CIRC: Planning C: Community Three-Dimensional Image Infrastructure for Sustainable Innovation in Biofilm Research

About This Grant

Microbial biofilms are composed of diverse microorganisms and are widespread in natural, human, and engineered environments. Biofilm-related problems exist across major economic and societal sectors, costing billions of dollars each year in energy losses, equipment damage, product contamination, agricultural losses, and medical infections. For over 30 years, scientists have sought to understand biofilms with much of the focus being on single species bacterial biofilms. While much has been learned from single organism studies, biofilms exist as multi-species, multi-domain consortia. Understanding biofilms is crucial, particularly in how their heterogeneous structures and community organization affect their resilience, nutrient access, and susceptibility to antimicrobial therapies. Digital imaging is essential for biological studies and is a backbone of biofilm analyses because of the non-invasive nature and compatibility with live samples. More specifically, imaging has become an essential instrument in biofilm research because of the ability to provide 3D information of hydrated biofilms in real-time. However, a major barrier in biofilm research has been the absence of robust image analysis methods that are easily accessible, centralized, computationally efficient, sensitive, and reproducible. This has hindered the meaningful and statistically robust integration of image analysis into biofilm studies. The Biofilm Imaging Library (BIL) planning project will lay the groundwork for an open-access, community-driven repository of standardized, high-quality biofilm images and the development of open-source easy-to-use computationally efficient tools aided by machine learning. This award will focus on planning the development of the BIL, ensuring that it meets the needs of the research community by establishing key collaborations, identifying data collection strategies, and designing the foundational platform architecture. Indicative of the interest, nine research groups have already begun contributing images following discussions at the 2024 GRC on Streptococcal Biology. Outreach to the biofilm and computer science/engineering communities is planned at the American Society of Microbiology Biofilms Meeting, the IEEE Signal Processing in Medicine and Biology Symposium and the Center for Biofilm Engineering’s Montana Biofilm Meeting. The BIL framework will be established for building a collection of images and metadata, open-source tools, and associated computational models. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.