Microscopy

Housed within the Institute for Molecular Bioscience (IMB), the Australian Cancer Research Foundation (ACRF) funded Cancer Biology Imaging Facility (CBIF) supports advanced methods in optical microscopy, including laser scanning and spinning disc confocal microscopy, deconvolution, high-throughput multi-well imaging, and large sample imaging.

The facility is home to 23 high-performance microscopes and supporting image data analysis workstations (with relevant visualisation and analysis software packages), with facility staff on-site to provide users with expert technical support and training.
With such a breadth of equipment and capabilities, the IMB Microscopy core facility welcomes users from within UQ as well as the greater community to contact us about utilizing the following resources.

Techniques and services

• Manual and automated brightfield and multi-channel fluorescence microscopy
• Confocal laser scanning microscopy
• Rapid, live-3D imaging (from molecules, cells to whole organisms)
• High-throughput imaging and analysis of multi-well plates and dishes
• Super-resolution imaging (STED ~30nm XY resolution, Airyscan ~120nm XY resolution)
• Large sample imaging
• SPIM (selected plane illumination / light-sheet microscopy)
• TIRF (total internal reflection fluorescence)
• FLIM (fluorescence lifetime imaging microscopy)
• FRET (Förster resonance energy transfer)
• FRAP (fluorescence recovery after photobleaching)
• 2-photon imaging (for deep tissue imaging or SHG)
• Image processing and analysis including automation in ImageJ/FIJI & commercial packages
• 3D printing (and design) of custom microscopy parts and sample holders
• Data visualisation (3D, 4D and in virtual reality)
• Consulting on sample preparation, image analysis pipelines, and big data storage
• Presentations of image analysis and processing training workshops

Equipment

23 instruments available, including:

 

3x Zeiss LSM710, 1x Zeiss LSM880, 1 x Zeiss LSM990 confocal laser scanning microscopes

• Upright and inverted
• 405, 458, 488, 514, 561, 594, 633nm and NIR 2Photon laser lines
• Fast Airyscan detectors for 120nm XY super-resolution imaging
• GaAsP photodetectors for imaging of dim or sensitive fluorphores
• Ideal for most imaging requirements
• Full environmental control (temperature & CO2)

Leica SP8 STED 3X confocal laser scanning microscope

• 405, 445nm, white light laser 467-670nm lasers
• STED super-resolution imaging to 30nm XY, 80nm Z
• Resonant scanning
• Falcon FLIM/FRET
• Lightning deconvolution
• Navigator
• Ideal for super-resolution and FLIM imaging
• Full environmental control (temperature & CO2)

Andor Dragonfly spinning disc confocal microscope

• Dual Andor Zyla 4.2 CMOS 100fps cameras
• 405, 440, 488, 514, 561 and 640nm laser lines
• TIRF module for imaging surface adhesions
• Ideal for developmental biology time-lapse imaging
• Full environmental control (temperature & CO2)

CREST X-Light v3 spinning disk confocal microscope

• Single and multi-well sample formats
• Confocal and Widefield modes
• Photometrics BSI Express 95% QE sCMOS Camera
• 405, 450,477,518,545,639,750nm laser lines
• Ideal for immunofluorescence and live cell imaging

3i Lattice Light-sheet microscope

• Dual flash 4.0 CMOS cameras
• 440, 488, 560 and 640nm laser lines
• 3D volumes acquired in under a second (100fps)
• Superior axial resolution compared to conventional light-sheet microscopes
• Ideal for multi-colour, high speed, long duration, time-lapse microscopy

Nikon inverted deconvolution microscope

• 4Mp sCMOS monochrome camera
• Detection of DAPI, CFP, GFP, YFP, mCherry, A594, Cy5
• Single and multi-well sample formats
• Maximum framerate: 1000fps (2048x100)
• Ideal for immunofluorescence and live cell imaging
• LIDA light source for high-speed colour brightfield
• Full environmental control (temperature & CO2)

Zeiss Inverted deconvolution microscope

• 4Mp BI sCMOS monochrome camera
• 5Mp colour camera
• Detection of DAPI, CFP, GFP, YFP, mCherry, A594, Cy5, Cy7
• Single and multi-well sample formats
• Maximum framerate: 500fps (2048x100)
• Apotome.2 for optical sectioning
• Ideal for immunofluorescence and live cell imaging
• Full environmental control (temperature & CO2)

OPT and Light-sheet Microscopy

• Optical projection tomography microscope
• openSPIM Light-sheet microscope
• Ideal for imaging whole cleared embryos and organs

Zeiss upright Apotome microscope

• 5Mp monochrome and colour cameras
• Detection of DAPI, CFP, GFP, YFP, mCherry, A594, Cy5, Cy7
• Ideal for immunofluorescence and brightfield slide scanning

Various stereo, upright and inverted widefield microscopes

• Ideal for brightfield/phase contrast/DIC and fluorescence

Image analysis servers

• 3x Dell r740 1-1.5TB RAM, 3xV100 16GB VRAM GPUs, 2x28 Core CPUs
• 2x AMD 96 and 128 core CPU, 2TB RAM, 3xA40/L40s 48GB VRAM GPUs

Image analysis software

• Imaris, Arivis, Amira, Huygens, Microvolution, Zeiss Zen, Nikon NIS-Elements, Leica

HPC Analysis Software

• Bespoke website GUI for ease of use
• Multi-GPU image deconvolution for widefield, confocal & Light-sheet modalities (Microvolution)
• Parallelised batched file conversion

Contact

Life Science and Soft Matter Electron Microscopy

The Life Science & Soft Matter Facility is located on the ground floor of the Australian Institute for Bioengineering and Nanotechnology (AIBN) building. This purpose-built laboratory houses two state of the art transmission electron microscopes, a serial blockface scanning electron microscope and two Focussed Ion Beam Dual Beam scanning electron microscopes plus a range of sample preparation facilities. In addition, the laboratory is equipped with a benchtop scanning electron microscope and a sophisticated optical microscopy suite including a laser microdissection confocal.

Equipment

• FEI Apreo – High resolution FESEM with a VolumeScope Serial Block Face System
• FEI Scios FIB – Dual Beam SEM
• Hitachi HT7700 120kV TEM (x2)
• Hitachi NX5000 ETHOS FIB-SEM
• Hitachi TM4000 plus SEM
• Zeiss Sigma Cryo SEM

Contact

Services

The Hawken laboratory houses electron microscopes, electron beam lithography and novel imaging instruments.  There are a series of scanning electron microscopes that can examine a very broad range of sample types.  Many of these instruments are capable of microanalysis using a wide variety of techniques. The laboratory houses a microprobe instrument that provides quantitative elemental analysis from polished specimens.

Equipment

• JEOL JSM-7800F SEM EDS & EBSD
• JEOL JSM-7100F SEM EDS
• JEOL JXA-iHP200F EPMA/Microprobe
• JEOL JXA-8200 EPMA/Microprobe
• Hitachi SU3500 SEM EDS x2
• Hitachi HF5000 TEM EDS & Diffraction & EELS
• Olympus DSX1000 Digital Optical Microscope

(For more CMM equipment located at Hawken Labs, see Mass Spectrometry and Nanofabrication)

Contact

The X-ray Analysis and Particle Characterisation lab at CMM is based on level two of the Chemistry building.

We provide a range of X-ray techniques, including diffraction, scattering, spectroscopy and imaging, for studying chemical composition, nano-scale size and crystalline phases in a range of materials. In addition we also have capabilities for particle characterisation, including size and shape analysis and interfacial tension/contact angle. We can also provide access to some partner instruments outside CMM. Please consult the instrument list below, or contact the lab manager if you don’t see the instrument you are looking for here, and we will do our best to direct you to the correct contact.

The lab provides complementary techniques to the electron-based methods afforded by the AIBN, QBP and Hawken Laboratories and to the macromolecular diffraction facilities in the QBP laboratories through small-angle scattering and small-molecule diffraction techniques.

Equipment

X-ray instruments:

• Bruker D8 Advance Powder XRD
• iXRF ATLAS X XFM
• Kratos Axis Supra Plus XPS
• Rigaku Smartlab Thin-film and Micro-diffraction XRD
• Xenox Xeuss 2.0 SAXS

Particle Characterisation Instruments:

• Microtrac Sync, equipped with Flow Sync wetmodule and TurboSync dry module
• Kruss Droplet Shape Analysis
• Malven Zetasizer Ultra
• Malvern Zetasizer 3000
• NanoFCM NanoAnalyzer

Contact

Located in the Queensland Bioscience Precinct, the Structural Biology facility is a laboratory that was purpose-built for standard and cryo-TEM sample preparation and analysis, as well as electron tomography of both resin-embedded and cryo-samples (for three-dimensional analysis).

Equipment

• 2x automated Cryo-Field Emission TEMs with energy filter and Gatan K2/K3 direct detectors: JEOL-Z200FCS Cryo ARM and JEOL-Z300FCS Cryo ARM
• FEI GLACIOS-2
• JEOL JEM-1400FLASH
• Refeyn-One optical mass photometry system
• A BalTec HPM010 high-pressure freezing system
• Two plunge freezing systems FEI Vitrobot MK-IV and Leica EM-GP2
• Diener Femto plasma cleaner
• Leica EM UC6 Ultramicrotome with FC6 cryo-box & Leica EM Crion antistatic controller

(For more equipment in CMM QBP labs see Protein and Small Molecule Crystallography)

Contact

Services

SCMB provides a wide range of microscopy, imaging equipment, and image analysis workstations.
The facility has four confocal laser scanning microscopes (one with super-resolution) and a high-end inverted research epifluorescent microscope housed within PC2 facilities. A high-end upright research epifluorescent microscope and laboratory-grade microscopes are also available.

Fluorescence microscopy is a research technique in optical microscopy that relies on the excitation of fluorescent molecules with a specific wavelength region to produce an image generated by the secondary fluorescence emission at longer wavelengths. Confocal microscopy is a precision mode of optical microscopy in which a focused laser beam at a defined wavelength is scanned laterally along the x and y axes of a specimen in a raster pattern. Single photons emitted away from the focal plane are blocked by a pinhole aperture located in a plane confocal with the specimen.

Full specifications and capabilities of SCMB imaging equipment can be obtained from the Facility Manager. The SCMB Microscopy and Imaging Facility is available to SCMB users as well as all UQ staff and students.

Equipment

• ZEISS LSM510 META upright confocal microscope with 3xPMT’s and AxioCam colour imaging camera
• ZEISS LSM510 META inverted confocal microscope with 3xPMT’s and AxioCam MRm imaging camera
• ZEISS LSM710 inverted confocal microscope with 3xPMT’s and environmental chamber (temperature and CO2 control)
• ZEISS LSM900 upright confocal microscope with 2xPMT’s plus Airyscan2 for super-resolution and multiplex imaging
• Nikon Ti2 high-end motorised research-class optical microscope with SPECTRA X LED 7 line illumination system, environmental chamber and Digital Sight 50M Microscope Camera (PC2 room with BSCII and CO2/O2 incubator available)
• ZEISS AxioImager.M2 high-end, motorised, research-class microscope with Colibri 7 LED Illumination system for epi-fluorescence, colour and mono cameras, and Apotome.2 for 3D optical sectioning
• Dedicated workstations for image visualisation, manipulation, and analysis – software includes Imaris, ZEISS advanced deconvolution and ZEISS Intellesis
• Nikon TS100 inverted bright-field and epi-fluorescent microscope with colour imaging system
• Nikon Ts2 inverted bright-field microscope with colour imaging system
• Nikon stereo dissecting microscope with imaging camera

Contact

Services

• Single-photon and two-photon scanned light-sheet microscopy
• Super-resolution microscopy (SIM, PALM/STORM/sptPALM)
• Two-photon laser-scanning microscopy
• Confocal laser-scanning microscopy
• Spinning disk confocal microscopy
• Bright-field and wide-field epifluorescence microscopy
• Slide scanning
• Stereology
• Calcium imaging
• FRAP
• TIRF, FLIM, FRET
• Image processing and analysis: Huygens Professional, Imaris, Amira, Neurolucida 360, ImageJ/FIJI, ilastik, CellProfiler, ZEN, NIS Elements

Equipment

• Custom-built single- and two-photon scanned light-sheet microscope
• Zeiss LSM 710 two-photon laser-scanning microscope
• Zeiss LS M510 META laser-scanning confocal microscope
• Zeiss Elyra PS.1 SIM/PALM/STORM
• Roper iLas2 sptPALM
• Andor Diskovery spinning disk confocal microscope
• 3i Yokogawa W1 spinning disk confocal microscope
• 3i Marianas TIRF FLIM FRET
• 2 x MetaSystems bright-field and fluorescence slide scanners
• MBF stereology microscope
• 4 x Zeiss Axio Imagers for bright-field and wide-field epifluorescence
• 2 x Zeiss Axio Observers for live-cell and high-speed imaging
• Zeiss StereoDiscovery V8 stereomicroscope
• Nikon Ti Eclipse wide-field epifluorescence microscope

Contact

Services

Self and full service:

• Confocal microscopy
• Multiphoton microscopy
• Digital deconvolution
• Epifluorescence microscopy
• Automated data analysis
• Stereology
• Image analysis functions development

Equipment

• Diskovery Spinning Disk Confocal Microscope
  High-speed multi-channel fluorescent confocal imaging, with live cell and super-resolution TIRF and STORM capabilities. The instrument can also act as a high-content imager for screening applications.
  • STORM super-resolution, TIRF Imaging
  • 405, 445, 488, 561, 633nm laser lines
  • Andor iXon888 EMCCD and sCMOS monochrome cameras and a Nikon sCMOS colour camera
• 2x Leica DMi8 SP8 Inverted Incubated Point Scanning Confocal Microscope
  Leica SP8 modules, perfect for multi-colour imaging, spectral unmixing and scanning, 3D imaging of sections, 96 well plate imaging, live cell imaging, FRET and FRAP.
  • 8 lasers, 6 detectors (3 HyD ultra-sensitive detectors)
  • 12k resonant scanner
  • Incubated for live cell applications
• Aperio XT slide scanner for bright field slide scanning
  Used to digitalise traditional histochemically stained tissues mounted on microscope slides. 20x and 40x magnifications with 120-slide capacity.
• Zeiss AxioScan Z1 Fluorescent Imager
  ​​​​​High Speed and Throughput Brightfield and Fluorescent Slide Scanner that is able to perform imaging of histological sections in a fully automated manner. Fluorescent imaging combines speed, gentle treatment and the optimal wavelength to perform true multispectral fluorescence imaging.
  • 100 automated slide scanning
  • 7 high powered LED light sources, 355nm, 430nm, 488nm, 561nm, 594nm, 640nm, 720nm
  • Pentaband emission filters to allow high speed imaging with no moving parts during acquisition
  • Ultra-sensitive sCMOS Hamamatsu Flash 4 monochrome camera
• Zeiss Upright Stereology microscope for Bright Field Neuron training and cell counting
• Nikon Eclipse Upright Fluorescent Slide scanner and Stereology Microscope with MBF Neurolucida and MBF Stereoinvestigator Software
  Fully automated fluorescent microscope with installed Stereoinvestigator and Neurolucida software (https://www.mbfbioscience.com/webinars) enables accurate cell counting and neuron tracing of brightfield and fluorescently stained samples. Installed NIS-Elements software also allows fluorescent slide imaging and automated image capture.
• Zeiss PALM Laser ablation and capture microscope
  PALM MicroBeam is designed to give you advanced laser microdissection capabilities. Suitable for laser microdissection, sample capture, and analysis for DNA, RNA, and protein isolation from archive material or live cells.
  • A system that completes the step from laser-microdissection to integrated imaging workstation - Applicable to cryosections, FFPE (formalin fixed and paraffin embedded) tissue
  • Performing LCM even from standard glass slides, e.g. archived material, with ZEISS-patented sample capture technology
  • Extendibility – add digital cameras from the AxioCam camera range for fluorescence, bright field, multi-channel fluorescence and extended focus
  • Ability to integrate additional components into MicroBeam and create simple workflows, whether for individual experiments or automation with flexible collectors
    • Calibration routines that allow you to easily adjust MicroBeam for laser parameters appropriate to your chosen specimen. PALM MicroBeam uses a focused laser beam to cut out and isolate your selected specimen without contact. The patented laser catapult isolates your target area fast and uncontaminated
• Leica DMi8 Live cell high content imaging system and high-speed fluorescent slide scanning
  High-speed multi-channel fluorescent imaging with rapid stage movement, enabling whole 96-well plates to be imaged. Deconvolution software enables the creation of confocal-quality images and increased resolving power.
  • 7 colours using a SpectraX LED light source: 390, 438, 475, 510, 542, 575, 633nm
  • Andor Zyla sCMOS camera system, Leica colour camera
  • Incubated for live cell work
  • Software for plate scanning and high-content imaging
• Leica M205FA Fully automated fluorescent stereomicroscope
  Suitable for fluorescent and brightfield imaging and the recording of instructional videos for teaching and training. Used to create macro-images of whole animals.
• Nikon fluorescent automated microscope
  Fast scanning stage, multi-fluorescent illumination sources. NIS-Element AR software for image acquisition.
• General upright and inverted fluorescent microscopes with CCD and sCMOS cameras
• 2x Zeiss 510 inverted confocal microscope, 1x multiphoton laser source
• Nikon electrophysiology upright microscope with Andor Mosaic light module for FRAP and FRET, SpectraX high-speed illumination and EMCCD Andor iXon888 camera
• Imaris licences 2x floating for image data analysis
• Amira licence for data analysis 1x floating
• Huygens deconvolution software
• Neurolucida 360
• Tissue Maker software – 3D image reconstruction
• Dedicated Cloud-based supercomputers with Volta GPU cards, 15000 core processors, 1T RAM and 200T of storage space

Contact

Services

The Translational Research Institute (TRI) offers outstanding microscopy facilities and expertise. We are available to assist with equipment selection, training, inductions, operation, optimisation and advice on how to get the best images from your samples, as well as subsequent image analysis.

Equipment

The following equipment is available to all users as part of the 'Core Facilities at TRI':

• Nikon 50i upright brightfield microscope
• Nikon Cres-Optics Spinning Disc confocal microscope with DeepSIM Super-resolution
• Zeiss AxioObserver 7 widefield live cell imaging microscope
• Zeiss LMS 980 upright confocal with Multi-photon laser and AiryScan 2 Super-resolution
• Olympus VS120 brightfield slide scanner (full service)
• Olympus VS200 brightfield and fluorescence slide scanner (full service)
• Olympus BX63 upright motorised fluorescence microscope
• Olympus IX73 inverted manual fluorescence microscope
• Olympus FV3000 inverted confocal microscope (x2)
• Olympus OLS4100 laser surface scanner
• Tissue Gnostics TissueFAXS SL spectral slide scanner (full service)
• Phasefocus Livecyte live cell holographic imaging system
• Sartorius S3 and SX5 Incucyte live cell imaging system
• Revvity Operetta high content imaging system
• Suite of high spec analysis workstations with software packages including Imaris, ZEN, NIS Elements-ai, StrataQuest as well as ImageJ and QuPath.

Contact