Beth A Cimini

Principal Researcher, Broad Institute

Joined

July 2021

Names

Beth A Cimini (Preferred)

Beth Cimini

Beth A. Cimini

Emails

****@broadinstitute.org (Confirmed)

Personal Links

Career & Education History

Principal Researcher

Broad Institute (broadinstitute.org)

2021 – Present

Researcher

Broad Institute (broadinstitute.org)

2016 – 2021

PhD student

University of California, San Francisco (ucsf.edu)

2007 – 2016

Undergrad student

Boston University (bu.edu)

2003 – 2007

Advisors, Relations & Conflicts

Coworker

Anne Carpenter

2016 – Present

PhD Advisor

Elizabeth Blackburn

2007 – 2016

Expertise

Image analysis

Present

Publications

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 Dinov, Brian Athey, nicolas clement rivron, Anne E Carpenter, Beth A Cimini, Shantanu Singh, Matthew J. O'Meara
- GenBio 2025 Poster
- Readers: Everyone
Tyche: Stochastic In-Context Learning Model for Medical Image Segmentation
Marianne Rakic, Hallee E. Wong, Jose Javier Gonzalez Ortiz, Beth A Cimini, John Guttag, Adrian V Dalca
- CVPR 2024
- Readers: Everyone
MorphoDiff: Cellular Morphology Painting with Diffusion Models
Zeinab Navidi, Jun Ma, Esteban Miglietta, Le Liu, Anne E Carpenter, Beth A Cimini, Benjamin Haibe-Kains, BO WANG
- ICLR 2025 Spotlight
- Readers: Everyone
Moving beyond the desktop: prospects for practical bioimage analysis via the web
Wei Ouyang, Kevin W. Eliceiri, Beth A. Cimini
- Published: 01 Jan 2023, Last Modified: 08 Nov 2023
- Frontiers Bioinform. 2023
- Readers: Everyone
Understanding metric-related pitfalls in image analysis validation
Annika Reinke, Minu Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A. Emre Kavur, Tim Rädsch, Carole H. Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B. Blaschko, Florian Büttner, M. Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A. Cimini et al. (58 additional authors not shown)
- 2023 (modified: 02 Mar 2023)
- CoRR 2023
- Readers: Everyone
The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions
Jun Ma, Ronald Xie, Shamini Ayyadhury, Cheng Ge, Anubha Gupta, Ritu Gupta, Song Gu, Yao Zhang, Gihun Lee, Joonkee Kim, Wei Lou, Haofeng Li, Eric Upschulte, Timo Dickscheid, José Guilherme de Almeida, Yixin Wang, Lin Han, Xin Yang, Marco Labagnara, Sahand Jamal Rahi et al. (19 additional authors not shown)
- Published: 01 Jan 2023, Last Modified: 02 Oct 2023
- CoRR 2023
- Readers: Everyone
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
- Published: 01 Jan 2023, Last Modified: 08 Nov 2023
- IJCAI 2023
- Readers: Everyone
Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl
Juan C Caicedo, Allen Goodman, Kyle W Karhohs, Beth A Cimini, Jeanelle Ackerman, Marzieh Haghighi, CherKeng Heng, Tim Becker, Minh Doan, Claire McQuin, Mohammad Hossein Rohban, Shantanu Singh, Anne E Carpenter
- 10 Jun 2022
- OpenReview Archive Direct Upload
- Readers: Everyone
Open-source deep-learning software for bioimage segmentation
Alice M Lucas, Pearl V Ryder, Bin Li, Beth A Cimini, Kevin Eliceiri, Anne E Carpenter
- 10 Jun 2022
- OpenReview Archive Direct Upload
- Readers: Everyone
ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis
Ellen TA Dobson, Beth A Cimini, Anna H Klemm, Carolina Wahlby, Anne E Carpenter, Kevin Eliceiri
- 10 Jun 2022
- OpenReview Archive Direct Upload
- Readers: Everyone

View all 16 publications

Co-Authors

View all 188 co-authors