The Center for Open Bioimage Analysis

University Of Wisconsin-Madison, Madison WI

Investigators

Abstract

Project Summary The R24 funded 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 Cimini laboratory at the Broad Institute and the Eliceiri laboratory at the University of Wisconsin-Madison, and in doing so unifies 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 user-friendly software for use in biology under real-world conditions, the Center will focus on three specific aims: 1) Maintain state-of-the-art access to evolving image analysis methods in established user-friendly tools such as ImageJ, Fiji, CellProfiler, and Piximi 2) Improve access to and accessibility within open-source image analysis tools, embracing additional deployment approaches and 3) Improve interoperability of open-source image analysis tools and methods, including cross-language interoperability across Java, Python, and JavaScript This work will not occur in isolation; rather, the Center will nucleate a larger community working on these three areas and serve as a catalyst and organizing force to create software and resources shared by all. Our teams are accustomed to working deeply and iteratively on problems side by side and with frequent feedback from biologists. 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 user-friendly software, further developing ImageJ and CellProfiler, and training the biological community to apply advanced software to important and diverse problems in biology.