{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T17:59:22Z","timestamp":1790359162097,"version":"4.1.0"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"vor","delay-in-days":24,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Tefor Infrastructure under the Investments for the Future program of the French National Research Agency","award":["ANR-11-INBS-0014"],"award-info":[{"award-number":["ANR-11-INBS-0014"]}],"id":[{"id":"https:\/\/ror.org\/00rbzpz17","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag665","type":"journal-article","created":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T09:48:56Z","timestamp":1790243336000},"source":"Crossref","is-referenced-by-count":0,"title":["The\n                    <i>BIP<\/i>\n                    software: high-level abstraction for reproducible biological image analysis"],"prefix":"10.1093","volume":"42","author":[{"given":"Eric","family":"Biot","sequence":"first","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin for Plant Sciences , 78000, Versailles,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandrine","family":"Lefranc","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin for Plant Sciences , 78000, Versailles,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayoub","family":"Ouddah","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin for Plant Sciences , 78000, Versailles,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erwan","family":"Guerrier","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin for Plant Sciences , 78000, Versailles,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9007-8722","authenticated-orcid":false,"given":"Jasmine","family":"Burguet","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin for Plant Sciences , 78000, Versailles,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5932-6863","authenticated-orcid":false,"given":"Philippe","family":"Andrey","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin for Plant Sciences , 78000, Versailles,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,24]]},"reference":[{"key":"2026092513141563900_btag665-B1","doi-asserted-by":"publisher","first-page":"jcs254151","DOI":"10.1242\/jcs.254151","article-title":"A guide to accurate reporting in digital image processing\u2014can anyone reproduce your quantitative analysis?","volume":"134","author":"Aaron","year":"2021","journal-title":"J Cell Sci"},{"key":"2026092513141563900_btag665-B2","doi-asserted-by":"publisher","first-page":"W83","DOI":"10.1093\/nar\/gkae410","article-title":"The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update","volume":"52","author":"Abueg","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026092513141563900_btag665-B3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v094.c01","article-title":"Using GNU make to manage the workflow of data analysis projects","volume":"94","author":"Baker","year":"2020","journal-title":"J Stat Soft"},{"key":"2026092513141563900_btag665-B4","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1111\/tpj.13189","article-title":"Strategy and software for the statistical spatial analysis of 3D intracellular distributions","volume":"87","author":"Biot","year":"2016","journal-title":"Plant J"},{"key":"2026092513141563900_btag665-B5","doi-asserted-by":"publisher","first-page":"871228","DOI":"10.3389\/fnins.2022.871228","article-title":"Microscopy-BIDS: an extension to the brain imaging data structure for microscopy data","volume":"16","author":"Bourget","year":"2022","journal-title":"Front Neurosci"},{"key":"2026092513141563900_btag665-B6","doi-asserted-by":"publisher","first-page":"e1008645","DOI":"10.1371\/journal.pcbi.1008645","article-title":"Ten simple rules for getting started with command-line bioinformatics","volume":"17","author":"Brandies","year":"2021","journal-title":"PLoS Comput Biol"},{"key":"2026092513141563900_btag665-B8","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1111\/jmi.13227","article-title":"ModularImageAnalysis (MIA): assembly of modularised image and object analysis workflows in ImageJ","volume":"296","author":"Cross","year":"2024","journal-title":"J Microsc"},{"key":"2026092513141563900_btag665-B9","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1038\/nmeth.2075","article-title":"Icy: an open bioimage informatics platform for extended reproducible research","volume":"9","author":"de Chaumont","year":"2012","journal-title":"Nat Methods"},{"key":"2026092513141563900_btag665-B10","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di Tommaso","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2026092513141563900_btag665-B11","first-page":"179","volume-title":"Focus on Bio-Image Informatics, Volume 219 of Advances in Anatomy, Embryology, and Cell Biology","author":"Dietz","year":"2016"},{"key":"2026092513141563900_btag665-B12","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1038\/s41592-022-01744-4","article-title":"JIPipe: visual batch processing for ImageJ","volume":"20","author":"Gerst","year":"2023","journal-title":"Nat Methods"},{"key":"2026092513141563900_btag665-B13","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.12688\/f1000research.26977.2","article-title":"TAPAS: towards automated processing and analysis of multi-dimensional bioimage data","volume":"9","author":"Gilles","year":"2020","journal-title":"F1000Res"},{"key":"2026092513141563900_btag665-B14","doi-asserted-by":"publisher","first-page":"160044","DOI":"10.1038\/sdata.2016.44","article-title":"The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments","volume":"3","author":"Gorgolewski","year":"2016","journal-title":"Sci Data"},{"key":"2026092513141563900_btag665-B15","doi-asserted-by":"publisher","first-page":"2472","DOI":"10.1002\/1873-3468.14451","article-title":"A Hitchhiker\u2019s guide through the bio-image analysis software universe","volume":"596","author":"Haase","year":"2022","journal-title":"FEBS Lett"},{"key":"2026092513141563900_btag665-B16","author":"ImageMagick Studio LLC","year":"2024"},{"key":"2026092513141563900_btag665-B18","doi-asserted-by":"publisher","first-page":"2520","DOI":"10.1093\/bioinformatics\/bts480","article-title":"Snakemake\u2014a scalable bioinformatics workflow engine","volume":"28","author":"K\u00f6ster","year":"2012","journal-title":"Bioinformatics"},{"key":"2026092513141563900_btag665-B20","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1083\/jcb.201004104","article-title":"Metadata matters: access to image data in the real world","volume":"189","author":"Linkert","year":"2010","journal-title":"J Cell Biol"},{"key":"2026092513141563900_btag665-B22","doi-asserted-by":"publisher","first-page":"e2005970","DOI":"10.1371\/journal.pbio.2005970","article-title":"CellProfiler 3.0: next-generation image processing for biology","volume":"16","author":"McQuin","year":"2018","journal-title":"PLoS Biol"},{"key":"2026092513141563900_btag665-B23","doi-asserted-by":"publisher","first-page":"e105889","DOI":"10.15252\/embj.2020105889","article-title":"Reproducible image handling and analysis","volume":"40","author":"Miura","year":"2021","journal-title":"EMBO J"},{"key":"2026092513141563900_btag665-B24","doi-asserted-by":"publisher","DOI":"10.1101\/2025.04.28.651001","article-title":"Cellpose-SAM: superhuman generalization for cellular segmentation","author":"Pachitariu","year":"2025"},{"key":"2026092513141563900_btag665-B25","doi-asserted-by":"publisher","first-page":"320","DOI":"10.12688\/f1000research.52569.1","article-title":"Bioimage analysis workflows: community resources to navigate through a complex ecosystem","volume":"10","author":"Paul-Gilloteaux","year":"2021","journal-title":"F1000Res"},{"key":"2026092513141563900_btag665-B26","doi-asserted-by":"publisher","first-page":"3009","DOI":"10.1093\/bioinformatics\/bts543","article-title":"ImgLib2\u2013generic image processing in Java","volume":"28","author":"Pietzsch","year":"2012","journal-title":"Bioinformatics"},{"key":"2026092513141563900_btag665-B27","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat Methods"},{"key":"2026092513141563900_btag665-B28","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1038\/nmeth.2089","article-title":"NIH Image to ImageJ: 25 years of image analysis","volume":"9","author":"Schneider","year":"2012","journal-title":"Nat Methods"},{"key":"2026092513141563900_btag665-B29","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1186\/s12859-021-04344-9","article-title":"CellProfiler 4: improvements in speed, utility and usability","volume":"22","author":"Stirling","year":"2021","journal-title":"BMC Bioinformatics"},{"key":"2026092513141563900_btag665-B30","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1038\/s41592-020-01018-x","article-title":"Cellpose: a generalist algorithm for cellular segmentation","volume":"18","author":"Stringer","year":"2021","journal-title":"Nat Methods"},{"key":"2026092513141563900_btag665-B31","first-page":"42","article-title":"GNU parallel\u2014the command-line power tool","volume":"36","author":"Tange","year":"2011","journal-title":"login USENIX Mag"},{"key":"2026092513141563900_btag665-B32","doi-asserted-by":"publisher","first-page":"6618","DOI":"10.21105\/joss.06618","article-title":"G\u2019MIC: an open-source self-extending framework for image processing","volume":"10","author":"Tschumperl\u00e9","year":"2025","journal-title":"JOSS"},{"key":"2026092513141563900_btag665-B34","doi-asserted-by":"publisher","first-page":"e57613","DOI":"10.7554\/eLife.57613","article-title":"Accurate and versatile 3D segmentation of plant tissues at cellular resolution","volume":"9","author":"Wolny","year":"2020","journal-title":"eLife"},{"key":"2026092513141563900_btag665-B35","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1007\/10968987_3","volume-title":"Job Scheduling Strategies for Parallel Processing","author":"Yoo","year":"2003"},{"key":"2026092513141563900_btag665-B36","first-page":"586","article-title":"Engineering and algorithm design for an image processing API: a technical report on ITK\u2013the Insight Toolkit","volume":"85","author":"Yoo","year":"2002","journal-title":"Stud Health Technol Inform"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag665\/71379138\/btag665.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/9\/btag665\/71379138\/btag665.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/9\/btag665\/71379138\/btag665.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T17:14:25Z","timestamp":1790356465000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag665\/8833504"}},"subtitle":[],"editor":[{"given":"Virginie","family":"Uhlmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,31]]},"references-count":31,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,8,31]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag665","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,8,31]]},"article-number":"btag665"}}