Image J / Fiji

ImageJ/Fiji is a highly flexible freeware image processing and analysis tool from NIH.

Available as standard ImageJ or the advanced Fiji version, which includes additional commonly used plugins. Functionality of either package can be extended further using a vast online library of peer-reviewed plugins.


  • Widely-used tool for image processing, featured in numerous peer-reviewed publications.
  • The standard ImageJ release mostly focuses on image processing. Functions include image filtering, denoising, binarisation for segmentation, cropping/scaling and intensity measurements.
  • An extended version, Fiji (also available for free) comes with a wider-range of pre-installed plugins. These include functionality for particle tracking, colocalisation analysis and advanced image segmentation.
  • Compatible with many proprietary imaging formats such as Leica .lif and Zeiss .czi (requires BioFormats reader – included as standard in Fiji).
  • Facility for automation of processes using macro recording functionality.


  • Batch processing and automation possible using macros. Preparation of which is simplified through inclusion of a macro recorder, which keeps tracks of all operations performed.
  • Extendable through large online library of peer-reviewed and published plugins.
  • Additional functionality can be included through development of custom Java plugins.
  • Contact us for more information


  • Guidelines for citing ImageJ and Fiji can be found here.


  • Open source and free to download.
  • Can be installed without elevated user rights.
  • Available on image processing computer in room C27/U (data analysis suite). Access to this computer can be booked on PPMS.
  • Free half-day workshops are held regularly to help researchers get started with ImageJ/Fiji, explore ImageJ/Fiji macro writing.

Additional information

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