The Center for Open Bioimage Analysis (COBA) was supported by an NIH P41 grant through November 2025, advancing open, accessible bioimage analysis tools and training for the global research community. Through software development, education, and direct user support, COBA empowered scientists worldwide to analyze complex imaging data and build reproducible workflows.
Building on the success of this first phase, the center is now continuing its mission under a newly funded program: Center for Open Bioimage Analysis (R24GM158834). This next phase expands efforts to support open-source bioimage analysis tools, training, and collaboration across the international imaging community.
Key Accomplishments
55+ Publications
Projects supported by COBA contributed to more than 55 peer-reviewed publications, advancing methods and tools for open bioimage analysis.
56 Trainings, Workshops, and Tutorials
COBA delivered hands-on workshops, conference tutorials, and virtual training programs, reaching 2,000+ researchers and learners worldwide.
110+ Hours of Office Hours Support
Bi-weekly consultations provided individualized troubleshooting and guidance for analysis pipelines using tools such as CellProfiler, Distributed CellProfiler, and Piximi.
292,000+ Educational Video Views
COBA’s training videos reached a global audience across multiple platforms:
Center for Open Bioimage Analysis YouTube Channel: 216,922+ views
I2K Workshops: 27,024+ views
Ask Erin / Dear Beth: 1,000+ views
These resources continue to expand access to expert-led bioimage analysis training for researchers worldwide.
The mission now continues under the Center for Open Bioimage Analysis (R24GM158834).
Team
The Center for Open Bioimage Analysis brings together the Cimini and Carpenter laboratories at the Broad Institute and the Eliceiri laboratory at the University of Wisconsin-Madison, and in doing so brings together the two most popular open-source bioimage analysis projects, ImageJ (including ImageJ2 and FIJI) and CellProfiler.
Organizational Structure
TR&D1 (Deep Learning)
Component leads:
Beth Cimini, PI (Broad Institute)
Anne Carpenter, PI (Broad Institute)
Kevin Eliceiri, PI (U Wisc-Madison)
Andréa Papaleo
Additional team:
Nodar Gogoberidze*
Ed Evans
Curtis Rueden*
* Funded by CZI
TR&D2 (Algorithm Accessibility)
Component leads:
Beth Cimini, PI (Broad Institute)
Anne Carpenter, PI (Broad Institute)
Kevin Eliceiri, PI (U Wisc-Madison)
Mark Hiner
Additional team:
Ed Evans
Curtis Rueden*
Gabe Selzer
Nodar Gogoberidze*
Driving Biological Projects (DBPs)
Component leads:
Beth Cimini, PI (Broad Institute)
Anne Carpenter, PI (Broad Institute)
Kevin Eliceiri, PI (U Wisc-Madison)
Additional team:
Ed Evans
Shatavisha Dasgupta
Each DBP will be assigned a DBP lead from among this team
Community Engagement
Component leads:
Beth Cimini, PI, (Broad Institute)
Anne Carpenter, PI (Broad Institute)
Kevin Eliceiri, PI (U Wisc-Madison)
Additional team:
Ed Evans
Shatavisha Dasgupta
Esteban Miglietta
Erin Weisbart
External Advisory Committee
The External Advisory Committiee (EAC) for the Center for Open Bioimage Analysis gives input into trends and directions for the center to pursue in our technology development, driving biological projects, and community engagement.
EAC Members:
Anna Kreshuk (EMBL Heidelberg)
Maddy Parsons (King's College London)
Emma Lundberg (KTH Royal Institute of Technology, Sweden)
Kota Miura (Max Planck BioImaging and NEUBIAS)
Badri Roysam (University of Houston)
Ross Whitaker (University of Utah)
Mary Ann Wu (NIH Program Officer)
Anne Gershenson (NIH Program Officer)