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 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. https://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy
Diffraction (EM)      
SAXS/WAXS/XRD Crystallography Open Data Base Open-access collection of organic and inorganic crystal structures http://www.crystallography.net/cod/
  NIST Macros SAXS simulations/fitting  
  Motofit XRR simulation/fitting http://motofit.sourceforge.net/
  ConvX Programme for converting between different XRD file formats http://www.ccp14.ac.uk/ccp/web-mirrors/convx/convx.zip
SEM Analytics & Simulation Tools (EDX, WDX, EBSD, CL) Original Casino Electron volume information, MonteCarlo modelling software http://www.gel.usherbrooke.ca/casino/index.html
  WinCasino2 Electron volume information, MonteCarlo modelling software http://www.gel.usherbrooke.ca/casino/What.html
  WinCasino3 Electron volume information, MonteCarlo modelling software http://www.gel.usherbrooke.ca/casino/What.html
  MC X-ray MonteCarlo modelling software http://montecarlomodeling.mcgill.ca/download/download.html
  Win X-ray MonteCarlo modelling software http://montecarlomodeling.mcgill.ca/download/download.html
  DTSA-II Post processing EDS spectra http://www.cstl.nist.gov/div837/837.02/epq/dtsa2/
  PfEPMA Probe for EPMA, Donovan http://www.probesoftware.com
  Probe for EPMA (Donovan) Advanced EPMA mapping http://www.probesoftware.com
  Probe Image (Donovan) Advanced EPMA mapping http://www.probesoftware.com
  EBSD EBSD-Image is a free open-source software to analyze EBSD diffraction patterns and mappings. http://www.ebsd-image.org/
TEM Analytics (STEM, EDX, EELS)      
TEM Autoslice TEM image simulation multislice  
  EMAN TEM & 3D data processing (single particle etc.) http://blake.bcm.edu/emanwiki/EMAN/
  Relion single particle 3D-reconstruction http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
  MotionCorr Drift correction for K2 image series http://cryoem.ucsf.edu/software/driftcorr.html
  Fiji/image J Image processing https://fiji.sc
  Gimp Image editor https://www.gimp.org
  SPRING Single Particle Helical Reconstruction http://www.sachse.embl.de/emspring/?_ga=1.81330654.898076223.1480317641
  UCSF Chimera Extensible molecular modeling system and volume viewer https://www.cgl.ucsf.edu/chimera/
Tomography (EM, Xray, 3view, 3D-FIB/SEM, APT) NCViewer NetCDF viewer  
  Drishti 3D visualisation software https://github.com/nci/drishti/wiki