Zuckerberg funds
How to "make friends" with optical technologies and biomedicine
Ed McCleskey, Medium: Better tools, increased collaboration between optical engineers and biomedical researchersTranslation: Alexey Statsenko, Habr
For links, see the translation or the original of the article – VM.
To speed up biomedtech, the creator of Facebook decided to finance Imaging Scientists (scientists engaged in the science of collecting, storing, searching and processing visual information).
Confocal microscopy of fibroblasts, which are important in connective tissue. The nuclei are marked in blue, the actin fibers are red, and the tubulins are green. Photo: iStock.com .
The invention of the microscope at the end of the XVI century allowed scientists to explore the microscopic world for the first time, but it took scientists another 200 years to evaluate the microscope as an important tool in clinical medicine. Today, images of molecules, cells and tissues are a critical step in biomedical research and clinical practice. However, shortcomings in image processing software and in the spread of new microscope technologies have slowed progress in this area.
The Chan Zuckerberg Initiative (CZI) held three seminars on image processing last year, which focused on computational tools for microscopy, cellular and subcellular imaging, and mesoscale and macroscale imaging, respectively. We also visited seven different image processing centers in the USA and Europe. In the feedback we received, we saw an opportunity to accelerate progress in the field of image processing through the use of technological expertise, which became the basis of our request for information systems for scientists engaged in the science of collecting, storing, searching and processing visual information (RFA)
CZI's new Imaging Scientists program aims to accelerate the development of biology and medicine by expanding collaboration between biologists and technology experts, thereby improving microscopy tools. The program will support up to 10 scientists in this program to work in image processing centers in the United States for three to five years. These scientists-inventors could be engineers, physicists, mathematicians, programmers or biologists who specialize in technology in the field of optical microscopy or data analysis.
Why image processing?
Microscopy, the main method of cell biology, occupies a central place in the basis of biology and medicine. Microscopy is also the key to pathology, which determines the causes and consequences of diseases. Along with microscopy, medical imaging provides a critical way to diagnose the disease at the level of the whole organism. Improving imaging techniques means improving broad areas of biomedicine, which is the main idea of CZI's mission to support science and technology, which will allow all diseases to cure, prevent or restrain their development by the end of this century.
In the past decade, technological progress has been achieved, which has dramatically increased the resolution of optical microscopy. Now it is possible, for example, to observe in living cells the movement of individual molecules that have been labeled with fluorescent markers. But many of these new microscopes have not been brought to market, and the software for analyzing these new kinds of data lags behind advances in hardware. We believe that this problem is due to insufficient interaction between biologists and engineers; our Imaging Scientists program aims to solve this problem.
The researcher checks whether the tissues are stained with a fluorescent antibody (Alexa Fluor 555). Photo: Jobelle Peralta.
Design support in image processing centers
Image processing centers use state-of-the-art microscopes, organ imaging tools, and related software among researchers at universities, medical centers, or affiliated research institutions. During our visits to image processing centers, we learned from biologists that they really appreciate contact with hardware and software engineers, but this technique is underestimated in biomedicine. For example, engineers in image processing centers in the United States are often funded by the provision of paid services. This lack of a trust fund hinders their creative ingenuity, does not allow them to use their experience to the full, and limits their attention to systemic progress that could improve the entire field. The funds from the CZI award will be used to bridge this gap by paying salary costs to scientists engaged in the science of collecting, storing, searching and processing visual information so that they can interact more deeply and creatively with people involved in experimental biology in their projects.
Improved image processing hardware and software
Modern microscopy is capable of generating 3D images at very high speeds or performing video timelapse for a long time. The biological community is trying to share such large volumes of processed images, analyze and visualize them. The existing ecosystem of open source tools meets the most pressing needs of scientists, but these tools remain difficult to use, difficult to interact with and do not yet include modern advances in the development and automation of the user interface using machine learning. In addition, many new microscopes, especially those under development, require special expertise to assemble and even work with them. We see how important it is for biologists and engineers to focus on their fields of knowledge, collaborating to solve problems that require the participation of advanced technologies.
Scientists working with CZI will work directly with biologists to use and improve the latest hardware and software for image processing. Through regular discussions and interactions, this team of on-site engineers will determine the needs of microscopy software and data infrastructure, determine which software packages are currently most useful, how these systems can be improved and whether it is necessary to develop completely new software. As part of our interest in open science, CZI has its own in-house engineering teams that develop software together with scientists from this environment, using open development sites such as GitHub, and releasing software developed by our own team and our funded partners under authorized open source licenses
Fluorescent view of human skin cells in culture under a microscope. The nuclei are marked in blue, the actin fibers are red, and the tubulins are green. Photo: iStock.com .
Wider and faster exchange of new image processing methods
It is not enough just to develop new technologies, these new technologies must be widely and quickly distributed. In addition to daily one-on-one interaction with biologists, scientists working with CZI will have to teach courses that disseminate modern microscopy techniques and that are open to scientists and students around the world. They are also expected to be part of a broader network of image processing experts to identify advances in the field and its needs. Twice a year, scientific seminars and meetings of CZI in the field of image processing and related biomedical fields will provide an opportunity to make acquaintances, exchange experience and knowledge and use each other's experience to create improvements in image processing technology.
CZI and Software
The unique design of the Chan Zuckerberg Initiative combines traditional philanthropic support with software development with the help of a full-time team of software engineers. The teams serve the three pillars of CZI: science, education and "justice &Opportunity". The developed software is freely distributed, usually open source, and is developed in collaboration with external developers and users. Interaction with scientists, teachers and the social service sector helps CZI identify areas where its engineers can provide maximum value for these diverse fields. To learn more about our technology team, subscribe to the CZI technology blog.
CZI expects through this Imaging Scientists program to contribute to microscopy and software specialists who are moving this field forward by identifying its current challenges and future potential. You can read the RFA and apply by October 3, 2018 at 17:00 Pacific Time. Please share these important perspectives and help us spread this information! For administrative and program issues, technical assistance or other issues related to RFA, please contact sciencegrants @ chanzuckerberg.com . To stay up to date on funding opportunities, subscribe to our newsletter. To learn more about working in science, visit our website or follow us on Twitter.
About the author:
Ed McCleskey has been a research associate at the Chan Zuckerberg Initiative since March 2017, and previously he was a research associate for 10 years at the Howard Hughes Medical Institute. He was a professor and scientist at the Vollum Institute at the University of Oregon Health & Science (1993-2007) and at the University of Washington School of Medicine (1986-1993). His research focuses on the biophysical properties of calcium-selective ion channels and the discovery of ion channels that cause various types of pain. He taught physiology and neurology and directed a neuroscience course at the Marine Biological Laboratory at Woods Hall.
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