The CMCA Cytometry core is one of the largest cytometry cores in WA, spanning genomics, imaging, mass spectrometry, and flow cytometry.

It provides access to critical state of the art platforms and dedicated professional staff. The facility not only operates a large variety of instruments but is a primary resource for:

  • Advice and dedicated training sessions in the use of cytometry, instrument operation and post-acquisition data analysis;
  • Access to new research and innovation opportunities;
  • Developing novel cytometric techniques to meet WA’s researchers diverse scientific needs;
  • Cell sorting/isolation.

We welcome users from the research community, other academic institutions, and external commercial groups (see access and rates for more information). The Core Facility is open Monday through Friday with user appointments from 9:00 AM until 5:00 PM. After hour appointments are also offered for independent users and for users with sort experiments that cannot be completed during regular business hours.

Training on the analysers: A theory course is held 3 times a year. We do one-on-one training for independent operation when your samples are ready, independent of the theory course.

Training on the Cell Sorter: Based on the project need and degree of experience, super-users can undertake operator training for the sorter. This request requires approval by the TGL on a case-by-case basis.

Contact the Group leader for discussions and advice on:

  • Advice on grant applications;
  • Formal teaching courses;
  • Academic/industrial collaboration for project development, experimental design, data analysis;
  • Clinical/GLP testing and projects.


Flow Cytometers

  • 405nm, 488nm and 633nm excitation lasers;
  • Eight fluorescence parameters;
  • Acquisition rate up to 10,000 events per second;
  • High throughput sampler (HTS) allowing sampling from 96- and 384-well plates.

Canto Configuration

  • 355nm, 405nm, 488nm (100 mW), 561nm and 640nm excitation laser;
  • Seventeen fluorescence parameters;
  • Acquisition rate up to 70,000 events per second;
  • High throughput sampler (HTS) allowing sampling from 96- and 384-well plates.

Fortessa Default Configuration

  • xMAP Technology is a bead-based immunoassay flexible array;
  • Simultaneous capture of up to 100 analytes in a single microplate well;
  • Small sample volume usage e.g. 20µl of serum can detect up to 100 analytes.
  • 405nm, 488nm and 633nm excitation lasers;
  • Eight fluorescence parameters;
  • Acquisition rate up to 10,000 events per second;
  • High throughput sampler (HTS) allowing sampling from 96- and 384-well plates.

FACS / Cell Isolation

  • 355nm, 405nm, 488nm, 561nm and 640nm excitation lasers;
  • Acquisition rate up to 200,000 events per second;
  • Up to four pure populations. Separation is based on the detection of fluorescent markers on cells, nuclei, bacteria or phytoplankton from 200nm – 60µm in size.
Coming soon
Coming soon

Mass Cytometry

  • The CyTOF2 is a tool that generates n-dimensional data to examine the properties of cells and materials;
  • This system can measure over 30 simultaneous parameters (metal mass range, 75–209 amu);
  • Please check the Fluidigm website for further information about mass spectrometry and the CyTOF2 brochure, and a great resource is the Nolan lab resource page;
  • A Panel Designer tool is available at

Beckman Coulter Z2

  • The Beckman Coulter Z2 makes use of the Coulter Principle known as the Electrical Sensing Zone Method for counting and sizing cells.

10x Chromium Genomics Platform

  • The 10X Genomics Chromium Platform offers a high throughput, microfluidics-based molecular barcoding solution that prepares sequencing libraries for whole genome sequencing, exome sequencing and single cell transcriptomics;
  • The platform provides software for detailed analysis and visualization of the products, enabling scientists to identify single-nucleotide and structural variants and dynamic gene expression of individual cells;
  • CMCA and the AGRF have partnered to assist researchers providing access to auxiliary equipment needed for library preparation and sequencing.

Data Analysis Software

  • Commercial: FlowJo, Cytobank Premium, Kaluza, BD Diva 8;
  • Open source: Spice, Flowing, Bioconductor, ViSNE, Wanderlust, PhenoGraph, Wishbone, Scenery;
  • 10X Genomics software (open source): Chromium Single Cell 3’ Solution: Cell Ranger, Loupe Cell Browser, Cell Ranger R Kit; Chromium Genome & Exome Solutions: Long Ranger, Loupe Genome Browser.

We are continually expanding the catalogue of open source software.

Common Applications

Cytometry refers to the quantitative measurement of single cells and particles, enabling sub- and whole-population characterisation and analysis. Modern day cytometry is increasingly applied to the biomedical/clinical and life science fields, including plant and marine biology, drug discovery, functional cell analysis and nanotechnology. Contact core staff for more information.

Common applications are listed below:

  • Immunophenotyping : Cells can be rapidly identified and quantified by staining with fluorescently or metal tagged antibodies to both extracellular and intracellular antigens;
  • DNA analysis : Using fluorescent dyes which bind to DNA, researchers measure cell cycle, cell kinetics and proliferation, determine ploidy, and genome size;
  • Cell viability or apoptosis : Flow cytometry offers numerous assays for the study of apoptosis and cell death;
  • Aquatic pico phytoplankton : Rapid and accurate identification of vast numbers of phytoplankton cells can be achieved by taking advantage of inherent auto fluorescent properties of different phytoplankton species;
  • Soluble protein quantitation : Bead-based assays allow detection and quantification of soluble proteins from serum, cell supernatant and tissue homogenates;
  • Biomarker assays : Protein concentration determination and disease panel profiling, antigen arrays for serology assays, gene expression and genotyping assays, microRNA assays, transcription factor profiling, and receptor specificity assays;
  • Cell Sorting (FACS) : Isolation of populations, high purity bulk sorts, and high-recovery and indexed single-cell sorting for e.g, cell cloning, particle enrichment, rare cell identification, adoptive transfer and sequencing;
  • Luminex 200 : Assay formats include: biomarker assays, disease panel profiling, antigen arrays, gene expression and genotyping assays, microRNA assays, transcription factor profiling, protein interactions and SNP;
  • Genomics : 10X Genomics are continually developing and optimising their Solutions for use on the 10X Chromium Controller platform, including the Single Cell 3’ Solution, Single Cell V(D)J Solution, Genome Solution, Exome Solution, and De Novo Assembly Solution.

Publishing in Cytometry

An acknowledgment to CMCA staff (this is considered a KPI for staff and is reported):

  • Personally acknowledge CMCA staff who have helped you in your activities;
  • Have CMCA staff helped you beyond simple instrument operation? If so, consider including them as authors on your publication.

An acknowledgment to CMCA:
‘The authors acknowledge the facilities, and the scientific and technical assistance of the Australian Microscopy & Microanalysis Research Facility at the Centre for Microscopy, Characterisation & Analysis, The University of Western Australia, a facility funded by the University, State and Commonwealth Governments.’

Best Practices in Publishing Cytometry Data:

  • MIFlowCyt describes the current best practice in documentation and publishing of cytometry data;
  • The FlowRepository operates under the auspices of ISAC with guidance provided by ICCS and ESCCA.

Together MIFlowCyt and FlowRepository provide a mechanism for researchers to access, review, download, deposit, annotate, share and analyze flow cytometry datasets.

Contact us

If you have any queries or would like to find out more about our team, please see our profiles below, or, alternatively, please email us and we will be happy to assist you.