Better tools, increased collaboration between optical engineers and biomedical researchers

New Imaging Scientists funding opportunity aims to accelerate biomedicine

Confocal microscopy of fibroblast cells, which are important in connective tissue. Nuclei are labeled with blue, actin filaments are red, and tubulins are green. Photo by

The invention of the microscope at the end of the 16th century allowed scientists to explore the infinitesimal world for the first time, yet it took another 200 years for scientists to appreciate the microscope as an important tool in clinical medicine. Today, imaging molecules, cells, and tissues is a critical step in biomedical research and clinical practice. However, weaknesses in imaging software and in the dissemination of novel microscope technologies has slowed progress in this area.

To understand how the Chan Zuckerberg Initiative (CZI) could aid in addressing this challenge, last year we hosted three workshops on the topic of imaging that focused on computational tools for microscopy, cellular and subcellular imaging, and meso/macro scale imaging, respectively. We also visited seven different imaging centers in the U.S and Europe. From the feedback we received, we saw the opportunity to accelerate progress in the field of imaging by leveraging technological expertise, which became the basis of our Imaging Scientists Request for Applications (RFA).

CZI’s new Imaging Scientists program aims to accelerate biomedical science by increasing collaboration between biologists and technology experts, thereby improving microscopy tools. The program will support up to 10 CZI Imaging Scientists to work at imaging centers in the U.S. for three to five years. These Imaging Scientists could be engineers, physicists, mathematicians, computer scientists, or biologists who focus on technology in either optical microscopy or data analysis fields.

Why Imaging?

Microscopy — the core method of cell biology — is central to basic biomedical science. Microscopy is also key to pathology, which identifies the causes and effects of diseases. Along with microscopy, medical imaging provides a critical way to diagnose disease at the level of the whole body. Improving imaging means improving broad areas of biomedicine, which is central to CZI’s mission of supporting the science and technology that will make it possible to cure, prevent or manage all diseases by the end of this century.

The past decade saw technical advances that dramatically increased the resolution of light microscopy. It now is possible, for example, to watch within living cells the movement of individual molecules that have been tagged with fluorescent labels. But many of these new microscopes have not been commercialized, and software for analyzing these new kinds of data lags behind the advances made in hardware. We believe that this bottleneck results from insufficient interaction between biologists and engineers; our Imaging Scientists program seeks to address this issue.

A researcher checks to see if tissues are stained with a fluorescent antibody (Alexa Fluor 555). Photo by Jobelle Peralta.

Supporting engineering at imaging centers

Imaging centers share advanced microscopes, organ imaging instruments, and associated software among researchers at universities, medical centers or affiliated research institutions. During our visits to imaging centers, we heard from biologists that they greatly value contact with both hardware and software engineers, but that engineering is undervalued in biomedicine. For example, engineers at imaging centers in the U.S. often are funded on a fee-for-service basis. This lack of dedicated funding inhibits their creativity, underuses their expertise, and limits their focus on systemic progress that could improve the whole field. Funds from CZI’s award will address this gap by paying salary costs of Imaging Scientists so that they can interact more deeply and creatively with experimental biologists on their projects.

Improving imaging hardware and software

Modern microscopy is capable of generating 3D images at very fast rates or for prolonged time-lapse video. The biological community struggles to analyze, visualize, and share such large volumes of imaging data. An existing ecosystem of open-source tools meets some of scientists’ most immediate needs, but these tools remain complex to use, difficult to interoperate, and do not yet incorporate modern advances in user interface design and automation through machine learning. In addition, many new microscopes, especially those in the pre-commercial stage, require special expertise to assemble and even to operate. We see value for biologists and engineers to focus on their individual areas of expertise while collaborating to solve problems that require cutting-edge technology.

CZI Imaging Scientists will work directly with biologists to use and improve cutting-edge imaging hardware and software. Through regular discussions and interactions, this cohort of on-the-ground engineers will identify the software and data infrastructure needs of the microscopy field, what software packages are presently most useful, how these systems can be improved, or whether entirely new software should be developed. As part of our commitment to open science, CZI has internal engineering teams that develop software collaboratively with scientists in the community using open development sites like GitHub, and it releases software developed by our own team and our funded partners under maximally permissive open-source licenses.

Fluorescence microscopic view of human skin cells in culture. Nuclei are labeled with blue, actin filaments are red, and tubulins are green. Photo by

Sharing new imaging methods faster & more widely

It is not enough to develop new technology — that new technology must be shared broadly and rapidly. In addition to their daily one-on-one interactions with biologists, CZI Imaging Scientists will be required to teach in courses that disseminate advanced microscopy methods and that are open to scientists and students around the world. They will also be expected to participate in a broader network of imaging experts to identify advances and needs of the imaging field. Twice-yearly CZI scientific workshops and meetings in imaging and adjacent biomedical areas will offer an avenue for this network to connect, to share experiences and knowledge, and to leverage each other’s expertise to create improvements in imaging technology.

CZI and software

The Chan Zuckerberg Initiative’s unique design combines traditional philanthropic giving with software development by its internal teams of software engineers. The teams serve the three pillars of CZI: Science, Education, and Justice & Opportunity. Software that is developed is shared freely, is generally open source, and is developed in collaboration with external developers and users. Interactions with scientists, with educators, and with the social service sector help CZI to determine areas where its engineers can provide maximal value to these varied arenas. To learn more about our technology team, follow the CZI technology blog.

With this Imaging Scientists program, CZI expects to contribute to the network of microscopy and software experts who drive this field forward by identifying its present bottlenecks and its future potential. You can read the RFA and apply before October 3, 2018 at 5pm PT. Please share with relevant prospects and help us spread the word! For administrative and programmatic inquiries, technical assistance, or other questions about this RFA, please contact To stay updated on funding opportunities, sign up for our mailing list. To learn more about work in science, visit our website or follow us on Twitter.

Ed McCleskey, Science Officer

Ed McCleskey has been a Science Officer at the Chan Zuckerberg Initiative since March 2017, and he previously was a Science Officer for 10 years at the Howard Hughes Medical Institute. He was a professor and scientist at the Vollum Institute of OHSU (1993–2007) and at Washington University School of Medicine (1986–1993). His research addressed the biophysical properties of Calcium-selective ion channels and the discovery of ion channels that trigger different types of pain. He taught physiology and neuroscience, and directed the Neurobiology course at Woods Hole Marine Biology Labs.



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Chan Zuckerberg Initiative Science

Supporting the science and technology that will make it possible to cure, prevent, or manage all diseases by the end of the century.