Caterina Strambio De Castillia and her team advance efforts to establish microscopy data standards
Caterina Strambio De Castillia, PhD, researcher at UMass Chan Medical School and imaging scientist at the Chan Zuckerberg Initiative, and her team are on a mission to defend one of the foundations of science: well-documented data, which in turn are essential to guarantee the quality, reproducibility of data and exchange. Dr. Strambio De Castillia, Assistant Professor of Molecular Medicine and Cell Biologist, is the lead author of two articles and co-author of four others published in the December issue of Natural methods. This issue of the journal also includes a profile of Strambio De Castillia.
The publication focuses on the progress made in recent years to improve documentation, quality control, publication and sharing standards for bioimaging experiments. One of the central topics of the issue is the development of standards and tools for the exchange of imaging results and metadata, information on the experimental, technical and image analysis context of image data.
The production of high-quality quantitative results and the possibility of replicating experiments are scientific cornerstones. And to ensure rigor and reproducibility, scientists must agree on common terminologies to describe the details of how an experiment was performed, what were the specifications of the technical equipment used, and how the images were analyzed. .
These aspects have sometimes been overlooked as scientific research has become more complex.
Strambio De Castillia explained that as scientists delved into the molecular details of cellular functions over the past half-century, it became important to know how the information gleaned could be incorporated into a broader understanding of biological systems. .
âWe’re not just looking at all the DNA in the nucleus, all the RNA, all the proteins. We are trying to understand how all of these individual components work together, are dynamically organized in three dimensions and move in time, for example to ensure the proper functioning of genetic material inside the nucleus, âshe said. . To achieve this goal, the quantitative and rigorous use of imaging data has become increasingly important in recent years.
To cope with this level of information complexity and to learn how the informational content of image data could be managed and exchanged between researchers, Strambio De Castillia acquired an in-depth knowledge of computer science.
“I am really interested in how to organize the information, so that we can talk with each other about experiments, we can guarantee the scientific rigor and we can publish enough experimental and technical details to guarantee the reproducibility and a meaningful data exchange, âshe said.
Building on his pioneering work on integrated imaging pipelines for viral particle tracking in collaboration with the biomedical imaging group at UMass Chan, Strambio De Castillia was invited in 2018 to join the 4D Nucleome Consortium of National Institutes of Health as an associate member to develop microscopy and imaging. analysis metadata standards.
Metadata is “information about other data” needed to interpret the results, Strambio De Castillia said. It provides the essential context to ensure that the results can be properly assessed, interpreted and compared.
âMetadata exists in a lot of different contexts, but in biology it started to become something that people started paying attention to when we started doing genomics,â she said. âYou just couldn’t keep track of everything you were doing, materials and methods, in your notebook like you did before big data. It’s a fundamental aspect of science, but we kind of lost track of it when we started to be inundated with data. “
Strambio De Castillia has partnered with a larger project called Open Microscopy Environment, an international consortium that developed an initial model on how to organize this information.
With the support of the Chan Zuckerberg initiative, Strambio De Castilla’s productivity in building integrated image data management and quality control pipelines âhas skyrocketed,â she said.
As a result, she was invited to organize and lead the Quality Control and Data Management Working Group of Bioimaging North America (BINA). BINA is a consortium formed to bring together the bio-imaging community in Canada, the United States and Mexico, foster communication, data sharing and dissemination of technology between base facilities, promote training and professional recognition of imaging scientists and being an advocate of bio-imaging for institutional partners and funding agencies, with whom to engage in strategic dialogue.
One of the key roles of BINA, now funded by the Chan Zuckerberg Initiative, is to serve as a counterpart to other global imaging organizations such as Global Bioimaging or the recent Quality Assurance and Reproductibility for Instruments & Images in Light training. Microscopy (QUAREP-LiMi) initiative.
As such, Strambio De Castillia is now involved at the forefront of a global effort under QUAREP-LiMi to develop standards and tools aimed at improving reproducibility, comparability, downstream data analysis and reuse of imaging data; promote rigorous record keeping, quality control and data management; develop international consensus on guidelines and tools to facilitate the evaluation and calibration of microscopes; and promote and disseminate guidelines and best practices.
It is important to note that the novelty of this effort is that QUAREP-LiMi was specifically designed as a bottom-up consortium involving all members of the imaging community, including microscope users, custodians and technicians. manufacturers, plant managers, imaging scientists, publishers, standards organizations. , and donors, said Strambio De Castillia.
“This creates a community that brings together all those who have an interest in ensuring that imagery can be used for scientific discovery for the specific purpose of generating consensus solutions that can be adopted by all,” she said. “But it also presents a unified voice of what would be needed and what kind of investments need to be made at the institutional and financial level to really move the field forward.”
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