CZI announces funding for open-source software efforts to improve image analysis in biomedicine

Reviewed by James Ives, M.Psych. (Editor)Dec 7 2018

Today, the Chan Zuckerberg Initiative (CZI) announced funding for open-source software efforts to improve image analysis and visualization in biomedicine. Microscopy -- critical to modern cell biology -- generates large volumes of complex data that pose significant challenges for analysis and visualization. The funding will support developers ("Imaging Software Fellows") from three projects to develop and maintain software tools, and begin collaborating to help create a cohesive, shared ecosystem of resources that can accelerate basic research and benefit the entire field.

"Better imaging software will make it faster and easier for biologists to extract quantitative information from imaging data, and share their methods and results with others," said CZI Head of Science, Cori Bargmann. "These grants highlight the impressive but underappreciated work of academic software developers in this area. We're excited to work with our grantees to accelerate a fundamental field in biomedicine."

The CZI Imaging Software Fellows work on three critical and widely-used tools: scikit-image, FIJI / ImageJ, and CellProfiler. After several workshops, hackathons, and discussions with the imaging community, these three projects were identified as playing a critical role in the imaging ecosystem, and their developers demonstrated an interest in improving the interoperability and capabilities of their tools.

The grants will be administered by the Chan Zuckerberg Initiative DAF, a donor-advised fund of Silicon Valley Community Foundation. The Imaging Software Fellows will collaborate within their projects and with others through frequent communication, open software development, and regular hackathons and meetings, with all code released under maximally permissive open-source licenses.

CZI believes that leveraging technology, encouraging collaborations, and supporting shared resources can move science forward faster. To this end, computational biologists and software engineers from CZI will collaborate with the Imaging Software Fellows to better understand the current ecosystem and work together to identify new ideas.