UBC Centre for High-Throughput Phenogenomics

The University of British Columbia, Vancouver, British Columbia
What the facility does

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

Areas 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.

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
  • Fisheries and aquaculture
  • Life sciences, pharmaceuticals and medical equipment
  • Manufacturing and processing
  • Mining, minerals and metals
Specialized labEquipmentFunction
Scanning Electron Microscopy ImagingFEI Helios Nanolab 650 Dual BeamA 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 SU3500The 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 SpectroscopyMALDI Duo LTQ Orbitrap XLA 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 ImagingScanco Medical μCT 100This 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 CT120The 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 MicroscopyZeiss Axioplan II Fluorescent MicroscopeA 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 MicroscopeOur 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 MicroscopeThe 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 MicroscopeThe 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 SystemThis 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 3001M3D 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 InstrumentsLeica EM MED020 CoaterThe 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/polisherThe 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 polpolisherThe VibroMet removes minor deformations following mechanical polishing for a variety of materials and applications, including EBSD.  
 Tousimis Samdri® -795 Critical Point DryerThe 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 SystemThis 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 CryostatThe 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.