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


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


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


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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