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10. Sept. 2021
Press Release;
The Central European Institute of Technology (CEITEC) in Brno received funding from the Chan Zuckerberg Initiative (CZI), founded by Dr. Priscilla Chan and Mark Zuckerberg. This open-source scientific software project led by Pavel Tomancak aims to support the maintenance, development and dissemination of key infrastructural software components for visualization and analysis of large image data called ImgLib2 and BigDataViewer. These components are the cornerstones of a diverse software ecosystem that addresses frontier challenges and scales to big bioimage data. The Chan Zuckerberg Initiative will support the project with 400 000 USD.
The bioimaging landscape is changing. State-of-the-art microscopy datasets reach scales previously unimaginable in the biology community. With the advent of big image data comes a paradigm shift in data analysis. Ready to use, point-and-click solutions (open source or proprietary) that work well for small images in memory are not designed to work on multi-terabyte datasets. One can argue that for data of the size and complexity we see today, they never will. “What the biomedical users need is a flexible platform on which they can, with the help of expert developers, rapidly prototype, implement and deploy custom image analysis solutions on their big image data,” explains Pavel Tomancak, one of the founding members of the Fiji community. Fiji (which stands for Fiji Is Just ImageJ) is the dominant open-source platform for biological image analysis, with tens of thousands of users worldwide.
ImgLib2/BDV, the cornerstone software libraries of Fiji, has proven to be one of the best platforms capable of delivering such functionality. The solutions built on top of ImgLib2/BDV cover all major activities performed on big data: visualization, reconstruction, segmentation (classical and deep learning driven), tracking and atlas registration. Several of the world’s largest biological image volumes have been processed with ImgLib2/BDV-based software.
Behind the development of ImgLib2 and BigDataViewer software stands the Fiji community – an international community of researchers interested in combining biology and image analysis. This strong developer community with deep knowledge of big image data processing actively tries to build bridges to other open-source bioimage informatics platforms and to address the current problems with datasets and image analysis that the scientific community is facing.
Biologists are beginning to realize that their bioimages are beyond the capabilities of existing software solutions, yet they may not be aware of the available big data solutions offered by the ImgLib2/BDV in Fiji. The image analysing possibilities of the ImgLib2/BDV ecosystem are very powerful but still not fully exploited. Barriers lie in the steep learning curve, low awareness among the researchers and the scarcity of experienced developers with interest and specific knowledge in this field.
The project aims to provide the vital funding to fully exploit the potential of this unique software, to attract new talents and to support knowledge exchange leading to innovative custom solutions for big data analysis. The main architect of ImgLib2/BDV, Tobias Pietzsch, and all current contributors to this codebase from around the world, rallied behind this proposal, ready to make it work. Another important goal of the project is to lower the entry barrier for newcomers, especially from the currently underrepresented communities. Big emphasis will be placed also on raising awareness of these existing solutions in the global scientific community and including regular knowledge sharing events between users and developers as well as tutorials for users, and mentoring activities targeting junior developers from underrepresented communities. The project will focus on non-European and non-US audiences leveraging the flourishing teleconferencing tools.
“This software addresses the need in the bioimaging community for building innovative software tools for big image data, and answers diverse biological questions with these tools. By consolidating and growing its developer community and spreading awareness of its capabilities amongst biologists, this project will enable the ImgLib2/BDV software ecosystem to assist scientists worldwide in weathering the incoming image data storm,” says Pavel Tomancak, adding that “Bringing ImgLib2/BDV to CEITEC in Brno marks a new chapter in the history of Fiji, establishing yet another centre, besides Dresden, Madison and others, that will contribute to long-term survival and continuing development of this powerful life science tool.”
About the Chan Zuckerberg Initiative
The Chan Zuckerberg Initiative (CZI) was founded in 2015 to help solve some of society’s toughest challenges — from eradicating disease and improving education, to addressing the needs of our local communities. Our mission is to build a more inclusive, just, and healthy future for everyone. For more information, please visit www.chanzuckerberg.com.
Pavel Tomancak
Pavel Tomancak is one of the founding members of the Fiji community. He has supported the community by providing funding, organizing hackathons and meetings (I2K) and promoting the platform among biologists for 15 years. Recently, he raised dedicated grants to support Fiji in Europe. Together with computer science collaborators he helped establish the flagship Fiji projects ImgLib2, image registration (TrakEM2, stitching), SPIM reconstruction, visualization (BigDataViewer) and tracking (Mastodon). He runs an independent research group at the MPI-CBG in Dresden, where he studies the evolution of morphogenesis using advanced microscopy and image analysis. He serves as a Director of the CEITEC consortium.