Imaging

To cure, prevent, and manage all diseases by the end of the century, we need a much deeper understanding of biological systems. Existing imaging tools provide a limited view, tending to focus on a specific biological scale without the necessary context. Researchers struggle to handle large volumes of data and to make quantitative insights, and substantial access and training gaps remain.

CZI’s imaging program aims to drive the development of: 

  • A suite of new imaging tools capable of observing biological processes across spatial scales at the level of tissues, cells, and proteins; and 
  • Robust frameworks to quantify, analyze, and share imaging data and share methods and tools.

Scientific imaging research and technology will play a critical role in enabling a deeper mechanistic understanding of health and disease, driving diagnostics, and informing directed treatments.

A scientist inspects a lime green slide to be placed under a microscope.
CZI Imaging Scientist Michelle S. Itano at the University of North Carolina, Chapel Hill, Neuroscience Microscopy Core. Photo provided by Michelle S. Itano.
CZI Imaging Scientist Michelle S. Itano at the University of North Carolina, Chapel Hill, Neuroscience Microscopy Core. Photo provided by Michelle S. Itano.

CZI Imaging Tools: napari

napari

Imaging

A community-built, Python-based, open-source tool for browsing, annotating and analyzing large multi-dimensional images.

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napari

We want napari to help not just Python practitioners, but also biologists and other scientists who want to access Python's enormous scientific ecosystem.

Juan Nuñez-Iglesias
Super-resolution light microscopy allows scientists to view the details of subcellular organelles — units in cells with specialized functions — in living cells. Photo provided by Aaron Taylor, University of Michigan, BRCF Microscopy Core.
Super-resolution light microscopy allows scientists to view the details of subcellular organelles — units in cells with specialized functions — in living cells. Photo provided by Aaron Taylor, University of Michigan, BRCF Microscopy Core.
A two-day-old zebrafish heart viewed through a microscope. The heart muscle membrane is shown in blue and its nuclei in red. Photo provided by CZI imaging scientist Michael Weber of the Morgridge Institute for Research, in affiliation with the University of Wisconsin-Madison.
A two-day-old zebrafish heart viewed through a microscope. The heart muscle membrane is shown in blue and its nuclei in red. Photo provided by CZI imaging scientist Michael Weber of the Morgridge Institute for Research, in affiliation with the University of Wisconsin-Madison.
A forest of nerve cells (axons, dendrites, and dendritic spines of neurons) in the brain. Photo by Gao, Asano, Upadhyayula et al, Science 2019.
A forest of nerve cells (axons, dendrites, and dendritic spines of neurons) in the brain. Photo by Gao, Asano, Upadhyayula et al, Science 2019.
These nuclear proteins (histones) in a living roundworm embryo were imaged using a dual-view inverted selective plane illumination microscopy (diSPIM). Maximum intensity projection images are rendered in different colors for visualization. Photo provided by Abhishek Kumar, Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering.
These nuclear proteins (histones) in a living roundworm embryo were imaged using a dual-view inverted selective plane illumination microscopy (diSPIM). Maximum intensity projection images are rendered in different colors for visualization. Photo provided by Abhishek Kumar, Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering.
The carotid artery of a mouse with atherosclerosis. Red, yellow, and green immune cells take up cholesterol and help regulate inflammation in the arterial wall (blue). Photo by Sara McArdle, La Jolla Institute for Immunology, LJI Microscopy Core.
The carotid artery of a mouse with atherosclerosis. Red, yellow, and green immune cells take up cholesterol and help regulate inflammation in the arterial wall (blue). Photo by Sara McArdle, La Jolla Institute for Immunology, LJI Microscopy Core.
A zebrafish embryo at one day old, imaged in the Tissue Microscopy Laboratory at Texas A&M University. Photo provided by Holly Gibbs, Texas A&M University, Microscopy and Imaging Center.
A zebrafish embryo at one day old, imaged in the Tissue Microscopy Laboratory at Texas A&M University. Photo provided by Holly Gibbs, Texas A&M University, Microscopy and Imaging Center.
  • Super-resolution light microscopy allows scientists to view the details of subcellular organelles — units in cells with specialized functions — in living cells. Photo provided by Aaron Taylor, University of Michigan, BRCF Microscopy Core.
  • A two-day-old zebrafish heart viewed through a microscope. The heart muscle membrane is shown in blue and its nuclei in red. Photo provided by CZI imaging scientist Michael Weber of the Morgridge Institute for Research, in affiliation with the University of Wisconsin-Madison.
  • A forest of nerve cells (axons, dendrites, and dendritic spines of neurons) in the brain. Photo by Gao, Asano, Upadhyayula et al, Science 2019.
  • These nuclear proteins (histones) in a living roundworm embryo were imaged using a dual-view inverted selective plane illumination microscopy (diSPIM). Maximum intensity projection images are rendered in different colors for visualization. Photo provided by Abhishek Kumar, Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering.
  • The carotid artery of a mouse with atherosclerosis. Red, yellow, and green immune cells take up cholesterol and help regulate inflammation in the arterial wall (blue). Photo by Sara McArdle, La Jolla Institute for Immunology, LJI Microscopy Core.
  • A zebrafish embryo at one day old, imaged in the Tissue Microscopy Laboratory at Texas A&M University. Photo provided by Holly Gibbs, Texas A&M University, Microscopy and Imaging Center.
An illustration on a black background of a blue T-cell attaching to an orange cancer cell, surrounded by three orange cancer cells.
In this illustration, T lymphocytes (orange), a type of white blood cell, attack a cancer cell (blue).
In this illustration, T lymphocytes (orange), a type of white blood cell, attack a cancer cell (blue).

Frontiers of Imaging

What if researchers could view how drugs alter the behavior of cancer cells and invade immune cells deep in the body? Or visualize how viral or bacterial pathogens hijack normal cellular functions to reproduce themselves? Such insights would open up new avenues for developing treatments and cures for many diseases.

Although there have been significant advances in biomedical imaging, we are far from the ultimate goal: to observe cells and subcellular processes in living organisms and in a minimally invasive manner. CZI’s Frontiers of Imaging effort aims to accelerate the development of disruptive imaging technologies that connect biological scales—such as proteins to cells and cells to organisms. This will allow researchers to directly visualize biological processes at the necessary resolution and in context to obtain a mechanistic understanding of health and disease.

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A scientist wearing a protective gown looks into a microscope
CZI imaging scientist Sara McArdle of the La Jolla Institute for Immunology looks into a microscope. Protective gowns are required, as this microscope is used in studies of infectious agents, such as Zika and Dengue viruses, in addition to a range of inflammatory disorders. Photo provided by Sara McArdle.
CZI imaging scientist Sara McArdle of the La Jolla Institute for Immunology looks into a microscope. Protective gowns are required, as this microscope is used in studies of infectious agents, such as Zika and Dengue viruses, in addition to a range of inflammatory disorders. Photo provided by Sara McArdle.

Creating Community & Building Capacity

Innovations in imaging science—new technologies, imaging modalities, and data analysis approaches—are becoming increasingly important in advancing biomedical research. To accelerate the promotion, dissemination, and efficient use of new methods and tools, CZI is supporting scientists who operate imaging facilities, which serve as hubs of imaging expertise for local communities of biomedical researchers. CZI is also supporting imaging software fellows who develop and maintain three critical imaging tools: scikit-image, FIJI / ImageJ, and CellProfiler.

On a larger scale, fostering international communities of imaging experts, scientists, imaging facility operators, and policymakers is vital to address current scientific, technical, and data challenges. To facilitate these activities, CZI supports Global BioImaging (GBI), the international network of cutting-edge imaging facilities and communities, and GBI member BioImaging North America, which brings together imaging communities spanning the United States, Canada, and Mexico.

Learn About Our Grantees

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Imaging Team

Ed McCleskey Program Officer, Imaging
Stephani Otte Program Officer, Imaging
Stephen Jett Program Manager, Imaging
Vladimir Ghukasyan Program Manager, Imaging
Melissa Gorham Project Manager, Imaging and Neurodegeneration
Nicholas Sofroniew Group Product Manager, Imaging

Advisory Board

Jono Bacon Jono Bacon Consulting
Muyinatu Bell Johns Hopkins University
Amy Bernard Allen Institute
Tobias Bonhoeffer Max Planck Institute for Neurobiology
Richard Henderson MRC Laboratory of Molecular Biology
Viren Jain Google
Robert Tijan Howard Hughes Medical Institute; University of California, Berkeley
Rebecca Willet University of Chicago
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