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.

Features

• 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.

Advantages

• 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

Citing

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

Availability

• 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

• ImageJ/Fiji Level 1: Basics of image processing and analysis
• ImageJ/Fiji Level 2: Automation and batch processing using macros
• Download ImageJ 
• Download Fiji 
• List of plugins
• Wikipedia ImageJ
• Wikipedia Fiji