TRI Microscopy core facility

The TRI has an outstanding microscopy facility including inverted fluorescence microscopes on most research floors and a fully equiped facility room of high end instruments. For analysis purposes, computers containing a range of analysis software are also available for use.  

The facility staff provides researchers with the training and knowledge to efficiently generate high quality reproducible images.

The facility is open to all users including external and commercial with the same charge rate.

Please contact m[email protected] for all enquiries.

CHARGES AND TERMS OF USE

To enquire about facility charges please email microscopy[email protected] or access the PPMS booking system.

FACILITY TERMS OF USE

EQUIPMENT AND SERVICES

 

Nikon Eclipse 50i Brightfield Microscope

Upright

Manual

Facility room 4026

Objectives: 4X, 10X, 20X, 40X, 60X and 100X Oil objectives

Camera/Detector: DS-Fi1 colour camera

Light Source: Halogen lamp for brightfield

Software: NIS-Elements Basic Research

Application: For slides only e.g. H&E, DAB and other histological stains

 

Olympus VS120 Slidescanner Microscope

Upright

Fully automated

Facility room 4026

Objectives: 2X (overview), 10X, 20X or 40X for actual scanning. Polarization also available

Camera/Detector: Allied Pike 505 colour camera

Light Source: Halogen lamp for brightfield

Software: VS-ASW

Application: For batch scanning up to 100 histologically stained slides. Service run by facility

 

Olympus IX73 Microscope

Inverted

Manual

Rooms 4035, 4066, 5026 and 6067

Objectives: 2X, 4X, 10X, 20X, 40X, 60X Oil

Camera/Detector: XM10 monochrome camera (room 4066, 5026 and 6067). DP73 colour camera in room 4035

Light Source: Halogen lamp for brightfield. Metal halide lamp for fluoresence (DAPI, GFP, CY3, CY5).

Software: Cell Sense

Application: For checking slides, dishes, plates, staining quality, transfection efficiency and taking simple images

 

Olympus BX63 Microscope

Upright

Motorised

Facility room 4026

Objectives: 4X, 10X, 20X and 40X, 60X Oil and 100X Oil

Camera/Detector: DP80 monochrome/colour camera

Light Source: Halogen lamp for brightfield. X-Cite LED for fluoresence (DAPI, GFP, CY3, CY5)

Software: Cell Sense

Application: Slides only, automated imaging of multiple colours and single slide tile scanning

Perkin & Elmer Vectra III Spectral Scanner Microscope

Upright

Automated

Facility room 4026

Objectives: 4X, 10X, 20X and 40X

Camera/Detector: Perkin & Elmer Spectral camera

Light Source: Halogen lamp for brightfield. Metal halide lamp for fluoresence (DAPI, GFP, CY3, CY5).

Software: Vectra, Phenochart, Inform

Application: Slides only, automated imaging of up to 6 slides, H&E, IHC, IF, OPAL stains. Spectral detection and separation of overlapping biomarkers.

Olympus IX81 Live imaging Microscope

Inverted

Motorised

Room 4024

Objectives: 1.25X, 2X, 4X, 10X, 20X, 40X, 60X Oil

Camera/Detector: Hamamatsu Orca Flash 2.8 monochrome camera

Light Source: Halogen lamp for brightfield. Metal halide lamp for fluoresence (DAPI, GFP, CY3, CY5)

Software: Cell Sense

Application: Slides, dishes, plates. For long term fast live imaging of cells/spheroids, etc. in multiple fluorescent colours plus brightfield, phase or DIC. Temperature and gas controlled.

Phasefocus Livecyte Live imaging Microscope

Inverted

Automated

Room 4024

Objectives: 4X (preview), 10X, 20X and 40X imaging

Camera/Detector: Monochrome sCMOS camera

Light Source: LED for brightfield and fluoresence (DAPI, GFP, CY3), 650nm laser for quantitative phase imaging

Software: Cell Analysis Toolbox and associated APPs

Application: Slides, dishes, plates. For long term ptychography and fluorescence live imaging of cells. Fully automated focusing and imaging. Adjustable QPI field of view. Temperature and gas controlled. Dedicated data processing unit and network storage.

Olympus FV1200 Confocal Microscope

Inverted

Motorised

Facility room 4026

Objectives: 4X, 10X, 20X, 40X, 40X Oil, 60X Oil and 100X Oil

Camera/Detector: 2 spectral and 1 filter PMT, 2 GaASP PMT and 1 transmitted light detector

Light Source: Halogen lamp for brightfield, metal halide lamp for fluoresence (DAPI, GFP, CY3). Lasers: 405, 473, 559, 635 and  748nm

Software: FluoView 10 ASW

Application: Slides, dishes, plates. For high resolution confocal imaging, Z-stacks, Mosaic, high-end imaging. Resolving power 250-350nm in X/Y and 500-700nm in Z

Olympus FV3000 Confocal Microscope

Inverted

Motorised

Facility room 4026

Objectives: 4X, 10X, 20X, 40X, 40X Oil, 60X Oil and 100X Oil, 30X and 60X Silicone Oil

Camera/Detector: 4 GaASP spectral PMTs and 1 transmitted light detector

Light Source: LED for brightfield, metal halide lamp for fluoresence (DAPI, GFP, CY3). Lasers: 405, 445, 488, 514, 561, 594 and 640nm

Software: FluoView 31S

Application: Slides, dishes, plates. For high resolution, confocal imaging, Z-stacks, Mosaic, high-end imaging. Resolving power 250-350nm in X/Y and 500-700nm in Z. Includes a hybrid resonant/galvonometer scanner for faster imaging and a stagetop incubator

Nikon/Spectral Spinning Disc Confocal Microscope

Inverted

Motorised

Facility room 4026

Objectives: 4X, 10X, 20X, 40X, 40X Oil, 60X Oil and 100X Oil

Camera/Detector: Andor Clara CCD camera 1392 x 1040, 6.45x6.45um pixel size , 11fps. Photometics Evolve Delta EMCCD camera 512 X 512, 16X16um pixel size, 33.7fps.

Light Source: Halogen lamp for brightfield, LED for fluoresence (DAPI, GFP, CY3). Lasers: 405, 445, 514, 488, 561 and 640nm.

Software: NIS-Elements Advanced Research

Application: Slides, dishes, plates. For high resolution, fast, confocal imaging, Z-stacks, Mosaic, high resolution intra cellular live imaging. Temperature and gas controlled. 355nm laser ablation system from Roper, TIRF imaging

Olympus LEXT OLS 4100 Microscope

Upright

Motorised

Facility room 4026

Objectives: 5X, 10X, 20X, 50X, 50X Long Working Distance, 100X

Camera/Detector: High sensitivity PMT

Light Source: 405nm laser

Software: OLS LEXT Software

Application: For measuring surface features of materials up to 10nm resolution

Multiphoton Microscope

Upright and Inverted

Motorised

Facility room 4026

Objectives: 16X, 40X and 20X

Camera/Detector: 4 High sensitivity PMTs

Light Source: Tunable emission laser 690-1040nm. OPO included to modulate output wavelength to IR spectrum (Optical Parametric Oscillator)

Software: LaVision Biotek software, Imspector and Imaris on floating license

Application: Deep imaging into samples (up to 2mm), Live imaging of mice or ex-vivo organs at the cellular level. Wide variety of dyes and fluorophores can be imaged. Supports two Nikon microscopes: Eclipse Ti-U inverted and Eclipse FN1 upright microscopes. Run by a Spectra Physics Ti:Sapphire pulsing. The Inverted microscope has a fully motorized X/Y/Z stage. Has a 64 beam splitter attached as well as high speed camera. Options also include 5 PMTs (including one ultrasensitive) and a selection of filters for flexibility. The upright microscope is fitted with a Z-motorised intravital stage, 4 PMTs (including ultrasensitive), and a wide selection of filters.

Peripheral equipment include oral anaesthetic for mice, warming blanket and monitoring equipment. Heated chamber as well as heated deep chamber to accommodate whole ex-vivo organs with gas perfusion including CO2 and/oxygen.

Access is limited by facility manager and prior arrangements made for use.

GE Healthcare OMX Blaze 3D Structured Illumination Microscope (SIM)

Inverted

Motorised

Facility room 4026

Objectives: 60X Oil

Camera/Detector: 2 sCMOS Cameras Custom liquid cooled, 15 bit, 5.5 Megapixel chip, 6.45 um pixels (3D-SIM operation at 512 x 512, Widefield operation 1024 x 1024)

Light Source: 405, 488 and 568nm lasers

Software: Deltavision OMX for acquisition and a separate reconstruction computer with SoftWoRx

Application: Structured illumination super-resolution microscope. Uses a frequency based interference pattern, unique deconvolution algorithms. When better resolution is needed to discern colocalisation or to resolve fine structures than that seen in confocal microscopy

90-130nm in X/Y compared to 180-250nm X/Y confocal

250-350nm in Z compared to 500-700nm Z in confocal

 

Analysis Software

4 physical computers + 2 virtual machines

Free software:

 
Image J / Fiji Freely available, open sourced, java based image processing software. Great for image processing and analysis with many useful plugins e.g. Bio-Formats Importer for opening proprietary files
OlyVIA Freely available viewing software for Olympus files (VSI, OIF, OIR, etc.) including the virtual slide files from the VS120 slide scanner, timelapse data from the IX81 live imaging microscope, etc.
FV10 Viewer / FV31S Viewer Freely available viewing software for the FV1200 OIF files and the FV3000 OIR files
NIS-Elements Viewer Freely available software for viewing Nikon ND2 files
 

Licensed Software:

 
NIS-Elements Advanced Research Nikon's acquisition and analysis software. Powerful software capable of image segmentation, measurements, tracking, morphology, counting, etc.
Visiopharm Automated trainable analysis software for batch whole section/slide analysis.
Cell Sense Olympus's acquisition and analysis software including Olympus's deconvolution.
Phenochart/Inform Perkin and Elmer's image analysis software for the spectral images from the Vectra 3.0 microscope.
Spotfire Tibco's data analysis software used mainly for extracting data genereated from Inform.
Cell Analysis Toolbox + associated APPs Phasefocus's analysis software for quantifying the QPI timelapse data acquired on the Livecyte microscope. Virtual machine access via remote connection.
Imaris Bitplane's powerful analysis software. Can open almost every proprietary file type and great at opening large files. Can view and render 3D datasets, automated tracking of cells from live imaging datasets. One physical computer and one virtual machine.

access to the facility

The Booking system is available at https://ppms.int.tri.edu.au/start/
New or unregistered users need to request an account via https://ppms.int.tri.edu.au/start/

For any queries regarding this system, please contact: [email protected]

If you cannot book the instrument you want:
Instruments cannot be booked until a certificate has been issued. The certificate represents your level of training/expertise on a particular instrument.  Contact the TRI Microscopy team for further information on ext: 37772 or email m[email protected]  

Microscopy Club

The Microscopy Club launched in September 2017 to bring together the collective knowledge and experience of those using the Microscopy Facility at TRI. See what was covered at the first Microscopy Club meeting here or stay tuned to the weekly events email for details about upcoming sessions. 

> News: Introducing the TRI Microscopy Club