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The Visium Spatial Transcriptomics system from 10x Genomics captures RNA from frozen or FFPE tissue sections to create a high resolution RNA-seq map.  The grid of 5000 uniquely-barcoded oligonucleotide spots captures and tags mRNAs, permitting determination of the specific transcriptome of each spot.  Expression profiles can then be compared and mapped back to the tissue morphology by overlay on a standard H&E stained or immunofluorescence image of the tissue slice. 

The Arts & Sciences Imaging Center is a participant in the 10x Genomics Visium Enablement Program, which verifies 10x Genomics authorized reagents and methods for spatial transcriptomics.  Contact us to learn more or to discuss your project.

The Arts & Sciences Imaging Center is operational for approved Phase 2 Research Resumption activities. Most of our services and instrumentation will be available, albeit with procedural changes to mitigate coronavirus infection risk. Self-service instrument operation for trained independent users, TEM sample preparation, and 10x Genomics services are now available. Please note that in-person new user instrument training is not expected to be available through August. Please use the web contact form if you have any questions.

We ask your assistance in implementing procedural modifications for Imaging Center activities to make the environment as safe as possible for other users and staff. Some of the important changes include:

Projects to be conducted in the Imaging Center must have independent Phase 2 approval

The Arts & Sciences Imaging Center and Markey Cancer Center Oncogenomics Shared Resource Facility (a part of the UK HealthCare Genomics Core) announce the establishment of the UK Single Cell Researchers Network.  The goal of the scRN is to serve as a community resource and user forum for investigators across campus to learn and share experiences and expertise with single cell analysis methods.  Both current and potential users of single cell techniques are encouraged to participate.  We anticipate periodic group meetings several times per year.

Please join us for our first meeting:


Planning a Single Cell RNA-seq Experiment Monday, September 30 at 12 Noon Nursing Bldg 502A (


Single Cell Solutions for Genomics, Transcriptomics, and Epigenomics

Keith Cockrum, Technical Sales Specialist, 10x Genomics

Wednesday, June 5 at 2:00PM

Jacobs Science Building, Room 221

The ability to recover and individually barcode nucleic acids from single cells for high throughput sequencing analysis is a powerful new tool with many applications. The technology allows researchers to characterize and profile gene expression in hundreds to tens of thousands of single cells, sequence paired, full-length B-cell or T-cell repertoires, or profile hundreds to thousands of single cell genomes to reveal genome heterogeneity and understand clonal evolution. Technical Specialist Keith Cockrum from 10x Genomics, a world leader in development of this technology, will provide an introduction to single cell

The 10x Genomics Chromium is a microfluidics instrument that partitions single cells into nanoliter emulsions, allowing isolation of nucleic acids from individual cells. The Arts & Sciences Imaging Center now offers preparation of single cell cDNA libraries ready for RNA-seq on Illumina instruments. Please see Instrumentation & Services pages or inquire for more information.

(Image courtesy of Jeff Chalfant)

The sea lamprey is unusual amongst vertebrates for a number of reasons. One of the most surprising features is its elimination of about 20% of its entire genome in most of its embryonic cells. The lab of Jeramiah Smith in the Biology Department is examining this fascinating phenomenon. The loss of chromosomes can be observed in the mitotic figures of somatic cells during early embryogenesis. In the video and in yellow boxes of the single image, chromosomes that are in the process of being eliminated are seen lagging behind the retained chromosomes in some of the dividing cells. Here, early lamprey embryos were collected, fixed, and the DNA stained using Syto21. Stained embryos were cleared in RIMS, embedded in agarose and imaged by LSFM using the Zeiss Lighsheet Z.1. The entire embryo is approximately 1000 microns in diameter.

The unique optical design used in light sheet fluorescence microscopy (LSFM) (aka SPIM ) allows for imaging of very thick specimens at much greater speeds than other fluorescence microscopy methods. Recent advances in tissue clearing methods have made it possible to perform such imaging on samples that are naturally opaque. Tissues such as whole rodent brains can be rendered clear, labelled with fluorescent markers or antibodies, and imaged intact.  As opposed to sectioning, all relational and positional information is retained, making it possible to see the three-dimensional relationships of cells and structures within the tissues.  Imaging a cleared mouse hemi-brain can be performed in about an hour, many times faster than confocal microscopy.

Thanks to the Office of the VPR, we are now able to offer optimized cleared sample imaging for the Zeiss Lightsheet Z.1.

The Arts & Science Imaging Center now offers preparation of biological samples for TEM (Transmission Electron Microscopy). Please see Instrumentation & Services pages or inquire for more information.

(Image courtesy of Robin Cooper and Andrew Johnstone)

Arts &Sciences Imaging Center, 158 Jacobs Science Building

The Arts & Sciences Imaging Center invites UK researchers to participate in a workshop and demonstration using the Zeiss Lightsheet Z.1 to image cleared fluorescent samples.  Because of the high speed and excellent sample penetration, light sheet microscopy is ideally suited to imaging of thick, optically clear fluorescent specimens.  New clearing methods for biological samples, such as CLARITY, have made it possible to image specimens that are otherwise opaque.  During the workshop, Zeiss technical specialist Courtney Akitake will mount and image cleared specimens provided by participants.  Reservations are not necessary to observe sample mounting and imaging or to speak with the Zeiss representative.  Observers are welcome to come

The egg of the fruit fly, Drosophila melanogaster, is constructed through the coordinated efforts of many cells.  The nurse cells, whose large nuclei can be seen in purple, maintain connections with each other and the oocyte through ring canals (blue circles).  These bridges allow nurse cells to dump their products into the oocyte at maturation.  The follicle cells are smaller and surround the outside of the egg chamber.  Their nuclei are visible as small round purple structures.  The follicle cells mediate yolk deposition in the egg and create the eggshells.  Polar cells (green) are a specialized pair of follicle cells at the anterior (left) and posterior (right) of each egg chamber.  These polar cells organize and determine fates of the other follicle cells.  Anterior polar cells also form extensions that create a channel in the egg