This is an open source flexible visualisation, processing and analysis tool developed by NIH. It is available as standard ImageJ or Fiji, which includes plugins. Functionality can be extended further using plugins or macros.


  • Widely-used and free.
  • Functions include image filtering, denoising, binarisation for segmentation, cropping/scaling and intensity measurements.
  • FIJI contains functionality for particle tracking, colocalisation analysis and advanced image segmentation.
  • Facility for automation of processes using macro recording functionality.


  • Batch processing and automation possible using macros. 
  • Extendable through large online library of peer-reviewed and published plugins.


  • Open source and free to download.
  • Can be installed without elevated user rights.
  • Available on all the workstations in the imaging department.

Additional information