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.
@article{arxiv.2312.11256,
title = {Bio-Image Informatics Index BIII: A unique database of image analysis tools and workflows for and by the bioimaging community},
author = {Chong Zhang and Alban Gaignard and Matus Kalas and Florian Levet and Felipe Delestro and Joakim Lindblad and Natasa Sladoje and Laure Plantard and Alain Latour and Robert Haase and Gabriel Martins and Paula Sampaio and Leandro Scholz and NEUBIAS taggers and Sébastien Tosi and Kota Miura and Julien Colombelli and Perrine Paul-Gilloteaux},
journal= {arXiv preprint arXiv:2312.11256},
year = {2023}
}
Comments
5 pages of main article including one figure and references, followed by the lis of taggers, the description of the ontologies in uses and some example of usage