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

J Phys D Appl Phys. 2019 Apr 17;52(16):163001. doi: 10.1088/1361-6463/ab0261. Epub 2019 Feb 18.


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.

Keywords: Fiji; ImageJ; fluidics; image analysis; image quality assessment; single-particle analysis; super-resolution microscopy.

Publication types

  • Review