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Data Analysis Suite

The Data Analysis Suite is part of the Curtin MRI research facilities and provides dedicated computing infrastructure for analysing biological and imaging data, especially from microscopy and flow cytometry.

  • It consists of dedicated high-end workstations (at least four) used for post-acquisition data processing
  • Located in Building 305, Room 143 at Curtin
  • Designed to handle large datasets generated by advanced imaging systems

In simple terms:
It is not a Curtin MRI scanner software itself, but a post-processing and analysis environment where researchers turn raw imaging data into usable scientific results.

Main functions of the suite:

The suite supports three broad categories of work:

1. Microscopy and imaging analysis

  • Visualisation of 2D and 3D biological images
  • Image segmentation, quantification, and reconstruction
  • Handling large datasets from confocal and advanced microscopes

2. Flow cytometry data analysis

  • Cell population analysis
  • Fluorescence intensity measurement
  • Cytokine and biomarker quantification

3. Data analysis, statistics, and presentation

  • Statistical testing
  • Graphing and publication-ready figures
  • General scientific computing

Software used in the Data Analysis Suite:

Microscopy & image analysis software

These are the core imaging tools:

  • ZEN (Zeiss)
    → Proprietary software for Zeiss microscopes, used for image acquisition and analysis
  • Imaris (Oxford Instruments)
    → Advanced 3D/4D visualisation, tracking, and modelling of biological structures
  • NIS-Elements (Nikon)
    → Imaging software for Nikon systems, supports acquisition, analysis, and automation
  • Volocity (PerkinElmer)
    → 3D visualisation and quantification tool for microscopy datasets
  • FIJI / ImageJ
    → Open-source image processing platform widely used in biomedical research

These tools together enable:

  • 3D reconstruction
  • Cell tracking
  • Quantitative image analysis
  • Custom pipelines via plugins (especially in ImageJ/FIJI)

Flow cytometry analysis software

  • FlowJo
    → Industry-standard software for analysing flow cytometry data
  • FCAP Array Software
    → Used for cytokine bead array analysis

(Additional tools used in related facilities include FlowLogic and Attune software)

These tools handle:

  • Cell population gating
  • Fluorescence analysis
  • Multi-parameter datasets

Data analysis, statistics, and plotting

  • GraphPad Prism
    → Statistical analysis and scientific graphing (very common in life sciences)
  • R
    → Programming language for statistical computing and reproducible analysis
  • Microsoft Windows (workstation OS)
    → Platform environment for running the above tools

How the software fits together (workflow)

  • A typical workflow in the Curtin MRI Data Analysis Suite looks like this:

    1. Data acquisition
      • Microscopes or cytometers generate raw data
    2. Pre-processing & visualisation
      • ZEN, NIS-Elements, or Imaris
    3. Advanced analysis
      • ImageJ / FIJI or Volocity
      • FlowJo for cytometry
    4. Statistical analysis
      • GraphPad Prism or R
    5. Output
      • Figures, graphs, and quantified datasets for publications

Key characteristics of the suite

  • Multi-software ecosystem, not a single platform
  • Mix of commercial high-end tools and open-source tools
  • Focus on biomedical imaging and cell biology, not purely clinical MRI
  • Integrated with other Curtin MRI facilities like:
    • Microscopy and Histology Suite
    • Flow Cytometry Facility

Important clarification

Despite the name “Curtin MRI”:

  • This suite is not primarily for clinical MRI brain analysis software like:
    • FreeSurfer
    • SPM
    • FSL

Instead, it is focused on:
microscopy imaging + cellular analysis + lab-based imaging workflows

Summary

The Curtin MRI Data Analysis Suite is:

  • A dedicated research computing environment
  • Built around specialised imaging and biological data analysis tools
  • Using software such as:
    • Imaging: ZEN, Imaris, NIS-Elements, Volocity, FIJI/ImageJ
    • Cytometry: FlowJo, FCAP Array
    • Statistics: GraphPad Prism, R

Its strength is in integrating multiple tools into a complete analysis pipeline, rather than relying on a single software platform.

Training and access

All users must complete facility-specific training before gaining independent access to shared research equipment.

Training includes:

  • General Inductions: Covering fundamental principles, equipment operation, and safety protocols.
  • Instrument-Specific Training: Hands-on instruction tailored to researchers’ specific applications.
  • Refresher & Advanced Training: Ongoing skill development and troubleshooting support.

Bookings and facility use

  • Licensed users have access to online booking systems for equipment scheduling.
  • Contact facility staff for training, troubleshooting, or equipment-specific queries.

Attribution and authorship

All research using Curtin MRI facilities must acknowledge the relevant facility in publications. Where significant intellectual contributions are made by facility staff, authorship should be considered.

For more information

Contact

Michael Nesbitt
Technical Specialist
Email:michael.nesbit@curtin.edu.au
Tel: +61 (08) 9266 2201

Data Analysis Suite

The data analysis suite provides a range of software tools for analysing microscopy and flow cytometry data, along with applications for statistical analysis and data visualisation. It is widely used by researchers across Curtin MRI.