Mission Statement

UC San Diego Seal
The mission of NCMIR is to develop technologies to bridge understanding of biological systems between the gross anatomical and molecular scales and to make these technologies broadly available to biomedical researchers. NCMIR provides expertise, infrastructure, technological development, and an environment in which new information about the 3D ultrastructure of tissues, cells, and macromolecular complexes may be accurately and easily obtained and analyzed.
Read More >>

Research Highlights IconResearch Highlights

thumbnail 1

Astrocytes Devour Neuronal Mitochondria in a Newly Documented Process Called Transmitophagy


Scientific canon long held that when the tiny energy producers within cells, called mitochondria, become damaged or dysfunctional, these tiny organelles are degraded and recycled within the cell that produced them. But a paper appearing in the Proceedings of the National Academy of Sciences (PNAS) from The Johns Hopkins University and NCMIR scientists now shows that, instead, particularly in the long axons of the brain’s nerve cells, damaged mitochondria are transferred to nearby glial cells for elimination. This process, in effect, outsources a substantial portion of the neurons’ housekeeping. Read More >>
thumbnail 1

A New Model System for Neural Development Produces Nanoscale-resolution Animations that Inspires Music


Neural circuit development in mice is characterized by early exuberant innervation followed by competition and pruning to mature innervation topography. Several neural systems (e.g., the neuromuscular junction and climbing fiber innervation of Purkinje cells) have served as models to study neural development in part because they establish a recognizable endpoint of mono-innervation of their targets, and the presynaptic terminals are large and easily monitored. The calyx of Held (CH) innervation of its target, which forms a key element of auditory brainstem binaural circuitry, exhibits these same characteristic. Read More >>
thumbnail 1

De-coating Caveolae: Understanding the Caveolar Protein Machinery in Endocytosis


Caveolae are flask-shaped invaginations with a diameter of 50-80nm in the plasma membrane of many types of mammalian cells. They are particularly abundant in fat cells, muscle cells, and cells that line blood vessels and serve as a source for clathrin-dependent endocytosis. Although they are likely to be important for cellular responses to mechanical stress, intracellular trafficking, and signaling events, the precise molecular mechanisms that determine how they form and carry out these functions have yet to be understood. Read More >>
thumbnail 1

Three Types of Microscopy Go To the Limit to Determine Ryanodine Receptor Calcium Release Channels in Cardiac Myocytes


A research team led by UCSD recently published results of their work using various kinds of microscopy to reveal the relative distribution of ryanodine receptors and caveolin-3 in mouse ventricular myocytes in the cytosol and near the cell surface. Ryandine Receptors are important to investigate because they comprise a class of intracellular calcium channels that mediate the release of calcium in various types of mammalian tissue like muscles and neurons. Read More >>
thumbnail 1

Liprin-α1/SYD-2 Determines Size of Electron-dense Projections in Presynaptic Active Zones in C. elegans


Fast synaptic neurotransmission relies on triggered release of neurotransmitters from synaptic vesicles after fusion with the plasma membrane. The release of synaptic vesicles is a highly regulated process of sequential events: First synaptic vesicles are recruited to the presynaptic active zone, then docked to the plasma membrane in a release-competent state, which guarantees their rapid release after the influx of calcium into the presynaptic terminal. Read More >>
thumbnail 1

Big Data Analysis: Applying Electron Microscopy to Semi-automated Neuron Boundary Detection and Non-branching Process Segmentation


Reconstructing neural circuits is important to studying neural circuit connectivity and its behavioral implications. Understanding the differences between neuronal classes, patterns, and connections is critical to enable a more general understanding of how neural circuits process information. Electron microscopy is a useful method to determine the anatomy of individual neurons and their connectivity because it has a resolution that is high enough to identify features such as synaptic contacts and gap junctions, which define connectivity and, therefore, are required to reconstruct the neural circuit. But because the complexity and size – often approaching tens of terabytes -- of this data make for very difficult and labor-intensive interpretation, new segmentation techniques for identifying neurons in these data sets are needed. Read More >>
thumbnail 1

Efficient, Scalable, and Cost-effective 3D Microscopy Image Segmentation Using a Microlabor Workforce


In an applications note published in Bioinformatics, a team of researchers from the National Center for Microscopy and Imaging Research at UCSD described a new scalable, semi-automated approach to segment 3D structures revealed in serial block-face scanning electron microscopy (SBEM) images. The team used the Dual Point Decision Process (DP2) to divide the segmentation problem into discrete tasks distributed to a large pool of individual workers. Read More >>
thumbnail 1

Adenovirus Protein may be a Key to Strategic New Cancer Therapies


A team of scientists led by Clodagh O’Shea’s group at The Salk In100stitute for Biological Studies in collaboration with NCMIR scientists (Mark Ellisman, Tom Deerinck, Andrew Noske) and Dr. Roger Tsien and his laboratory suggest that cold viruses could serve as a valuable tool in the fight against cancer. Adenovirus, a type of cold virus, has developed proteins that allow it to hijack a cell's molecular machinery particularly those involved in growth, replication and cancer suppression. Read More >>
thumbnail 1

Origins of Aggressive Brain Tumors


Scientists have long believed that glioblastoma multiforme (GBM), the most aggressive type of primary brain tumor, begins in glial cells that make up supportive tissue in the brain or in neural stem cells. In a paper published in Science, researchers at the Salk Institute for Biological Studies and the National Center for Microscopy and Imaging Research have found that the tumors can originate from other types of differentiated cells in the nervous system, including cortical neurons. Read More >>
thumbnail 1

Ocean Bacteria Infected by Strange Looking Viruses


NCMIR researchers aided in the discovery of the most abundant virus in the ocean. This virus, called a Pelagiphage, attacks the most abundant microorganism in our oceans, a type of marine bacteria called SAR11, with significant implications for how carbon moves between the atmosphere and our oceans. SAR11, a bacterium that's the most abundant organism in the oceans, survives where most other cells would die and plays a major role in the planet's carbon cycle. It had been theorized that SAR11 was so small and widespread that it must be invulnerable to attack. Pelagiphages are so strange-looking that scientists previously didn't even recognize what they were. Read More >>
thumbnail 1

Accumulated Excess Protein Linked To Development Of Parkinson’s Disease By Progressively Disrupting Neuronal Function And Viability


NCMIR scientists have shown that overexpression of a protein called alpha-synuclein appears to disrupt vital recycling processes in neurons, starting with the terminal extensions of neurons and working its way back to the cells’ center, with the potential consequence of progressive degeneration and eventual cell death. Published in the February 6, 2013 issue of The Journal of Neuroscience, this study has major implications for more fully understanding the causes and mechanisms of Parkinson’s disease (PD), a neurodegenerative movement disorder that affects an estimated 1 million Americans. Read More >>
thumbnail 1

Electron Microscopy Achieves A New APEX


Chemists from MIT together with NCMIR Scientists, Mark Ellisman, Tom Deerinck and Gina Sosinsky, have now designed a GFP equivalent for electron microscopy — a tag that allows scientists to label and visualize proteins with unprecedented clarity that offers much higher resolution than fluorescence microscopy. The new tag developed by Jeff Martell and Alice Ting, lead and senior authors of a paper describing the new tag in the Oct. 21 online edition of Nature Biotechnology, could help scientists pinpoint the locations of many cell proteins, providing new insight into those proteins’ functions. This new tag can label proteins throughout the cell — not only within mitochondria but also in the nucleus, the endoplasmic reticulum and the cytosol. Read More >>
thumbnail 1

It's Not What You Eat But When You Eat


Researchers at the Salk Institute led by Dr. Satchidananda Panda with NCMIR collaborators, published a provocative paper In the June issue of Cell Metabolism showing that mice fed a high calorie/high fat diet on a time restricted feeding schedule were protected against obesity and related complications compared to mice eating the same amount of calories ad libitum. Read More >>

In The News IconIn The News

thumbnail 1

UC San Diego and NCMIR Researcher Roger Tsien is awarded the first annual Golden Goose Award from Congress


Roger Tsien, PhD, Professor of Pharmacology at UC San Diego and Nobel laureate for Chemistry 2008, for work related to NCMIR at UC San Diego, received the Golden Goose Award in September 2012. This award “showcases researchers who pursue oddball topics that eventually lead to significant health and economic benefits, the awards were created by a coalition of science organizations (including AAAS, publisher of Science Insider) Read More >>
thumbnail 1

The Microscopy Society of America awards the Maser Award to NCMIR’s own Gina Sosinsky


At the 2012 Microscopy & Microanalysis meeting held in Phoenix this July, Gina Sosinsky, Assistant Director of NCMIR and a UCSD Professor-In-Residence in Neurosciences was awarded the Morton D. Maser Ward for Distinguished Service to the Microscopy Society of America. This major society award recognizes outstanding volunteer service to the Society. Read More >>
thumbnail 1

NCMIR at the MET


NCMIR Commissioned to Provide Artwork for the New Medical Education and Telemedicine Center at UCSD

La Jolla, CA , December 2011- Researchers from the National Center for Microscopy and Imaging Research (NCMIR) have been charged with providing science-based artwork for the public areas of the new +100,000 square foot Medical Education and Telemedicine Center on the campus of the School of Medicine at UCSD. The new center will be a hub of learning that incorporates state-of-the-art design and technology to prepare medical students to become physicians and innovators of tomorrow. It will also be used for physicians to learn new skills utilizing the latest advances in medical and surgical technology, such as surgical robotics. Read More >>
thumbnail 1

Two Top Biological Imaging Centers Offer Powerful Free Online Tool to Researchers, Educators, and Public


ASCB’s The Cell: An Image Library and NCMIR’s Cell Centered Database introduce new interface to spur health discoveries and science education

BETHESDA, MD, USA, DECEMBER 1, 2011 – The collaboration of two leading cell image resource centers now provides a more extensive and advanced facility for archiving, sharing, and analyzing microscope images in great detail. The American Society for Cell Biology (ASCB) and the National Center for Microscopy and Imaging Research (NCMIR) at the University of California, San Diego (UCSD), have joined forces to provide a unified interface. This union extends ASCB’s The Cell: An Image Library website with new capabilities and an extensible software infrastructure. Read More >>
thumbnail 1

Waitt Family Foundation Project Develops Whole Brain Catalog


At the year’s biggest international meeting of neuroscientists, researchers from the University of California, San Diego will unveil a tool that could revolutionize the way scientists and students explore and map the mysteries of the brain. Read More >>

Image Gallery

Gallery of Covers

View our Gallery of Covers

User Application

Share to Facebook Share to Twitter Email This More...

Affiliated Sites