Microscopy and Micro Imaging

Monash Micro Imaging


Monash Micro Imaging (MMI) at the Alfred Research Alliance (MMI@ARA) provides optical imaging expertise and instrumentation. Located on level 6, Burnet Tower in Monash’s Central Clinical School, the team coordinates and facilitates training, research support and access to core microscopy resources.  MMI@ARA is a node of the MMI platform.


Technologies and expertise includes light microscopy, fluorescence and confocal microscopy, supporting a diverse range of applications for morphological and functional characterisation in the biomedical and life sciences. All technologies are underpinned by training in bioimage analysis and research methodology. MMI@ARA staff are available to assist with experimental design, and techniques such as:

  • live and fixed cell imaging
  • time-lapse microscopy
  • Optical sectioning and 3D analysis of samples
  • Tiling and stitching to generate high resolution images of large areas
  • Digital Interference Contrast microscopy to enhance contrast for improved visibility
  • Fast image capture for ion imaging e.g. Ca2+ and pH.



  • A1r Plus si – Inverted confocal microscope, four colour with Galvo & Resonant scanner in PC2 laboratory
  • Nikon A1r Plus si – Inverted confocal microscope, four colour with Galvo & Resonant scanner. Includes VAAS super resolution in PC2 laboratory
  • Nikon Ti-E – inverted motorised microscope with live cells incubator and time lapse capacity in PC2 laboratory
  • Olympus IX83 Cell TIRF – Inverted microscope with four colours and live cell incubator
  • Olympus BX51 – upright microscope in PC2 laboratory


  • Image J FIJI
  • Imaris
  • HALO
  • NIS Analysis

Access and Contact

For further information about equipment specifications, imaging hardware and software, and locations of the instrumentation contact the Platform Manager.

A range of services are offered depending on researcher need and access to the equipment is available to researchers by agreement with the local Platform Manager. For general research enquiries contact:

Dr Iska Carmichael
Platform Manager, MMI@ARA
Monash University


Baker Institute Microscopy Platform


The Baker Institute Microscopy Platform enables researchers to perform leading-edge microscopy to advance the treatment of cardiovascular disease, diabetes, and related disorders. As an open-access facility, the Baker Institute Microscopy Platform aims to advance optical imaging throughout the Baker Institute and surrounding precinct.

The Platform houses a wide range of equipment and staff expertise to enable brightfield and fluorescent imaging experiments. The Platform can assist and lead research teams across all facets of optical imaging from providing education, assisted imaging through to the development of analysis pipelines.


Platform houses state of the art equipment enable:

  • Live cell confocal imaging
    • Integrated temperature and CO2 control for live cell imaging
    • Conventional or fast imaging (30 fps, faster with small frames)
    • Optional Piezo Z-stage for rapid volume imaging
    • Simultaneous imaging with photo-activation or bleaching
    • 32 channel spectral detector
  • Live intravital mouse imaging
    • Integrated temperature incubation system
    • 32x channel spectral array for spectral linear un-mixing
    • Airyscan module for super-resolution imaging (120nm XY, 350nm Z resolution)
    • Fast Airyscan imaging mode
  • Dedicated Advanced Image Analysis Workstations and software solutions

All users, regardless of experience, must be inducted and trained by a Baker Institute Microscopy Platform Member prior to any microscope equipment use. The Imaging Facility will provide:

  • Quick guides, FAQs, software walk-throughs.
  • Educational resources.
  • Internal workshops developed by facility or vendors.

For more information about training requirements, contact Adam Parslow.


  • Nikon A1r Plus si NIR Modified — inverted confocal microscope
    • Observation modes: Brightfield, Fluorescence, Phase
  • Zeiss LSM880 Airyscan — upright multiphoton microscope
    • Observation Modes: Brightfield, Fluorescence
    • Laser Ablation System
    • 6x external (NDD) detectors including:
      • 2x external MA-PMTs and 2x GaAsP PMTs in cascade
      • Ultra-sensitive external multiphoton detection with 2x Nosepiece GaAsP detection
  • Olympus BX61 — upright motorised microscope
    • Observation Modes: Brightfield, Fluorescence, Phase, DIC
    • Camera: Olympus DP80. Dual CCD Monochrome and Colour Camera
  • Image analysis workstation
    • Hardware
      • HP Z6 Workstation
    • Software
      • Imaris 9.9
      • HALO and HALO AI
      • Arvis 3.2
      • FIJI
      • QuPath
      • Rstudio
      • Zen Blue 2.3
      • Zen Black 2.3

Access and Contact

Equipment is available through collaborative research or by fee for service by contacting the Microscopy Manager below requested access and completed induction and/or training. For general research enquiries contact:

Dr Adam Parslow
Microscopy Manager
Baker Institute
Microscopy platform

Burnet Cell Imaging Facility