UBC Centre for High-Throughput Phenogenomics

The University of British Columbia, Vancouver, British Columbia
Area(s) of Expertise

The Centre for High-Throughput Phenogenomics offers a comprehensive suite of imaging technologies. Its broad goal is to provide two- and three-dimensional information and structural analysis of specimens using scanning electron microscopy, optical imaging, X-ray imaging and mass spectroscopy. The Centre is a fee-for-service core facility, and welcomes collaborative, interdisciplinary research projects from across universities, research organizations and corporate users.

What the facility does

High-resolution imaging of biological and materials science specimens and in vivo models.

Research Services

Specimen micro-CT imaging, in vivo micro-CT imaging, optical projection tomography, confocal microscopy, fluorescent microscopy, laser dissection microscopy, MALDI mass spectroscopy, scanning electron microscopy (with focused ion beam milling/ crystalline structure and analysis), sample preparation, image analysis

Sectors of Application
  • Automotive
  • Clean technology
  • Energy (renewable and fossil)
  • Fisheries and aquaculture
  • Life sciences, pharmaceuticals and medical equipment
  • Manufacturing and processing
  • Mining, minerals and metals

Name of specialized lab

Name of equipment in use

Description of function

Scanning Electron Microscopy Imaging

FEI Helios Nanolab 650 Dual Beam

A state-of-the-art scanning electron microscope designed for 2D and 3D surface characterization at nanometer resolution.  Electron backscatter diffraction (EBSD) and Energy dispersive spectroscopy (EDS) detectors provide elemental analysis and crystal structure characterization.  The focused ion beam can mill and view in 50 nm slices to create 3D reconstructed images of the sample.

 

Hitachi SU3500

The variable pressure tungsten filament emission instrument has the capability for 7 nm lateral resolution at 3 keV for SE imaging and 10 nm at 5 keV for BSE imaging.  Also, this machine is very suitable for imaging specimens at relatively large working distances (65 mm—resulting in a large depth of field), high tilt angles (up to 90°), and an observation area of 130 mm.

Mass Spectroscopy

MALDI Duo LTQ Orbitrap XL

A laser rasters across a tissue section and converts molecules into ions, which are then analyzed by mass spectrometry.  It can detect different classes of molecules (e.g. proteins, peptides, hormones, drugs, or metabolites) without affinity reagents or labels, and convert this information into a highly multiplexed image of their abundance and distribution in the tissue.

X-ray Imaging

Scanco Medical μCT 100

This micro-CT system provides 3D X-ray images of specimens up to 10 cm in diameter and 16 cm in length.  It can sequentially image up to 12 samples at high resolutions ranging from 5-100 μm.

 

TriFoil eXplore CT120

The TriFoil eXplore CT 120 is an in vivo micro-CT imaging system capable of resolutions ranging from 25-100 μm. Physiological gating can be used to capture rodent heart and/or lungs at specific points in the cycle.  The imaging field of view is 8.5 cm in diameter and up to 27.5 cm in length.

Optical Imaging and Microscopy

Zeiss Axioplan II Fluorescent Microscope

A standard fluorescence/light microscope with filter cubes for DAPI/Hoechst, Fluorescein/Alexa 488 and Rhodamine/Alexa Red fluorescence detection. The system has a Q Imaging Retiga monochrome camera with a colour slider.

 

Nikon Laser Confocal Microscope

Our Nikon Eclipse Laser Confocal Microscope allows high-resolution confocal imaging with blue/green/red fluors corresponding to 405, 488 and 543 nm.

 

Olympus LEXT OLS3100 Confocal Microscope

The Olympus confocal microscope allows for surface characterization and is ideal for imaging featureless or very low contrast surfaces as well as transparent surfaces such as ceramic or glass.

 

Leica  TCS SP5 X Confocal Microscope

The white light laser emits a broad spectrum of wavelengths between 470 to 670 nm for simultaneous tunable excitation and detection of multiple fluorophores.  Live cell imaging is also available with this microscope.

 

Zeiss PALM Laser Capture Microdissection and Imaging System

This system allows laser microdissection, excision and capture of areas of interest in cell culture & histological sections for microanalysis.  The system uses an Axio observer inverted microscope platform with light and fluorescence beam paths, Axiocam for imaging and a highly user-friendly Axiovision Zeiss software system.

 

Bioptonics Optical Projection Tomography Scanner 3001M

3D optical imaging of samples up to 1 cm X 1 cm X 1.5 cm in size using bright field or fluorescence imaging.  Three fluorescent channels are available: Texas Red, FITC Green or broad spectrum green.

Sample Preparation Instruments

Leica EM MED020 Coater

The Leica EM MED020 is a precision modular high vacuum coating system for sputtering and carbon thread, carbon rod, evaporation applications.

 

Buehler Cast N’ Vac 1000

 

This is a vacuum impregnation system for epoxy resin embedding for all sample materials, including temperature-sensitive samples.

 

Buehler Automet 250 Pro grinder/polisher

The Automet 250 Pro is a semi-automated grinder/polisher for producing very smooth polished surfaces.  The power head can accommodate single or multiple samples and the automated burst dispensing system improves productivity and consistency of the final polished surface.

 

BuBuehler VibroMet® 2 vibratory polpolisher

The VibroMet removes minor deformations following mechanical polishing for a variety of materials and applications, including EBSD.  

 

Tousimis Samdri® -795 Critical Point Dryer

The Tousimis Samdri® -795 is a semi-automatic critical point dryer with a chamber diameter of 3.2 cm and depth of 3.2 cm; it is capable of accommodating samples of various sizes with the accessories provided.

 

PELCO 3470 Hornet Microwave System

This microwave-assisted system is user-friendly and ideal for enhancing rapid processing of protocols including, but not limited to, tissue in electron microscopy, formalin and glutaraldehyde fixation, EDTA decalcification, paraffin tissue processing and special stain, immunolabelling, and confocal microscopy. 

 

Leica CM 1950 Cryostat

The Leica CM 1950 Cryostat is a microtome that produces frozen sections for biological, medical, and industrial applications. This cryostat is a high-performance cryostat with a frost-free, encapsulated microtome.  It features a UV disinfection system that is effective against most bacteria, viruses, and fungi, and an integrated vacuum extraction system for removing section waste.

Title

URL

CHTP Newsletter https://secure.campaigner.com/csb/Public/show/eondq--bnjrk-5kqw2nq0
NCOHR Summer Institute http://phenogenomics.dentistry.ubc.ca/news/2014/NCOHR/default.asp

Dentistry’s Imaging Facility Popular with UBC Scientists and Corporate Users, UBC Dentistry Impressions magazine Spring 2013 p12

http://www.dentistry.ubc.ca/impressions/documents/Impressions-Spring2013.PDF

New $10.1 M imaging facility will unlock medical, engineering secrets

http://www.publicaffairs.ubc.ca/2013/02/20/new-10-1-m-imaging-facility-will-unlock-medical-engineer…

Bioimaging Centre Moves to New Location and New Capability, UBC Dentistry Impressions magazine Fall 2012 p3

http://www.dentistry.ubc.ca/impressions/documents/Impressions-Fall2012.pdf

Bioimaging Equipment: It’s Here!, UBC Dentistry Impressions magazine Fall 2011 p4

http://www.dentistry.ubc.ca/impressions/documents/Impressions-Fall2011.pdf

New Home for Bioimaging Facility, UBC Dentistry Impressions magazine Fall 2010 p3

http://www.dentistry.ubc.ca/Impressions/documents/Impressions-Fall2010.pdf

Governments of Canada and BC Invest in UBC Dentistry’s Bioimaging Facility, UBC Dentistry Impressions magazine Fall 2009 p3

http://www.dentistry.ubc.ca/impressions/2009/fall/Impressions-Fall2009.pdf

Moving to the Forefront of Bioimaging : A new High-Throughput Centre at UBC Dentistry, UBC Dentistry Impressions magazine Fall 2009 p20-22

http://www.dentistry.ubc.ca/impressions/2009/fall/Impressions-Fall2009.pdf