CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis. - David R. Stirling; Anne E. Carpenter; Beth A. Cimini (Bioinform., 2021)

CellProfiler 4: improvements in speed, utility and usability. - David R. Stirling; Madison J. Swain-Bowden; Alice M. Lucas; Anne E. Carpenter; Beth A. Cimini; Allen Goodman (BMC Bioinform., 2021)

Metrics reloaded: Pitfalls and recommendations for image analysis validation. - Lena Maier-Hein; Annika Reinke; Evangelia Christodoulou; Ben Glocker; Patrick Godau; Fabian Isensee; Jens Kleesiek; Michal Kozubek 001; Mauricio Reyes 001; Michael A. Riegler; Manuel Wiesenfarth; Michael Baumgartner 001; et al. (CoRR, 2022)

Distributed-Something: scripts to leverage AWS storage and computing for distributed workflows at scale. - Erin Weisbart; Beth A. Cimini (CoRR, 2022)

Pseudo-Labeling Enhanced by Privileged Information and Its Application to In Situ Sequencing Images. - Marzieh Haghighi; Mario C. Cruz; Erin Weisbart; Beth A. Cimini; Avtar Singh; Julia Bauman; Maria E. Lozada; Sanam L. Kavari; James T. Neal; Paul C. Blainey; Anne E. Carpenter; Shantanu Singh (IJCAI, 2023)

Understanding metric-related pitfalls in image analysis validation. - Annika Reinke; Minu Tizabi; Michael Baumgartner 001; Matthias Eisenmann; Doreen Heckmann-Nötzel; A. Emre Kavur; Tim Rädsch; Carole H. Sudre; Laura Ación; Michela Antonelli; Tal Arbel; Spyridon Bakas; et al. (CoRR, 2023)

The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions. - Jun Ma 016; Ronald Xie; Shamini Ayyadhury; Cheng Ge; Anubha Gupta; Ritu Gupta; Song Gu; Yao Zhang 010; Gihun Lee; Joonkee Kim; Wei Lou; Haofeng Li; et al. (CoRR, 2023)

Defining the boundaries: challenges and advances in identifying cells in microscopy images. - Nodar Gogoberidze; Beth A. Cimini (CoRR, 2023)

Moving beyond the desktop: prospects for practical bioimage analysis via the web. - Wei Ouyang; Kevin W. Eliceiri; Beth A. Cimini (Frontiers Bioinform., 2023)

Tyche: Stochastic in-Context Learning for Medical Image Segmentation. - Marianne Rakic; Hallee E. Wong; Jose Javier Gonzalez Ortiz; Beth A. Cimini; John V. Guttag; Adrian V. Dalca (CVPR, 2024)

MorphoDiff: Cellular Morphology Painting with Diffusion Models. - Zeinab Navidi; Jun Ma 016; Esteban Miglietta; Le Liu; Anne E. Carpenter; Beth A. Cimini; Benjamin Haibe-Kains; Bo Wang 044 (ICLR, 2025)

Foreground-aware Virtual Staining for Accurate 3D Cell Morphological Profiling. - Alexandr A. Kalinin; Paula Llanos; Theresa Maria Sommer; Giovanni Sestini; Xinhai Hou; Jonathan Z. Sexton; Xiang Wan; Ivo D. Dinov; Brian D. Athey; Nicolas Rivron; Anne E. Carpenter; Beth A. Cimini; et al. (CoRR, 2025)