SciJava Ops: An Improved Algorithms Framework for Fiji and Beyond

• DOI: 10.48550/arxiv.2405.12385
• Publication Date: 2024-05-20
• Authors: Gabriel J. Selzer; Curtis Rueden; Mark Hiner; Edward L. Evans; David Kolb; Marcel Wiedenmann; Christian Birkhold; Tim-Oliver Buchholz; Stefan Helfrich; B. Northan; Alison Walter; Johannes Schindelin; Tobias Pietzsch; Stephan Saalfeld; Michael R. Berthold; Kevin W. Eliceiri
• Keywords: Software Engineering (cs.SE); FOS: Computer and information sciences; Computer Science - Software Engineering; analysis workflows; image analysis; Bioinformatics; Computer applications to medicine. Medical informatics; R858-859.7; scientific imaging; Fiji; algorithms; imaging software

Many scientific software platforms provide plugin mechanisms that simplify the integration, deployment, and execution of externally developed functionality. One most widely used in imaging space is Fiji, a popular open-source application for image analysis. Fiji incorporates builds on ImageJ ImageJ2 platforms, which powerful architecture by thousands plugins to solve wide variety problems. This capability major part Fiji's success, it has become biological analysis tool target new However, plugin-based cannot unify disparate operating incompatible data structures; interoperability necessitates creation adaptation or "bridge" layers translate invoke As result, while like enable high degree interconnectivity extensibility, they were not fundamentally designed integrate across many types, programming languages, architectural differences various platforms.To help address this challenge, we present SciJava Ops, foundational library expressing algorithms as unified extensible way. Continuing evolution mechanism, Ops enables users harness from within central environment. In addition, automatically adapts into appropriate structure each algorithm, allowing freely transparently combine otherwise tools. While initially distributed update site, framework does require ImageJ, ImageJ2, would be suitable integration with additional platforms.