Project Summary The Center for Open Bioimage Analysis will serve the cell biology community’s growing need for sophisticated software for light microscopy image analysis. Quantitative image analysis has become an indispensable tool for biologists using microscopy throughout basic biological and biomedical research. Quantifying images is now a critical, widespread need as imaging experiments continue to grow in scale, size, dimensionality, scope, modality, and complexity. Many biologists are missing out on the quantitative bioimaging revolution due to lack of effective algorithms and/or usable software for their needs, or lack of access to training. The Center brings together the Carpenter laboratory at the Broad Institute and the Eliceiri laboratory at the University of Wisconsin­Madison, and in doing so brings together the two most popular open source bioimage analysis projects, ImageJ (including ImageJ2 and FIJI) and CellProfiler. Through the collaborative development and dissemination of open source image analysis software, as well as training events and resources, the Center will empower thousands of researchers to apply advanced analytics in innovative ways to address new experimental areas. Building on the team’s expertise developing algorithms and user­friendly software for use in biology under real­world conditions, the Center will focus on two Technology Research and Development (TR&D) projects: deep learning­based image processing, and accessibility of image­processing algorithms for biologists. This work will not occur in isolation at the Center; rather, the Center will nucleate a larger community working on these two areas and serve as a catalyst and organizing force to create software and resources shared by all. The Driving Biological Projects (DBPs) will serve a major role in driving the TR&D work: our teams are accustomed to working deeply and iteratively on problems side by side and with frequent feedback from biologists. This will ensure that important cell biological problems drive the work of the Center. The DBPs reflect tremendous variety in terms of biological questions, model systems, imaging modalities, and researcher expertise and will ensure robustness of our tools for the widest possible impact on the community. Continuing the teams’ track record with ImageJ and CellProfiler, two mature open source bioimage analysis software projects critical to the work of biologists worldwide, the Center will also assist and train biologists in applying the latest computational techniques to important biological problems involving images. In short, the need for robust, accurate, and readily usable software is more urgent than ever. The Center for Open Bioimage Analysis will serve as a hub for pioneering new computational strategies for diverse biological problems, translating them into user­friendly software, further developing ImageJ and CellProfiler, and training the biological community to apply advanced software to important and diverse problems in cell biology.

Project Narrative Biologists studying a huge variety of diseases and basic biological processes need software to measure cells, tissues, and organisms in microscopy images. We will create the Center for Open Bioimage Analysis which will catalyze the scientific community, creating resources, free software, and training that allow biologists to analyze images using deep learning and other new image processing algorithms, offering improved accuracy, convenience, and reproducibility.