Instruments & Services

Light sheet fluorescence microscopy (LSFM) is an imaging method that uses one or more illumination objectives to excite fluorophores in a specimen with a thin sheet of light, which are then visualized with a separate imaging objective perpendicular to the sheet. LSFM has several advantages over confocal microscopy, including:

• Excellent sample penetration
• High speed
• Minimal phototoxicity and photobleaching

These properties make LSFM ideal for many biological imaging applications, including:

• Fluorescence imaging of thick samples
• Long-term imaging of live samples

The Zeiss Lightsheet Z.1 includes several additional features to optimize LSFM:

• Four-axis sample positioning permits rotation of the specimen for easy viewing from any angle.
• Multiview acquisition allows the same tissue to be imaged from multiple perspectives, then integrates these views for optimal resolution and accurate rendering.
• Two illumination objectives, one on each side of the sample chamber, enhance even illumination of the specimen.
• Pivot scanning slightly rotates the sample during acquisition to eliminate shadowing and striping artifacts observed in other systems
• Cleared tissue optics (5x objective) designed for CLARITY and similar clearing techniques (RI=1.45)

For more information about LSFM imaging methods, visit MicroscopyU and for details about the Lightsheet Z.1, visit the Carl Zeiss Microscopy. To discuss whether light sheet microscopy would be of benefit for your application, please contact us for a free consultation.

System specifications:

The Zeiss LightSheet Z.1 Dual Illumination Microscope System is ideally suited for imaging of thick and/or live specimens, because it uses separate illumination and detection light paths to minimize photobleaching and phototoxicity and maximize imaging depth. The 4-axis sample positioning system allows imaging from any perspective and Multiview acquisitions increase axial resolution. The system features two illumination objectives and uses ultrafast pivot scanning to reduce shadowing artifacts. The system includes temperature and CO₂ environmental control of the sample chamber. Solid-state lasers provide excitation lines at 405, 445, 488, 515, 561, and 638nm, with simultaneous two channel detection using PCO.edge 16-bit sCMOS cameras.  Imaging objectives include 5x dry and 20x and 40x water immersion lenses, with 2.5x system optical zoom, yielding effective magnifications of 2x-100x. Optics for cleared tissue imaging using a 5x objective are designed for a refractive index of 1.45, matching that used in CLARITY and similar techniques. Image acquisition and basic manipulation is performed with Zen software, that also integrates with Arivis Vision 4D for rendering and analysis. A separate workstation is available for these analyses.

The VAST Bioimager with Large Particle Sampler from Union Biometrica is an automated system for loading objects up to 700 microns into an imaging capillary and collecting a series of user defined images. Images may be captured by the positioning camera or using transmitted light or fluorescence modes at high resolution on the Zeiss AxioExaminer. The system was specifically designed for rapid automated imaging and screening of zebrafish. Fish may be loaded automatically in bulk from a 50ml conical tube or microtiter dishes using the LP Sampler or may be loaded individually using the handheld pipettor.

The Union Biometrica BioSorter Pro is a large object flow cytometer designed to sort objects beyond the capacity of standard FACS.  The instrument is capable of sorting objects based on fluorescence or size and, with the 1000 micron flow cell, easily accommodates specimens up to approximately 700 microns in size. The BioSorter is ideal for sorting intact small animals, such as zebrafish embryos and larvae, Drosophila embryos and larvae, C. elegans, small tissues, and organoids.

The 10x Genomics Chromium is a microfluidics device capable of partitioning single cells into nanoliter emulsions for transcriptomic and genomic analyses. The CGI Core offers full-service processing of single cells into bar-coded cDNA libraries ready for sequencing on an Illumina platform. The service includes:

• Evaluation, quantification, and viability assessment of cells for input
• Single cell capture of desired target number of cells (500-20,000)
• Generation and amplification of single cell cDNAs
• Construction of Illumina sequencing-ready libraries of cDNA
• Quality assessment and quantification of libraries

Note that services do NOT include Illumina sequencing or bioinformatic analysis. Sample processing must be scheduled at least two weeks in advance. Please contact us for more information or to schedule a consultation about a project.

The 10x Genomics Visium and Visium HD platforms power the interrogation of transcription within the spatial context of intact tissues. Starting with sections from frozen, fixed frozen, or FFPE tissues, the entire transcriptome is probed or captured onto a 6.5 x 6.5mm lawn of 55 micron spots (Visium) or 2 micron squares (Visium HD) for spatial barcoding and library generation. The services include:

• H&E staining and imaging of tissue sections
• Capture of transcripts onto Visium slides using the CytAssist instrument
• Generation of Illumina sequencing-ready libraries from captured transcripts
• Quality assessment and quantification of libraries

As with single cell, services do NOT include Illumina sequencing or bioinformatic analysis. Please contact us for more information or to schedule a consultation about a project.

The core has partnered with the Markey Cancer Center Oncogenomics Shared Resource Facility to create the University of Kentucky Single Cell Researchers Network, whose goal 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.  To receive news and announcements from the UK scRN, join the SingleCell email listserv.