#Imagej vs fiji download#

Developers maintain so-called “update sites”, where folders of plugins are deposited and offered to the public via the Internet. The developers of the Fiji platform accepted this challenge and developed a technical solution: The Fiji Updater. For sophisticated image analysis workflows this caused substantial workload on the user side because of an overwhelmingly large ecosystem of plugins and scripts in different versions modified by different people. However, as the number of publicly available plugins grew, this way of distributing plugins soon faced challenges: To make their workflows reproducible, scientists had to specify which ImageJ plugins in which version were used and how they were installed. At the same time, the ImageJ website exposed general-purpose plugins to a broader audience and a revolution started: more and more plugins were programmed inspired by the tight interaction between users and developers. The way these plugins were distributed until about 8 years ago was like follows: A developer packs her algorithms into a so called “.jar file” and ships it to collaborators asking them to “Please put it in the plugins folder of your ImageJ.”. Furthermore, these plugins could be used in workflows conveniently by scientists who did not necessarily have programming skills.

Algorithm developers distributed their algorithms as ImageJ plugins compatible to plugins from other developers. ImageJ was one of the first image data science platforms that promoted forming a community of developers and users. How Plugins Changed the World of Image Data Science In this article, I give some insights in how it works, why it is crucial in the rapidly growing image data science field, what new challenges it brings, and who ensures that the machinery keeps running behind the scenes.

I see it as my favorite image analysis tool because thinking back to all the projects I worked on in the past years, the Fiji Updater was part of the majority.

#Imagej vs fiji download#

It also represents a stronghold against the reproducibility crisis: As the updater allows us to just download plugins and tools from other scientists, we can easily reproduce their research. It is a major engine behind a highly diverse and dynamic community of scientists interested in solving questions in biology with quantitative bio-image analysis and computer science. For understanding why, an important role resides in a core component of Fiji: The Fiji Updater. When image analysts in life sciences, including myself, make statements like “Fiji is just ImageJ”, we are smiling, because we lie a bit.