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CELLULAR IMAGING

Revisiting colocalization via optimal transport

Nature Computational Science volume 1, pages 177–178 (2021)Cite this article

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The advent of STED microscopy, which allows observation at a sub-diffraction resolution, raises a challenge in studying spatial proximities of biomolecules’ distributions. In this issue, researchers have attempted to study colocalization of molecules by employing optimal transport.

Colocalization studies have notoriously been subject to misinterpretation due to difficulties in robust quantification and, more importantly, reproducibility, which results in a constant source of confusion, frustration, and error. Many quantitative colocalization analysis methods are proposed to ease these issues and provide a more objective measure3. Existing colocalization techniques can be broadly classified as pixel-based or object-based. Pixel-based methods quantify the level of colocalization in microscopy images by the degree of association between intensities at each pixel. This type of method, while intuitive and popular, is sensitive to resolution and, in particular, not suitable for high-resolution images (Fig. 1a). Also, the spatial information among different pixels is often not well utilized. On the other hand, object-based methods measure colocalization by the closeness between the estimated fluorophores’ locations. They are applicable to high-resolution images but often fail to take full advantage of valuable information represented by the intensities at each pixel. It is natural to wonder if one can have the best of both worlds. And Carla Tameling et al. showed us how.

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Fig. 1: Challenges in colocalization quantification and new colocalization measure proposed by Carla Tameling and colleagues.

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Authors and Affiliations

  1. Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, IL, USA

    Shulei Wang

  2. Department of Statistics, Columbia University, New York, NY, USA

    Ming Yuan

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  1. Shulei Wang
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  2. Ming Yuan
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Correspondence to Shulei Wang.

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Wang, S., Yuan, M. Revisiting colocalization via optimal transport. Nat Comput Sci 1, 177–178 (2021). https://doi.org/10.1038/s43588-021-00046-7

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