Reproducible image-based profiling with Pycytominer

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Authors: Erik Serrano, CHANDRASEKARAN N.R, Dave Bunten, Kenneth I. Brewer, Jenna Tomkinson, Roshan Kern, Michael Bornholdt, Stephen B. Fleming, Ruifan Pei, John Arévalo, Hillary Tsang, Vincent Rubinetti
+16 more Callum Tromans‐Coia, Tim Becker, Erin Weisbart, Charlotte Bunne, Alexandr A. Kalinin, Rebecca A. Senft, Stephen J. Taylor, Nasim Jamali, Adeniyi Adeboye, Hamdah Shafqat Abbasi, Allen Goodman, Juan C. Caicedo, Anne E. Carpenter, Beth A. Cimini, Shantanu Singh, Gregory P. Way
Cited by: 0

Abstract

What's Changed build(deps): bump pandas from 2.3.2 to 2.3.3 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/586 build(deps-dev): bump pytest-cov from 6.2.1 to 7.0.0 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/585 build(deps-dev): bump types-openpyxl from 3.1.5.20250822 to 3.1.5.20250919 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/584 build(deps): bump the python-packages group with 7 updates by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/583 build(deps): bump peter-evans/dockerhub-description from 4 to 5 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/587 build: End Python 3.9 support by @d33bs in https://github.com/cytomining/pycytominer/pull/588 build(deps): bump urllib3 from 1.26.19 to 2.5.0 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/590 build(deps): bump actions/upload-artifact from 4 to 5 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/592 build(deps): bump actions/download-artifact from 5 to 6 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/591 build(deps-dev): bump starlette from 0.47.2 to 0.49.1 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/593 build(deps): bump the python-packages group with 5 updates by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/594 build(deps-dev): bump ipython from 8.18.1 to 8.37.0 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/595 build(deps-dev): bump sphinx from 7.4.7 to 8.1.3 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/596 build(deps): bump pyarrow from 21.0.0 to 22.0.0 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/597 build(deps): bump sqlalchemy from 2.0.43 to 2.0.44 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/598 build(deps): bump actions/checkout from 5 to 6 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/599 build(deps-dev): bump pytest from 8.4.2 to 9.0.1 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/603 build(deps): bump the python-packages group with 6 updates by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/602 ci: add codeowners file for reviewer assignments by @d33bs in https://github.com/cytomining/pycytominer/pull/601 build(deps): bump urllib3 from 2.5.0 to 2.6.0 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/604 build(deps): bump actions/cache from 4 to 5 in /.github/actions/setup-env by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/607 build(deps): bump actions/upload-artifact from 5 to 6 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/605 build(deps): bump actions/download-artifact from 6 to 7 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/606 build(deps-dev): bump filelock from 3.13.3 to 3.20.1 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/608 build(deps-dev): bump the python-packages group with 6 updates by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/610 build(deps): bump sqlalchemy from 2.0.44 to 2.0.45 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/611 refactor: enable Python 3.14 compatibility by @d33bs in https://github.com/cytomining/pycytominer/pull/609 build(deps): bump aiohttp from 3.12.14 to 3.13.3 by @dependabot[bot] in https://github.com/cytomining/pycytominer/pull/612 bump: version 1.3.0 -> 1.3.1 by @d33bs in https://github.com/cytomining/pycytominer/pull/613 Full Changelog: https://github.com/cytomining/pycytominer/compare/v1.3.0...v1.3.1

Publication details

Journal / source
Zenodo (CERN European Organization for Nuclear Research)
Publication date
6 January 2026