Techniques instructed at CMM

Table of techniques available for instruction at the CMM




Light Microscopy

No previous skills assumed.

Operation of compound and stereo microscopes at a basic skills level. Topics include: light microscopy techniques (including: Brightfield field, Differential Interference Contrast (DIC), fluorescence), effects of light, resolution, digital image acquisition, system calibration, Koehler Illumination, sample loading, sample preparation.

Half Day Session

Scanning Electron Microscopy (SEM) for Biological and Physical Sciences

No previous electron microscope (EM) experience is assumed.

Operation of SEM up to an intermediate skills level. Topics include: sample loading, secondary and back scattered electron imaging, effect accelerating voltage has, depth of field, resolution, focusing, astigmatism and digital image acquisition. Sample preparation includes: sample mounting, sputter coating with metals, carbon coating, freeze drying, fixation, chemical dehydration, critical point drying.

This basic training is a prerequisite for upgrade to other SEMs and related techniques e.g. microprobe, ultrahigh resolution FEG, LaB6 cryoSEM, variable pressure (VP) SEM, energy dispersive spectroscopy (EDS), electron backscatter diffraction (EBSD), use of Alicona MEX 3D software.

23 hrs over a two week period

Subsequent upgrades for other SEMs and related techniques are 5 - 20 hours.

Transmission Electron Microscopy (TEM) for Biological Sciences, Polymer Sciences and General Morphology

No previous EM experience is assumed.

Operation of TEM at a basic level. Topics covered include: generation of beam, electron lenses and correction of astigmatism, image formation, resolution, sample insertion, staining and contrast, the vacuum system and contamination, and digitising of images. Sample preparation includes: fixation, microwave fixation, and resin embedding.

Sample preparation includes: fixation and resin embedding, both on bench and using the microwave oven, and ultramicrotomy (semi-thin and ultra-thin sectioning, staining and grid coating).

24 hrs covered over a 2 week period.

Ultramicrotomy alone: 6 hours including practice.

Transmission Electron Microscopy for Physical Sciences

No previous EM experience is assumed.

Part 1: Operation of TEM at basic level. Topics covered include: generation of the beam, condenser system, objective lens, intermediate and projector lenses, ray paths, specimen insertion, generation of high voltage, aperture insertion; microscope alignment, including alignment of the gun, condenser, beam tilt, objective and intermediate systems; correction of objective astigmatism; focussing the image, image capture, diffraction, specimen tilt, dark-bright field imaging, phase-contrast imaging, film exchange, digital image capture. EDS. PEELS. CBED

Part 2: Operation of TEM at an advanced level. Topics include: upgrade from simpler TEM operation, sample exchange and different specimen holders – cryo and or double-tilt or tilt-rotate, alignment for Nanodiffraction, alignment for STEM, alignment for GIF, how to operate EDS 
(requires microanalysis theory), how to operate GIF, software use for quantitation
Standards, computer simulation of HREM images and EELS spectra, diffraction theory and experimentation.

Part 1: 8 hrs plus individual practice 
Part 2: 20 hrs +


Basic SEM training required.


Technical operation of WDS Microprobe for quantitative analysis, mapping, and image acquisition. Advice on sample preparation: resin embedding, polishing and coating. Previous SEM experience/ training required, Plus completion of microanalysis theory.

18 hrs plus individual practice

Microanalysis Theory

[Microanalysis for SEM and Microprobe (EDS/WDS) and TEM]

Previous SEM/TEM experience/training required.

Provides an introduction to analysing the elemental composition of samples. Topics include: X-ray production, energy dispersive spectroscopy (EDS), wavelength dispersive spectroscopy (WDS), spectral artefacts and an introduction to matrix correction effects (ZAF).

8 hrs of theory and tutorial (across 3 days)

Sample Preparation for Physical Sciences

No previous experience is assumed.

Ion milling, dimple grinding, electropolishing, chemical polishing, cleavage, holey carbon films.

However, as our sample preparation facilities are limited, we recommend wherever possible that facilities outside the CMM are used. We can provide contact information.

Half day + practise

Advanced sample preparation for TEM

Previous EM experience is required.

Theory of freezing hydrated samples for electron microscopy, high pressure freezing, plunge freezing of particle suspensions, handling of frozen hydrated samples, freeze substitution.

Variable: at least 12 hrs plus individual practice.

It should be recognised that these techniques are time-consuming.

High Resolution SEM

Previous EM experience is required.

Operation of SEM at a high level. Topic includes: advanced sample preparation, sample loading, electron lenses, microscope alignment, including alignment of the gun, condenser lenses, beam tilt, secondary and back scattered electron imaging, focussing the image, correction of objective astigmatism and digital image acquisition.

10 hrs including practice

High Resolution Transmission Electron Microscopy

Previous TEM required.

Fine TEM alignment including correcting objective lens astigmatism using amorphous edge of TEM specimens; titling crystalline TEM specimens to the zone axis; choosing the correct condenser aperture, spot size, and objective aperture, and taking HRTEM images including justification of defocus of the microscope. TEM specimen preparation as the thickness of the TEM specimen for HRTEM should be less than 20 nm.

12 hrs

Cryo Scanning Electron Microscope

Previous SEM experience/ training required.

Operation of dedicated cryoSEM. Topics covered routinely include: CryoSEM setup and shutdown; sample preparation and mounting techniques; sample freezing (nitrogen slush plunge freezing); sample fracture techniques; specimen sublimation; sputter coating; sample storage and retrieval; energy dispersive spectroscopy (EDS); and artefacts.
Additional training is available for a high pressure freezer and a freeze drier.

3 hrs theory and 12 to 15hrs of practical

Variable Pressure SEM

Previous SEM experience/ training required.

Operation of variable pressure (VP) SEM. Topics include: theory and practical use of SEM chamber pressure to control specimens charge up; the imaging (backscattered and secondary) and X-ray analysis (EDS) of non-conductive samples in the VP SEM; freeze drying specimens using the VP SEM; artefacts and limitations of VP SEM.

5 to 6hrs practical including some theory

Electron Backscatter Diffraction (EBSD)

Previous SEM experience/ training required.

SEM training on the JEOL 6610 is a pre-requisite. Basic operation of EBSD. Topics include: overview, sample preparation, EBSD system, collection of crystallographic orientation data and analysis using Oxford Azetc software.

12 hrs


Previous sectioning experience/ training helpful. 

Sample preparation: generally biological (gelatin embedding) or polymer samples (resin embedding); knife making; operation of cryoultramicrotome ie correct orientation and trimming of blocks, ultrathin sectioning, picking up sections; troubleshooting.

6-8 hrs plus practice per individual (extended if no previous experience on ultramicrotomes for resin sectioning)

X-ray Diffraction (XRD)

No previous experience required but Queensland Health Use Licence is a pre-requisite (we can advise on obtaining license but be aware it takes about 6 months).

Operation of X-Ray Diffractometer in powder diffraction mode. Topics include: sample preparation, sample loading, creation of parameter file, creation of job file, processing of traces using Evaluation software, search match using PDF-2 Database, file conversion.

12 hrs


Previous TEM experience is required. 

Operating electron microscopes at an advanced level, imaging with high-end CCD-cameras, acquiring tilt-series of bilological/material samples using Serial EM, computing of tomograms using IMOD, basic segmentation of tomographic data.

Variable depending on research project 

It should be recognised that this techniques is extremely time-consuming.

Cryo TEM

Previous TEM experience is required. 

Handling of frozen hydrated samples, use of cryo-sample holders, insertion of cryo-samples into the microscope, low dose electron microscopy.

Variable: at least 12 hrs plus individual practice. 

It should be recognised that these techniques are time-consuming.

XPS - X-Ray Photoelectron Spectroscopy

An introduction to the basics of the XPS technique and the use of the CasaXPS data processing software

This half day seminar and tutorial (9am-12pm) must be attended before samples can be booked in for analysis

3 hrs