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

Aske L. Ejdrup (), Matthew D. Lycas, Niels Lorenzen, Ainoa Konomi, Freja Herborg, Kenneth L. Madsen and Ulrik Gether ()
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Aske L. Ejdrup: University of Copenhagen
Matthew D. Lycas: University of Copenhagen
Niels Lorenzen: University of Copenhagen
Ainoa Konomi: University of Copenhagen
Freja Herborg: University of Copenhagen
Kenneth L. Madsen: University of Copenhagen
Ulrik Gether: University of Copenhagen

Nature Communications, 2022, vol. 13, issue 1, 1-10

Abstract: 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’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.

Date: 2022
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DOI: 10.1038/s41467-022-32064-y

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