Architecture

Software construction

Software evolution

Open source software

Open source

Scripting language

Biology

Gene

Operating system

Image (mathematics)

Software engineering

Software system

Visual arts

Artificial intelligence

Transformation (genetics)

Data science

Software

Computer science

Plug-in

Biochemistry

Image processing

Nature Methods

Presented is an overview of the image-analysis software platform Fiji, a distribution of ImageJ that updates the underlying ImageJ architecture and adds modern software design elements to expand the capabilities of the platform and facilitate collaboration between biologists and computer scientists. Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

Fiji: an open-source platform for biological-image analysis