Imaging

To cure, prevent, and manage all diseases by the end of the century, we need a much deeper understanding of biological systems. To gain this knowledge, we need to develop hardware and software tools to visualize life’s processes at the level of tissues, cells, and proteins.

We also need to understand context — such as protein interaction in cells and cell signaling in living organisms. Enabling measurement and quantitative insights, and providing access and training to these tools, will allow researchers to make breakthroughs and build on each other’s discoveries.

CZI Imaging Tools: napari

napari

Imaging

An interactive, multi-dimensional image viewer for Python designed for browsing, annotating and analyzing large 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 2-day-old zebrafish heart viewed through a microscope. The heart muscle membrane is shown in blue and their 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 2-day-old zebrafish heart viewed through a microscope. The heart muscle membrane is shown in blue and their 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 the 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 the 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.
T lymphocytes (orange), a type of white blood cell, attack a cancer cell (blue).
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? 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 support innovations in imaging technology that could be transformative for medical applications and for understanding life at the cellular level.

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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.

CZI Imaging Scientists & Imaging Software Fellows

CZI’s Imaging Scientists program aims to advance the field of imaging by increasing collaboration between biologists and technology experts and improving the imaging tools that scientists use. CZI also supports Imaging Software Fellows to develop and maintain three critical tools: scikit-image, FIJI / ImageJ, and CellProfiler.

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Global BioImaging

CZI supports Global BioImaging (GBI), an international network of bioimaging facilities and communities. These networks of core imaging centers help researchers better understand and identify the biological mechanisms of health and disease using cutting-edge technology. GBI strengthens community building and training worldwide to address the practical challenges of operating open access tools for imaging technologies in the life sciences.

Scanning electron microscopy image of the surface of frozen daisy with pollen (false-colored). Photo by Daniel Gütl, winner of the 2017 Euro-BioImaging “Research. Captured” competition.
Scanning electron microscopy image of the surface of frozen daisy with pollen (false-colored). Photo by Daniel Gütl, winner of the 2017 Euro-BioImaging “Research. Captured” competition.

Imaging Team

Ed McCleksey (Program Officer, Imaging)
Ed McCleksey
Program Officer, Imaging
Stephani Otte (Program Officer, Imaging)
Stephani Otte
Program Officer, Imaging
Vladimir Ghukasyan (Program Manager, Imaging)
Vladimir Ghukasyan
Program Manager, Imaging
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