquidsCell Image Analysis Techniques

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Quantitative diffusion measurements using the open-source software PyFRAP

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Bläßle, Alexander, Soh, Gary, Braun, Theresa, Mörsdorf, David, Preiß, Hannes, Jordan, Ben M., Müller, Patrick·2018·Nature Communications
DOI 10.1038/s41467-018-03975-6PMC PMC5910415
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Abstract

Fluorescence Recovery After Photobleaching (FRAP) and inverse FRAP (iFRAP) assays can be used to assess the mobility of fluorescent molecules. These assays measure diffusion by monitoring the return of fluorescence in bleached regions (FRAP), or the dissipation of fluorescence from photoconverted regions (iFRAP). However, current FRAP/iFRAP analysis methods suffer from simplified assumptions about sample geometry, bleaching/photoconversion inhomogeneities, and the underlying reaction-diffusion kinetics. To address these shortcomings, we developed the software PyFRAP, which fits numerical simulations of three-dimensional models to FRAP/iFRAP data and accounts for bleaching/photoconversion inhomogeneities. Using PyFRAP we determined the diffusivities of fluorescent molecules spanning two orders of magnitude in molecular weight. We measured the tortuous effects that cell-like obstacles exert on effective diffusivity and show that reaction kinetics can be accounted for by model selection. These applications demonstrate the utility of PyFRAP, which can be widely adapted as a new extensible standard for FRAP analysis.

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  • The measured diffusion coefficients were in good agreement with literature values in aqueous solutions and their mass dependence.

    “Using this method, our measured diffusion coefficients were in good agreement with literature values in aqueous solutions23,24 and their mass dependence (inset to Fig. 1b).”

    From Brain clearance is reduced during sleep and anesthesia (2024) · cites this paper as [23]

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Metadata

Authors
Bläßle, A., Soh, G., Braun, T., Mörsdorf, D., Preiß, H., Jordan, B. M., & Müller, P.
Affiliations
Max Planck Society (DE)
Corresponding author
Müller, Patrick
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2018-04-20
Volume
9
Issue
1
Pages
1582-1582
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-018-03975-6
PMC
PMC5910415
OpenAlex
W2800923780
Cited by
49
References
1
Citations by year
2026: 8 · 2025: 8 · 2024: 5 · 2023: 6 · 2022: 4 · 2021: 6 · 2020: 4 · 2019: 4 · 2018: 4
FWCI
2.21
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • KOPS (University of Konstanz) (submittedVersion, cc-by)
  • Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • MPG.PuRe (Max Planck Society) (submittedVersion)
Funders
  • Deutsche Forschungsgemeinschaft
  • Max-Planck-Gesellschaft
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Diffusion Coefficients in Liquids
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
Keywords
FRAP, diffusion measurement, molecular mobility, reaction-diffusion kinetics, effective diffusion coefficient, model selection, open source software

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