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

authors

• Laine Romain F
• Tosheva Kalina L
• Gustafsson Nils
• Gray Robert D M
• Almada Pedro
• Albrecht David
• Risa Gabriel T
• Hurtig Fredrik
• Lindås Ann-Christin
• Baum Buzz
• Mercer Jason
• Leterrier Christophe
• Pereira Pedro M
• Culley Siân
• Henriques Ricardo

keywords

• Super-resolution microscopy
• ImageJ
• Fiji
• Image analysis
• Image quality assessment
• Fluidics
• Single-particle analysis

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.

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