A density-based enrichment measure for assessing colocalization in single-molecule localization microscopy data

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Standard

A density-based enrichment measure for assessing colocalization in single-molecule localization microscopy data. / Ejdrup, Aske L.; Lycas, Matthew D.; Lorenzen, Niels; Konomi, Ainoa; Herborg, Freja; Madsen, Kenneth L.; Gether, Ulrik.

In: Nature Communications, Vol. 13, No. 1, 4388, 2022.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Ejdrup, AL, Lycas, MD, Lorenzen, N, Konomi, A, Herborg, F, Madsen, KL & Gether, U 2022, 'A density-based enrichment measure for assessing colocalization in single-molecule localization microscopy data', Nature Communications, vol. 13, no. 1, 4388. https://doi.org/10.1038/s41467-022-32064-y

APA

Ejdrup, A. L., Lycas, M. D., Lorenzen, N., Konomi, A., Herborg, F., Madsen, K. L., & Gether, U. (2022). A density-based enrichment measure for assessing colocalization in single-molecule localization microscopy data. Nature Communications, 13(1), [4388]. https://doi.org/10.1038/s41467-022-32064-y

Vancouver

Ejdrup AL, Lycas MD, Lorenzen N, Konomi A, Herborg F, Madsen KL et al. A density-based enrichment measure for assessing colocalization in single-molecule localization microscopy data. Nature Communications. 2022;13(1). 4388. https://doi.org/10.1038/s41467-022-32064-y

Author

Ejdrup, Aske L. ; Lycas, Matthew D. ; Lorenzen, Niels ; Konomi, Ainoa ; Herborg, Freja ; Madsen, Kenneth L. ; Gether, Ulrik. / A density-based enrichment measure for assessing colocalization in single-molecule localization microscopy data. In: Nature Communications. 2022 ; Vol. 13, No. 1.

Bibtex

@article{763c9efc595f431691ed04d9c18459d3,

title = "A density-based enrichment measure for assessing colocalization in single-molecule localization microscopy data",

abstract = "Dual-color single-molecule localization microscopy (SMLM) provides unprecedented possibilities for detailed studies of colocalization of different molecular species in a cell. However, the informational richness of the data is not fully exploited by current analysis tools that often reduce colocalization to a single value. Here, we describe a tool specifically designed for determination of co-localization in both 2D and 3D from SMLM data. The approach uses a function that describes the relative enrichment of one molecular species on the density distribution of a reference species. The function reframes the question of colocalization by providing a density-context relevant to multiple biological questions. Moreover, the function visualize enrichment (i.e. colocalization) directly in the images for easy interpretation. We demonstrate the approach{\textquoteright}s functionality on both simulated data and cultured neurons, and compare it to current alternative measures. The method is available in a Python function for easy and parameter-free implementation.",

author = "Ejdrup, {Aske L.} and Lycas, {Matthew D.} and Niels Lorenzen and Ainoa Konomi and Freja Herborg and Madsen, {Kenneth L.} and Ulrik Gether",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

doi = "10.1038/s41467-022-32064-y",

language = "English",

volume = "13",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "nature publishing group",

number = "1",

}

RIS

TY - JOUR

T1 - A density-based enrichment measure for assessing colocalization in single-molecule localization microscopy data

AU - Ejdrup, Aske L.

AU - Lycas, Matthew D.

AU - Lorenzen, Niels

AU - Konomi, Ainoa

AU - Herborg, Freja

AU - Madsen, Kenneth L.

AU - Gether, Ulrik

PY - 2022

Y1 - 2022

N2 - Dual-color single-molecule localization microscopy (SMLM) provides unprecedented possibilities for detailed studies of colocalization of different molecular species in a cell. However, the informational richness of the data is not fully exploited by current analysis tools that often reduce colocalization to a single value. Here, we describe a tool specifically designed for determination of co-localization in both 2D and 3D from SMLM data. The approach uses a function that describes the relative enrichment of one molecular species on the density distribution of a reference species. The function reframes the question of colocalization by providing a density-context relevant to multiple biological questions. Moreover, the function visualize enrichment (i.e. colocalization) directly in the images for easy interpretation. We demonstrate the approach’s functionality on both simulated data and cultured neurons, and compare it to current alternative measures. The method is available in a Python function for easy and parameter-free implementation.

AB - Dual-color single-molecule localization microscopy (SMLM) provides unprecedented possibilities for detailed studies of colocalization of different molecular species in a cell. However, the informational richness of the data is not fully exploited by current analysis tools that often reduce colocalization to a single value. Here, we describe a tool specifically designed for determination of co-localization in both 2D and 3D from SMLM data. The approach uses a function that describes the relative enrichment of one molecular species on the density distribution of a reference species. The function reframes the question of colocalization by providing a density-context relevant to multiple biological questions. Moreover, the function visualize enrichment (i.e. colocalization) directly in the images for easy interpretation. We demonstrate the approach’s functionality on both simulated data and cultured neurons, and compare it to current alternative measures. The method is available in a Python function for easy and parameter-free implementation.

U2 - 10.1038/s41467-022-32064-y

DO - 10.1038/s41467-022-32064-y

M3 - Journal article

C2 - 35902578

AN - SCOPUS:85135146576

VL - 13

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

M1 - 4388

ER -

ID: 315761103

Department of Neuroscience