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NanoJ: a high-performance open-source super-resolution microscopy toolbox

Laine, RF; Tosheva, KL; Gustafsson, N; Gray, RDM; Almada, P; Albrecht, D; Risa, GT; ... Henriques, R; + view all (2019) NanoJ: a high-performance open-source super-resolution microscopy toolbox. Journal of Physics D: Applied Physics , 52 (16) , Article 163001. 10.1088/1361-6463/ab0261. Green open access

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Abstract

Super-resolution microscopy (SRM) has become essential for the study of nanoscale biological processes. This type of imaging often requires the use of specialised image analysis tools to process a large volume of recorded data and extract quantitative information. In recent years, our team has built an open-source image analysis framework for SRM designed to combine high performance and ease of use. We named it NanoJ—a reference to the popular ImageJ software it was developed for. In this paper, we highlight the current capabilities of NanoJ for several essential processing steps: spatio-temporal alignment of raw data (NanoJ-Core), super-resolution image reconstruction (NanoJ-SRRF), image quality assessment (NanoJ-SQUIRREL), structural modelling (NanoJ-VirusMapper) and control of the sample environment (NanoJ-Fluidics). We expect to expand NanoJ in the future through the development of new tools designed to improve quantitative data analysis and measure the reliability of fluorescent microscopy studies.

Type: Article
Title: NanoJ: a high-performance open-source super-resolution microscopy toolbox
Open access status: An open access version is available from UCL Discovery
DOI: 10.1088/1361-6463/ab0261
Publisher version: https://doi.org/10.1088/1361-6463/ab0261
Language: English
Additional information: © 2019 IOP Publishing Ltd. Original content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence (https://creativecommons.org/licenses/by/3.0/).
Keywords: super-resolution microscopy, ImageJ, Fiji, image analysis, image quality assessment, fluidics, single-particle analysis
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Physics and Astronomy
URI: https://discovery.ucl.ac.uk/id/eprint/10069492
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