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.
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 |
SAXS/WAXS/XRD | Crystallography Open Data Base | Open-access collection of organic and inorganic crystal structures | http://www.crystallography.net/cod/ |
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, CL) | OriginalCasino WinCasino2 WinCasino3
| Electron volume information, MonteCarlo modelling software | http://www.gel.usherbrooke.ca/casino/index.html |
MC X-ray 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 | |
TEM | 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/ | |
Gatan Microscopy Suite Software | Gatan 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) | Drishti | 3D visualisation software | https://github.com/nci/drishti/wiki |