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.




Find -  the techniques and facilities to fit your project

Use TechFiTM to identify and understand the microscopy and microanalysis techniques available to researchers through the AMMRF. 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 


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.
Diffraction (EM)      
SAXS/WAXS/XRD Crystallography Open Data Base Open-access collection of organic and inorganic crystal structures
  NIST Macros SAXS simulations/fitting  
  Motofit XRR simulation/fitting
  ConvX Programme for converting between different XRD file formats
SEM Analytics & Simulation Tools (EDX, WDX, EBSD, CL) Original Casino Electron volume information, MonteCarlo modelling software
  WinCasino2 Electron volume information, MonteCarlo modelling software
  WinCasino3 Electron volume information, MonteCarlo modelling software
  MC X-ray MonteCarlo modelling software
  Win X-ray MonteCarlo modelling software
  DTSA-II Post processing EDS spectra
  PfEPMA Probe for EPMA, Donovan
  Probe for EPMA (Donovan) Advanced EPMA mapping
  Probe Image (Donovan) Advanced EPMA mapping
  EBSD EBSD-Image is a free open-source software to analyze EBSD diffraction patterns and mappings.
TEM Analytics (STEM, EDX, EELS)      
TEM Autoslice TEM image simulation multislice  
  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
Tomography (EM, Xray, 3view, 3D-FIB/SEM, APT) NCViewer NetCDF viewer  
  Drishti 3D visualisation software