The ACRF Centre for Imaging the Tumour Microenvironment (CITE) integrates two high-end technology platforms: the Microscopy Platform and the Spatial Proteomics Platform. The Centre is committed to advancing our understanding of how tumours interact with, corrupt normal cells, and alter the surrounding microenvironment at the cellular and molecular levels. Equipped with cutting-edge instrumentation and analytical systems, CITE supports world-class research in cancer biology, tumour immunology, and the development of innovative therapeutic strategies.
Contact
If you would like to discuss opportunities to use our platform technologies and services, please contact:
Prof Sarah Ellis
Head, ACRF CITE Facility
Technologies
Embedding Station & Leica Blocking Centre
Embed tissue samples and cell pellets in paraffin wax ready for blocking and sectioning with a microtome.
- Embedding Station
- Station for Heating Cassettes
- Blocking Station
- Cold Plate
Microtomes
Cutting stations comprising a microtome and water bath for sectioning wax blocks from 2μm to 20μm
- Leica 2045
- Leica 2035
- Microtec CUT4055
Leica Cryostat CM1860 UV
Cut frozen tissue sections at sub-zero temperatures
Leica Vibratome
Cut thick sections of fresh or fixed tissue.
Olympus CKX53 Inverted Microscope
The Olympus CKX53 is ideal for imaging live cells in chamber slides or tissue culture plates.
Capabilities:
- Transmitted-light brightfield LED, phase contrast
- Filter Sets: DAPI, GFP, mCherry/TxRed & RFP
- Lumen Dynamics LED light source for epi-flourescence
- Long working distance objectives: 4x (NA 0.13), 10x (NA 0.25), 20x (NA 0.4), 40x (NA 0.55)
- Olympus DP27 colour camera
- CellSans standard software
Zeiss Inverted Axio Observer 5
The Zeiss Inverted Axio Observer 5 is ideal for imaging live cells in chamber slides or tissue culture plates.
Capabilities:
- Transmitted-light brightfield LED, phase contrast, and semi-motorised fluorescence imaging
- Filter Sets: BFP/DAPI, GFP, RFP
- Long working distance objectives: 5x (NA 0.15), 10x (NA 0.25), 20x (NA 0.35), 40x (NA 0.55), 100x (NA 1.25) oil
- Zeiss Axiocam 305 mono
- Zen Blue software
Zeiss Axioskop Upright Microscope
The Zeiss Axioskop upright microscope is ideal for imaging sections on slides.
Capabilities:
- Transmitted-light brightfield LED, phase contrast & fluorescence imaging
- Filter Sets: BFP/DAPI, GFP, mCherry/TxRed & Cy5/AF647
- Objectives: 4x (NA 0.1), 10x (NA 0.3), 20x (NA 0.6), 40x (NA 0.75), 100x (NA 1.3) oil
- SPOT RT Monochrome camera
- SPOT software
Olympus Inverted IX81 Microscope
The Olympus inverted IX81 microscope is ideal for live cell imaging with CO2 and temperature control.
Capabilities:
- Transmitted-light brightfield, phase contrast & fully motorised fluorescence imaging
- Filter Sets: DAPI, GFP, YFP, RFP, Cy5
- Objectives: 4x (NA 0.13), 10x (NA 0.3), 20x (NA 0.45 & 0.75), 40x (NA 0.6 & 0.95), 100x (NA 1.4) oil
- Motorised Stage (x-y-z)
- Sensitive monochrome camera
- Cellsens software with all modules
Aperio AT2 - High Volume, Whole Slide Scanner
The Aperio AT2 provides high-throughput digital scanning of slides at 20x or 40x resolution, with capacity for up to 400 slides and a scanning speed of 50 slides per hour (at 20x).
Key Features:
- Low rescan rate
- Z-stacking with up to 25 layers
- Remote access to scanned images via eSlideManager for collaborative research
- Integrated macros and algorithms via Aperio ImageScope software
- Easy export of images for analysis in third-party platforms
Zeiss LSM 980 with Airyscan 2 Confocal Microscope
Capabilities:
- Optical sectioning at high resolution or, with the Airyscan, superresolution
- Live-cell imaging with CO₂ and temperature control
- High-resolution Airyscan 2 imaging
- Lambda scanning
- Spectral linear unmixing
- Online fingerprinting
- Fluorescence Correlation Spectroscopy (FCS)
- Fluorescence Cross-Correlation Spectroscopy (FCCS)
- Tile Scanning
- Time Series Imaging
- Z-Stack Scanning
- Experimental Designer for automation of complex workflows
Hardware:
- 7 Laser Lines: 405, 458, 488, 514, 561, 591, 633nm
- Objectives: 5x (NA 0.16), 10x (NA 0.45), 20x (NA 0.8), 40x (NA 1.2) water, 40x (NA 1.3) Oil, 63x (NA 1.4) Oil
- Motorised Axio Observer 7 microscope with Definite Focus 2
- Integrated large incubation with temperature and CO₂ control
- Fast Airyscan module for super-resolution imaging (120 nm XY, 350 nm Z)
- Motorised XY stage and fast Z-piezo focus device
- Comprehensive range of stage inserts
- Detectors: 32 channel GaAsP array detection, 2xMA-PMT, Airyscan detector and Transmitted-PMT
- AxioCam 506 monochrome camera
- Zen Blue software
Zeiss LSM 980 Fast Airyscan Confocal and Multiphoton on an upright Microscope
Custom-built for ONJCRI specifications, this microscope was the first of its kind globally and is the only one in Australia. Combining multiphoton and confocal capabilities, it is ideally suited for the next generation of discoveries using in vitro and in vivo models of the tumour microenvironment.
Capabilities:
- Deep tissue intravital microscopy
- Second Harmonic Generation Imaging (SHG)
- High resolution Airyscan 2 imaging
- Lambda scanning
- Spectral linear unmixing
- Online fingerprinting
- Fluorescence Correlation Spectroscopy (FCS)
- Fluorescence Cross Correlation Spectroscopy (FCCS)
- Fluorescence Liftetime Imaging (FLIM)
- Tile Scanning
- Time Series Imaging
- Z-Stack Scanning
- Experimental Designer for automation of complex experiments
Hardware:
- 5 Solid State Laser Lines: 445, 488, 514, 561, 639nm
- Spectra-Physics Insight X3 Laser (690-1300nm plus 1045nm fixed line)
- Objectives: 20x (NA 0.8), 63x (NA 1.4), Multiphoton Immersion 20x (NA 1.0)
- Motorised Axio Examiner Z1 upright microscope
- Motorised XY stage: Prior Z-Deck stage with very large sample space
- Airyscan module for fast, gentle, super-resolution imaging (120nm XY, 350nm Z resolution)
- 5x Internal Detectors: 32 channel spectral array detector (GaAsP PMT), 2 x MA-PMT, Transmitted Light Detector (MA-PMT) and Airyscan 2 detector (GaAsP PMT)
- 4x External (NDD) detectors; 2x BiG detectors (GaAsP PMTs) and 2 x NDD detectors (MA-MPTs) in cascade
- Ultra-sensitive external multi photon detection with 2x Nosepiece (GaAsP PMTs) detectors
- Integrated large incubation with temperature control
- Integrated PicoQuant FLIM detection using 2x FLIM detectors
NanoString Molecular Barcoding Scanner
The NanoString nCounter® SPRINT Profiler system provides multiplexed analysis of up to 800 RNA, DNA, or protein targets with minimal sample preparation. Optimised for FFPE, tissue lysates, and biofluids, it enables reliable quantification without the need for cDNA amplification or library preparation.
Key Features:
- 15 minute hands-on sample preparation
- No need for cDNA amplification or library prep
- 24-hour scanning turnaround
- Curated human and mouse panels for oncology and immunology
Sample Types Supported:
- Total RNA
- Cell Lysates in GITC
- FFPE-derived total RNA
- PAXgene-lysed whole blood
Recommended starting material:
- RNA: 1 ng – 50 ng
- DNA: 5 ng – 300 ng
- Protein: 150 ng – 2.5 µg
The Spatial Proteomics Platform leverages advanced multiplexed imaging technologies to map the tumour immune microenvironment with high precision, supporting both hypothesis-driven and discovery-based research. The platform includes the BOND RX, Vectra 3, and PhenoImager HT 2.0 for targeted spatial proteomic analysis, alongside the PhenoCycler-Fusion system for ultra-high-plex discovery workflows, enabling the simultaneous profiling of over 100 biomarkers at subcellular resolution. Together, these systems empower researchers to uncover complex cellular phenotypes and interactions within tissue architecture, driving new insights into cancer biology and immune regulation.
BOND RX Automatic Immunostainer
The BOND RX automates IHC/IF, RNA Scope, ISH, FISH, CISH, and multiplex staining experiments, increasing reproducibility and efficiency.
Leverage standardised protocols or develop novel, reproducible staining methods tailored to your research needs.
Capabilities:
- Fully customisable staining protocols (baking, dewaxing, antigen retrieval, staining)
- Capacity for 30 slides with continuous loading of 10-slide trays
- Run up to three protocols simultaneously
- Reduces a manual seven-plex immuno-flourescence workflow from ~5 days to ~17 hours
VECTRA® 3 Microscope with Multispectral Camera
Capabilities:
- Brightfield and fluorescence Automated Scanner
- Simultaneous detection of up to 6 biomarkers plus the nuclear stain, DAPI, on a single tissue section using Opal chemistry
- Whole slide pre-scanning at 4x or 10x; high-resolution multispectral imaging at 20x or 40x
- Identify multiple cell phenotypes in tissue sections or Tissue Microarrays
- Automated spectral unmixing using Inform software
- Automated slide loader for up to 200 slides
PhenoImager HT 2.0 Microscope
Capabilities:
- Brightfield and fluorescence Automated Scanner
- Simultaneous detection of up to 8 biomarkers plus the nuclear stain, DAPI, on a single tissue section using Opal chemistry
- Whole slide scanning or multispectral imaging at 10x, 20x, or 40x magnifications
- Onboard spectral unmixing during whole slide scans for up to 6 biomarkers plus DAPI
- New QUPTIFF file format offers a more manageable data output
- Identify multiple cell phenotypes in tissue sections or Tissue Microarrays
- Automated slide loader for up to 80 slides
PhenoCycler-Fusion 2.0
Capabilities:
- Fully automated imaging system for ultra-high plex (over 100 targets) spatial information
- Images 1 million cells in 10 minutes in situ
- Uses barcoded antibody technology and fluorescence detectors
- Integrates advanced fluidics and imaging for seamless sample-to-data workflow
- Compatible with FFPE & fresh frozen tissue
- Supports customisable panels for targeted and discovery-based spatial analysis
- High-throughput capabilities with walk-away automation for multiple-sample runs
- Enables subcellular resolution imaging across entire tissue sections
- Generates spatial maps of cell phenotypes and interactions within the tissue microenvironment
- Streamlined data output compatible with downstream bioinformatics tools (e.g., HALO, QuPath, R)
In addition to the above technologies, the Zeiss LSM 980 with Airyscan 2 Confocal Microscope (see ‘Advanced Imaging’ section) offers advanced spectral detection and high-resolution optical sectioning to analyse tissues in 3D. Its spectral imaging capabilities allow for precise separation of overlapping fluorophores, enabling multiplexed imaging with exceptional clarity and minimal cross-talk. This system is ideally suited for applications requiring high sensitivity and flexibility, including validation of spatial proteomics findings, colocalization studies, and dynamic imaging of cellular processes within complex tissue environments
Image Analysis Software
A variety of imaging software platforms are available to support researchers with advanced image analysis, from free tools to licensed solutions:
- FIJI/ImageJ (free, 2D image analysis)
- HALO/AI (multiplex IHC/IF analysis)
- Inform (spectral unmixing for multiplex IF)
- Imaris (powerful software for 3D image analysis available via La Trobe University)
- Metamorph (2D image analysis software – legacy)
- Olyvia (free, 2D image analysis)
- Zen Blue (3D image analysis)
Support
Our team is here to help with:
- Experimental design
- Sample preparation
- Image acquisition
- Image analysis
- Multiplex panel development
- Grant pricing estimates
- Informal/formal supervision
- Training through workshops
Training and User Access
The ACRF Centre for Imaging the Tumour Microenvironment is an open-access facility, welcoming external researchers and industry partners. The Centre offers flexible access models, ranging from comprehensive, fee-for-service collaborations to user-led access following structured training.
Training programs are tailored to user needs and include:
- System overview and operational principles
- Hands-on training with expert support
- Pathway to independent instrument use
These training pathways ensure users are equipped to generate high-quality data, whether operating independently or working in collaboration with Centre staff.