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.

TechniqueSoftware NameDescriptionLink
Cryo Electron MicroscopySoftware Tools For Molecular MicroscopyThis link provides a comprehensive list and up-to-date distribution information of all of the software of interest to the cryoEM community.
SAXS/WAXS/XRDCrystallography Open Data BaseOpen-access collection of organic and inorganic crystal structures
 MotofitXRR simulation/fitting
 ConvXProgramme 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-IIPost processing EDS spectra
 PfEPMAProbe for EPMA, Donovan
TEMEMANTEM & 3D data processing (single particle etc.)
 Relionsingle particle 3D-reconstruction
 MotionCorrDrift correction for K2 image series
 Fiji/image JImage processing
 GimpImage editor
 SPRINGSingle Particle Helical Reconstruction
 UCSF ChimeraExtensible molecular modeling system and volume viewer
 Gatan Microscopy Suite SoftwareGatan 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)Drishti3D visualisation software