Online tools

MyScope Online teaching help

MyScope is an online teaching and learning resource. It may be of help to you before undertaking training with the Centre or as a refresher at any stage in your use of techniques. MyScope includes modules on scanning electron microscopy, transmission electron microscopy, confocal microscopy, scanning probe/ atomic force microscopy, microanalysis and X-ray diffraction. It provides theory, diagrams, videos, flowcharts for sample preparation and virtual microscopes / equipment. This is a good place to start if you want to know more about techniques and use of equipment. Link to MyScope.

To directly access the videos produced by CMM on use of equipment in the MyScope site click here.


Tech Finder

Find -  the techniques and facilities to fit your project.

Use TechFiTM to identify and understand the microscopy and microanalysis techniques available to researchers through Microscopy Australia. You will find the contact details of our expert staff for each technique. They can provide you with all the information you need and guide you through the planning, training, data collection and interpretation stages of your experiment. Link to TechFiTM 



Use ImagingTools to help you find and access digital characterisation resources, including online environments, computing facilities, data, training and events.  Link to ImagingTools.

What they do:

Deploying federated CVL desktop environment

  • Deploying web-based tools and software
  • Helping researchers use informatics tools
  • Improving interoperability
  • Building Community
  • Integrating instruments
  • Training researchers
  • Building sustainability through direct engagement with Institutions


This is a platform for researchers, research organisations, government agencies (state and commonwealth) and infrastructure providers who have a need to manage and analyse characterisation data. 


Scientific Freeware

The following list provides links to 'free' software specific to numerous scientifc techniques.

Technique Software Name Description Link
Cryo Electron Microscopy Software Tools For Molecular Microscopy This link provides a comprehensive list and up-to-date distribution information of all of the software of interest to the cryoEM community.
SAXS/WAXS/XRD Crystallography Open Data Base Open-access collection of organic and inorganic crystal structures
  Motofit XRR simulation/fitting
  ConvX Programme for converting between different XRD file formats
SEM Analytics & Simulation Tools (EDX, WDX, CL)

OriginalCasino WinCasino2 WinCasino3


Electron volume information, MonteCarlo modelling software

MC X-ray

Win X-ray


MonteCarlo modelling software
  DTSA-II Post processing EDS spectra
  PfEPMA Probe for EPMA, Donovan
TEM EMAN TEM & 3D data processing (single particle etc.)
  Relion single particle 3D-reconstruction
  MotionCorr Drift correction for K2 image series
  Fiji/image J Image processing
  Gimp Image editor
  SPRING Single Particle Helical Reconstruction
  UCSF Chimera Extensible molecular modeling system and volume viewer
  Gatan Microscopy Suite Software Gatan Microscopy Suite® (GMS) is the industry standard software for (scanning) transmission electron microscope experimental control and analysis.

Tomography (EM, Xray, 3view, 3D-FIB/SEM, APT) Drishti 3D visualisation software