Bio-Image Informatics Index BIII: A unique database of image analysis tools and workflows for and by the bioimaging community

TL;DR

Bio-Image Informatics Index (BIII) is a comprehensive, community-curated web database that consolidates bioimage analysis tools, workflows, and resources to aid biologists and developers in the field.

Contribution

This work introduces BIII, the first large-scale, crowdsourced database integrating bioimage analysis software, workflows, and resources following community standards and FAIR principles.

Findings

References over 1300 software tools and 20 image databases

Includes more than 70 training materials for bioimage analysis

Organizes tools as workflows, components, or platforms

Abstract

Bio image analysis has recently become one keystone of biological research but biologists tend to get lost in a plethora of available software and the way to adjust available tools to their own image analysis problem. We present BIII, BioImage Informatic Index (www.biii.eu), the result of the first large community effort to bridge the communities of algorithm and software developers, bioimage analysts and biologists, under the form of a web-based knowledge database crowdsourced by these communities. Software tools (> 1300), image databases for benchmarking (>20) and training materials (>70) for bio image analysis are referenced and curated following standards constructed by the community and then reaching a broader audience. Software tools are organized as full protocol of analysis (workflow), specific brick (component) to construct a workflow, or software platform or library (collection). They are described using Edam Bio Imaging, which is iteratively defined using this website. All entries are exposed following FAIR principles and accessible for other usage.