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Journal Articles Journal of Physics D: Applied Physics Year : 2019

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

Romain F Laine
  • Function : Author
Kalina L Tosheva
  • Function : Author
Nils Gustafsson
  • Function : Author
Robert D M Gray
  • Function : Author
Pedro Almada
  • Function : Author
David Albrecht
  • Function : Author
  • PersonId : 782089
  • IdRef : 181539047
Gabriel T Risa
  • Function : Author
Fredrik Hurtig
  • Function : Author
Ann-Christin Lindås
  • Function : Author
Buzz Baum
  • Function : Author
Jason Mercer
  • Function : Author
Pedro M Pereira
  • Function : Author
  • PersonId : 1044320
Siân Culley
  • Function : Author
  • PersonId : 1044321
Ricardo Henriques
  • Function : Author
  • PersonId : 1044322


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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hal-02073339 , version 1 (19-03-2019)



Romain F Laine, Kalina L Tosheva, Nils Gustafsson, Robert D M Gray, Pedro Almada, et al.. NanoJ: a high-performance open-source super-resolution microscopy toolbox. Journal of Physics D: Applied Physics, 2019, 52 (16), pp.163001. ⟨10.1088/1361-6463/ab0261⟩. ⟨hal-02073339⟩
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