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 

 


ImagingTools

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

Audience

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.https://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy
SAXS/WAXS/XRDCrystallography Open Data BaseOpen-access collection of organic and inorganic crystal structureshttp://www.crystallography.net/cod/
 MotofitXRR simulation/fittinghttp://motofit.sourceforge.net/
 ConvXProgramme for converting between different XRD file formatshttp://www.ccp14.ac.uk/ccp/web-mirrors/convx/convx.zip
SEM Analytics & Simulation Tools (EDX, WDX, CL)

OriginalCasino WinCasino2 WinCasino3

 

Electron volume information, MonteCarlo modelling softwarehttp://www.gel.usherbrooke.ca/casino/index.html
 

MC X-ray

Win X-ray

 

MonteCarlo modelling softwarehttp://montecarlomodeling.mcgill.ca/download/download.html
 DTSA-IIPost processing EDS spectrahttp://www.cstl.nist.gov/div837/837.02/epq/dtsa2/
 PfEPMAProbe for EPMA, Donovanhttp://www.probesoftware.com
TEMEMANTEM & 3D data processing (single particle etc.)http://blake.bcm.edu/emanwiki/EMAN/
 Relionsingle particle 3D-reconstructionhttp://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
 MotionCorrDrift correction for K2 image serieshttp://cryoem.ucsf.edu/software/driftcorr.html
 Fiji/image JImage processinghttps://fiji.sc
 GimpImage editorhttps://www.gimp.org
 SPRINGSingle Particle Helical Reconstructionhttp://www.sachse.embl.de/emspring/?_ga=1.81330654.898076223.1480317641
 UCSF ChimeraExtensible molecular modeling system and volume viewerhttps://www.cgl.ucsf.edu/chimera/
 Gatan Microscopy Suite SoftwareGatan Microscopy Suite® (GMS) is the industry standard software for (scanning) transmission electron microscope experimental control and analysis.

https://www.gatan.com/products/tem-analysis/gatan-microscopy-suite-software

Tomography (EM, Xray, 3view, 3D-FIB/SEM, APT)Drishti3D visualisation softwarehttps://github.com/nci/drishti/wiki