The BIP software: high-level abstraction for reproducible biological image analysis

Abstract Motivation The bioimage informatics community is increasingly facing needs for the reproducible processing and analysis of large batches of multi-dimensional images through complex pipelines. We introduce BIP, a new open-source software for addressing these needs. The distinctive features of BIP is to be natively designed for batch and pipeline processing, relying on a unified, simple, and human-readable high-level syntax for processing single or multiple images and for specifying individual or combined operations. As a command-line tool, BIP also lends itself seamlessly to high-performance computing applications. BIP invests an original niche in the ecosystem of bioimage informatics software and should contribute to the development of reproducible research in bioimage processing and analysis. Availability BIP is distributed as an open source software under the GNU General Public License, version 3. The source code is available at https://forge.inrae.fr/andreylab/bip and can also be found at the Software Heritage permalink https://archive.softwareheritage.org/swh:1:dir:dded82e71041943bdfdf7b4684c69dd742c67312. Executables for Linux and Windows are available from the BIP website at https://andreylab.versailles.inrae.fr/html/bip.html. The distribution also includes a detailed user manual (PDF and HTML formats). To enable users to identify the right operators for their tasks, the principles and effects of the operators are briefly exposed, and many illustrations are provided. The manual also includes a tutorial section, illustrating how to solve typical, commonly encountered problems in bioimage analysis. The material for the tutorials is publicly available at https://doi.org/10.57745/JIWVCE. Supplementary information Supplementary data are available at Bioinformatics online.