Zuckerberg finances: How to "make friends" optical technology and biomedicine

To speed up biomedtech, the creator of Facebook decided to finance Imaging Scientists (scientists involved in the science of collecting, storing, searching and processing visual information).



Confocal microscopy of fibroblasts that are important in connective tissue. The nuclei are marked blue, the actinic fibers are red, and the tubulins are green. Photo: iStock.com.
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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, flaws in image processing software and the proliferation of microscope technologies have slowed progress in this area.

The Chan Zuckerberg Initiative (CZI) last year held three workshops on image processing , which were focused on microscopic computational tools, cellular and subcellular visualization and macroscale and macroscopic visualization, respectively. We also visited seven different image processing centers in the USA and Europe. In the feedback we received, we saw the possibility of accelerating progress in image processing through the use of technological expertise, which became the basis of our request for information systems for scientists involved in the science of collecting, storing, searching and processing visual information (RFA)

The new CZI Imaging Scientists program aims to accelerate the development of biology and medicine by increasing 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 - is central to 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 a disease at the level of the whole organism. Improving visualization methods means improving broad areas of biomedicine, which is the main idea of ​​the CZI mission to support science and technology, which will allow all diseases to cure, prevent or inhibit their development by the end of this century.

In the past decade, technical progress has been achieved, which has dramatically increased the resolution of optical microscopy . Now you can, for example, observe the movement of individual molecules in living cells, which have been labeled with fluorescent markers. But many of these new microscopes have not been introduced to the market, and the software for analyzing these new types of data lags behind the advances in hardware. We believe that this problem is due to insufficient interaction between biologists and engineers; our Imaging Scientists program seeks 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 modern 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 greatly value contact with hardware and software engineers, but this technique is undervalued in biomedicine. For example, engineers at image processing centers in the United States are often funded by paid services. This lack of a trust fund hinders their creative ingenuity, does not allow their experience to be fully utilized, and limits their attention to systemic progress, which could improve the whole area. Funds from the CZI award will be used to close this gap by paying salary costs to scientists involved in the science of collecting, storing, searching and processing visual information so that they can more deeply and creatively interact with people involved in experimental biology in their projects.

Improved image processing hardware and software

Modern microscopy is able to generate 3D images at very high speeds or to perform time-lapse video 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, and do not yet include current advances in developing and automating user interfaces using machine learning. In addition, many new microscopes, especially those under development, require special expertise for assembly and even for working with them. We see how important it is for biologists and engineers to focus on their areas of expertise, working together 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 group of field engineers will determine the needs of software and data infrastructure in the field of microscopy, determine which software packages are currently most useful, how these systems can be improved and whether completely new software needs to be developed. As part of our interest in open science, CZI has its own full-time 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 within the permitted open source licenses



Fluorescent view of human skin cells in culture under a microscope. The nuclei are marked blue, the actinic fibers are red, and the tubulins are green. Photo: iStock.com.

Wider and faster exchange of new image processing methods

It is not enough to develop new technologies; these new technologies should be widely and quickly distributed. In addition to the one-on-one daily interactions 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 wider network of image processing experts to identify advances in this area and its needs. Twice a year, scientific seminars and CZI meetings in the field of image processing and related biomedical areas will provide the opportunity to make acquaintances, share experiences and knowledge, and use each other’s experiences 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. Interacting with scientists, educators, and the social services sector helps CZI identify areas where its engineers can provide the maximum value for these diverse areas. To learn more about our technology team, subscribe to the CZI technology blog .

CZI is counting on this Imaging Scientists program to contribute to specialists in the field of microscopy and software who are pushing this area forward, identifying its current problems and future potential. You can read the RFA and apply before October 3, 2018 at 5:00 p.m. Pacific Time. Please share these important perspectives and help us spread this information! For administrative, policy, technical assistance, or other RFA related issues, please contact sciencegrants@chanzuckerberg.com. Sign up for our newsletter to stay up to date on funding opportunities. To learn more about working in science, visit our website or follow us on Twitter .

Ed McCleskey, Researcher

Ed McCleskey has been a research fellow at the Chan Zuckerberg Initiative since March 2017, and previously he was a research assistant for 10 years at Howard Hughes Medical Institute. He was a professor and scholar at the Vollum Institute at the University of Oregon Helt & Science (1993–2007) and at the University of Washington Medical School (1986–1993). His research focuses on the biophysical properties of calcium-selective ion channels and the opening of ion channels that cause various types of pain. He taught physiology and neuroscience and guided the course of neuroscience at the Marine Biological Laboratory at Woods Hole.

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