The Chan Zuckerberg Initiative announced this month funding for open-source software efforts to improve image analysis and visualization in biomedicine. The announcement includes funding for scikit-image.
BIDS Researcher Stéfan van der Walt, the founder of scikit-image, is enthusiastic about this support for the open source community. "Many foundational open source scientific software packages are maintained by a handful of developers in their spare time. To strengthen the foundation we depend on so heavily, and to grow our potential pool of participants, we need to support the people at its core. We are excited that CZI, through their grant, recognizes this need and the role scikit-image plays in microscopy."
Microscopy — critical to modern cell biology — generates complex data at volumes that challenge its analysis and visualization. CZI cited scikit-learn among three critical, widely-used tools that can accelerate basic research and benefit the entire field.
Juan Nunez-Iglesias, a Research Fellow at Monash University in Australia, received the CZI funding. He has been named the CZI's scikit-image Imaging Software Fellow. His work will advance the technical capabilities of scikit-image and continue the community growth of image analysis in Python. According to Juan, "Image analysis is touching everything these days, so there is something for everybody: already we’ve seen scikit-image used to detect lung cancer, measure crop growth, study better solar panel materials, measure deforestation, and transcribe clay tablets from the 7th century BC. A better scikit-image can accelerate all these endeavors and more."
Nunez-Iglesias will collaborate with other CZI computational biologists and software engineers to improve the surrounding ecosystem, including NumPy and SciPy (software packages that form the basis of scientific computing in Python), CellProfiler (a graphical user interface for cell-based measurements in images), and dask (a library for computing on very large datasets). BIDS is currently home to grants from the Moore and Sloan Foundations that support NumPy, upon which scikit-image is built.
Van der Walt started scikit-image in 2009, and it has since grown into a community-driven project that includes a vast collection of high-quality, peer-reviewed image processing algorithms that are made available free of charge and free of restrictions. scikit-image now has over 285 contributing developers worldwide, and 14,000 packages that depend on it. The software plays a critical role across many domain areas of science, with applications including biomedical image processing, energy and environmental resource management, astronomy, and more.
At BIDS, Van der Walt and other researchers, developers and maintainers are provided institutional support and a home to advance open source software platforms such as scikit-image and NumPy. BIDS will be expanding these efforts in 2019 and beyond.
CZI Announces Support for Open-Source Software Efforts to Improve Biomedical Imaging
December 6, 2018 | Chan Zuckerburg Initiative