BIII — BioImage Informatics Index
Overview
BIII (BioImage Informatics Index, also known as BISE) is a community-curated knowledge database of software tools, benchmark image datasets, and training materials for biological image analysis. It was initiated at the 2013 European Biological Image Analysis Symposium and developed through a series of community taggathons organised by the NEUBIAS network. Funded successively by COST Action NEUBIAS (until May 2020) and COST Action COMULIS, it is now an ELIXIR service listed on the ELIXIR services catalogue. The registry holds over 1,300 software tools annotated using the EDAM-Bioimaging ontology, a controlled vocabulary for bioimaging analysis developed by the community specifically for BIII. Tools are classified as complete workflows, workflow components (bricks), or software platforms and libraries.
Scope and Annotation
Entries in BIII describe tools across the full range of biological imaging modalities and analysis tasks, including microscopy, cell segmentation, tracking, and image registration. Each tool is annotated with operations, topics, data types, and formats using EDAM-Bioimaging vocabulary, enabling structured search and comparison. Benchmark datasets and training materials are indexed alongside tools to support reproducible evaluation of analysis pipelines. All data is exposed via a JSON API.
Connections
- isPartOf: ELIXIR
- registeredIn: bio.tools (bio.tools/BISE)
- relatedTo: BioImage Archive (complementary bioimaging infrastructure — BIII indexes tools, BioImage Archive deposits image data)
- relatedTo: Euro-BioImaging (shared bioimaging community and ELIXIR imaging strategy)
Resources
- https://biii.eu
- https://biii.eu/about
- https://elixir-europe.org/services/bioimage-informatics-index-bise (ELIXIR service record)
- https://doi.org/10.48550/arXiv.2312.11256 (Zhang et al. 2023, BIII description paper)
- https://bio.tools/BISE (bio.tools entry)