Hyperion, Imaging mass cytometer (Fluidigm)


The Hyperion (imaging mass cytometer, IMC) consists of a CyTOF (Helios) instrument, with an imaging module attached to the front. Within the imaging module, a pulsed laser scans and ablates the tissue section in incremental 1 um shots. With each laser shot, vaporised material is carried into the mass cytometer, and the metal ions are analysed by time-of-flight mass spectrometry. 

Overview: The 'Hyperion' imaging mass cytometery (IMC) from Fluidigm was installed in the Charles Perkins Centre in August 2017. The Hyperion platform allows imaging of tissue sections, by combining a laser ablation module with a Helios mass cytometry platform.

Usage prices can be found here.


  • Image tissue sections, rather than cell suspensions

  • Run panels of over 40 parameters

  • Acquisition speed of approx. 0.75 mm^2 per hour

  • Gain full microenvironment and tissue architecture data

  • Minimal reporter overlap and low autofluorescence

Users who are interested in using the Hyperion can submit a project meeting request or can email the facility at cytof@sydneycytometry.org.au.

Mouse lymph node (sample provided by Benita Tse and Scott Byrne)

Mouse lymph node (sample provided by Benita Tse and Scott Byrne)

Mouse CNS (sample provided by Thomas Ashhurst and Nicholas King)

Mouse CNS (sample provided by Thomas Ashhurst and Nicholas King)

Virally infected CNS (sample provided by Thomas Ashhurst and Nicholas King)

Virally infected CNS (sample provided by Thomas Ashhurst and Nicholas King)



How many parameters can be measured?
As many as are measured on the CyTOF/Helios, where panels of around 45 parameters are common. An entire panel can be stained on the tissue section in one step, unless separate antigen retrieval steps are required. 

Can I use snap-frozen sections?
Yes. These should be compatible with most existing mass cytometry antibodies.

Can I use paraffin embedded/formalin fixed tissues?
Yes. Because no fluorescence is used in the system, fixation induced autofluorescence is not a problem. Antibody clones required for these sections may be different to existing CyTOF antibodies, but work is underway by multiple groups to validate protocols and clones for use with these tissues.

How fast is the IMC?
The IMC acquires data at approx. 0.75 mm^2 per hour.

What is the resolution of the IMC?
1 um spot size (i.e. 1 pixel = 1 um). Good enough for cellular analysis, but only basic sub-cellular resolution.

Can I run samples overnight?
Yes, because the IMC is acquiring only ions in a continuous phase, similar to traditional mass spec.

Can I still use algorithmic tools like SPADE and tSNE on my data?

Further reading:

Chang, Q., et al. (2017). Imaging Mass Cytometry. Cytometry A.

Giesen, C., et al. (2014). Highly multiplexed imaging of tumour tissues with subcellular resolution by mass cytometry. Nature Methods.

Data analysis

The raw data is similar to single cell data from traditional mass cytometry, but instead of relative abundance (of metal) per cell, this is relative abundance per spot.

Analysis of IMC data consists of:

  1. Image visualisation and management.

  2. Conversion of MCD files to TIFF/OME-TIFF files.

  3. Pixel classification and cell segmentation (the data can be processed to identify cell boundaries and converted into relative abundance per cell, similar to a normal FCS file).

  4. Clustering (PhenoGraph) and dimensionality reduction (tSNE).

  5. Neighbourhood analysis.


To gain access to our analysis protocols, please fill in your details here. These are only used for our internal reporting and won’t be used for marketing or other purposes. We may email you from time to time if substantial updates to the protocols are made.

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