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NanoJ-SQUIRREL: quantitative mapping and minimisation of super-resolution optical imaging artefacts

By Siân Culley, David Albrecht, Caron Jacobs, Pedro Matos Pereira, Bénédicte Dargent, Jason Mercer, Ricardo Henriques

Posted 02 Jul 2017
bioRxiv DOI: 10.1101/158279 (published DOI: 10.1038/nmeth.4605)

Most super-resolution microscopy methods depend on steps that contribute to the formation of image artefacts. Here we present NanoJ-SQUIRREL, an ImageJ-based analytical approach providing a quantitative assessment of super-resolution image quality. By comparing diffraction-limited images and super-resolution equivalents of the same focal volume, this approach generates a quantitative map of super-resolution defects, as well as methods for their correction. To illustrate its broad applicability to super-resolution approaches we apply our method to Localization Microscopy, STED and SIM images of a variety of in-cell structures including microtubules, poxviruses, neuronal actin rings and clathrin coated pits. We particularly focus on single-molecule localisation microscopy, where super-resolution reconstructions often feature imperfections not present in the original data. By showing the quantitative evolution of data quality over these varied sample preparation, acquisition and super-resolution methods we display the potential of NanoJ-SQUIRREL to guide optimization of super-resolution imaging parameters.

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