Zebrafish

Optical Microscopy

Light microscopes use visible light sources including lamps, LEDs and lasers to image live and fixed samples. There are many different optical microscopy techniques, including brightfield, phase contrast, differential interference contrast (DIC), reflected light microscopy, darkfield and fluorescence.

CMCA offers a number of instruments covering these basic techniques, as well as more advanced instruments for specialised applications, such as confocal, multiphoton and super-resolution microscopy.

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What can optical microscopy platforms do?

We can help with all your optical microscopy enquiries. We provide access to instruments, training, advice on different imaging techniques and support with research projects.

We are always happy to discuss your project and available options, without any obligations. If we cannot provide what you need, hopefully we can point you in the right direction.

Although most researchers become independent operators of our instruments, we also have some scope to take on fee-for-service work, if you would like to get your samples professionally imaged

Why us?

Our facilities are openly accessible to all researchers who require access to microscopes, including those from industry and institutions beyond UWA. We specialise in imaging a wide range of sample types, from biological specimens to materials and earth sciences.

We offer comprehensive training on all instruments and techniques to ensure you achieve the best results from your imaging. In addition to standard microscopy, we can assist with specialised imaging modes and techniques tailored to your needs. Our support extends beyond the lab—we can assist with project planning, such as grant applications, and provide ongoing guidance from project inception through to publication.

Our techniques

Basic optical microscopy

Basic optical microscopy techniques include brightfield, transmission, reflection, phase contrast, DIC and polarisation microscopy. The sample is placed in the microscope, and for transparent samples usually the light transmitted through the sample is observed; for opaque samples reflection microscopy can be used.

These techniques are generally suitable for both live and fixed samples, and can achieve subcellular resolution <0.5 µm, depending on the technique and objective. A colour camera is also available.

Instruments:

Brightfield image of a cat brain section.

Slide scanning

A slide scanner is an automated microscope that captures digital images from microscopy slides. It is used for high throughput screening, e.g. to look for diseases and abnormalities in tissue, bone, blood and serum samples, and analyse composition of geological and archaeological samples.

CMCA has a new Zeiss Axioscan 7 slide scanner that has been optimised for both biological and geological applications. It has options for brightfield, fluorescence and polarisation imaging, 100 slide capacity and magnifications from 5x to 40x. CMCA also has an older Aperio ScanScope OS oil scanner, which has 100x magnification and brightfield mode.

Instruments:

Geological sample imaged with Zeiss Axioscan 7

Fluorescence microscopy

Fluorescence microscopy uses a specific wavelength of light to excite fluorescent molecules. Emitted fluorescence, which is longer wavelength than the excitation light, is passed through an emission filter, which allows rejection of reflected light and imaging inside cells and tissues. Some molecules are naturally fluorescent (autofluorescent), and sometimes it is possible to use autofluorescence for imaging. However, in the biological field, fluorescent proteins (such as GFP) or antibodies with fluorescent dyes are often used, which allows the tagging of cellular structures with high specificity and high brightness.Fluorescence microscopy techniques are generally suitable for both live and fixed samples - CMCA has a Tokai Hit stage top incubator that can be fitted in most of our microscopes for live cell imaging.

 

Wide-field fluorescence

In a wide-field fluorescence microscope the whole sample is illuminated, typically using a coloured filter in front of a lamp to choose the excitation wavelength, and the image is collected using a CCD or a CMOS camera. For thick samples out-of-focus light can blur images making it difficult to resolve fine detail. However, data collection is fast, and the microscope is usually simple to operate.

Instruments:

Confocal fluorescence microscopy

Confocal microscopy is an optical imaging technique used to increase optical resolution and contrast by using a spatial pinhole to eliminate out-of-focus light in thicker specimens. It enables the reconstruction of three-dimensional structures from the obtained images. Confocal microscopy is our most popular Optical Microscopy technique, and usually the best choice for high quality fluorescence imaging of biological samples.

  • For spatial resolution >200 nm, sample size < 10mm
  • Suitable for both live and fixed samples (Tokai Hit chamber), and in-vivo imaging.
  • A range of magnifications from 4x-100x; four channels (405, 488, 561 and 640 nm excitation).

Instruments:

Confocal image of autofluorescence in a grass bud

Specialised optical techniques

Are you looking to go beyond what standard light microscopy can offer? We offer several specialised techniques that get around some limitations of conventional techniques:

  • Multiphoton microscopy can improve depth penetration in thick samples, and enable Second Harmonic Generation (SHG) label-free imaging mode (in addition to two-photon fluorescence).
  • Super-resolution techniques (e.g. SIM and STORM) improve spatial resolution beyond the classical diffraction limit, as recognised by the 2014 Nobel Prize in Chemistry. 
  • Fluorescence lifetime imaging (FLIM) enables mapping of the environment and interaction of fluorescent probes. One prominent FLIM application is the measurement of Förster Resonance Energy Transfer (FRET) to study protein interactions and conformational changes. FLIM is also used to image viscosity, temperature, pH, refractive index and ion and oxygen concentrations.
  • We can also help configure microscopes for special imaging modes, such as TIRF (total internal reflection fluorescence) and FRAP (fluorescence recovery after photobleaching).

Instruments:

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FAQ

  • Who can use the equipment?

    The platform is open to researchers from UWA, other academic institutions, and industry partners. Whether you’re experienced or new to optical microscopy, we welcome your use of our facilities.

  • How do I get started?

    To get started, you need to complete an induction, online training materials and hands-on training session(s). This ensures that all users are equipped to handle the equipment safely and efficiently. Please contact us via [email protected] to arrange a meeting to discuss your imaging requirements.

  • Do I need prior experience with microscopy to use the equipment?

    No prior experience is necessary! Our team provides comprehensive training for new users. After training, you’ll have the skills needed to use the equipment independently.

  • Is there a booking system for the equipment?

    Yes, we use an online booking system that allows you to reserve equipment at your convenience based on availability. Once you’ve completed your training, we’ll grant you access to the booking system. Please ensure you book well in advance to secure your preferred timeslot. At busy times some booking limits may apply to ensure everyone can access the equipment.

  • How do I know which microscope or technique is right for my project?

    If you’re unsure which equipment best suits your needs, our team is here to help. During your initial consultation, we’ll discuss your research goals and recommend the most appropriate microscopy techniques.

    Please contact us via: [email protected]

  • I’m not sure if a technique is suitable for my samples. What should I do?

    We may be able to provide a pilot test to see if a technique is suitable for your requirements.

    Please contact us via [email protected] to discuss.

  • Can you help with sample preparation?

    We are happy to provide basic advice on how to best prepare your samples for imaging when using our microscopes. However, we don’t offer full sample preparation services. We encourage you to discuss your sample requirements with us, and we’ll do our best to guide you in the right direction.

  • Do you offer imaging services in addition to equipment access?

    We provide training on all our equipment and specialised techniques so that you and your research team have the skills needed to use the equipment independently. We offer a limited range of imaging services, for researchers who prefer not to use the equipment directly. Due to our small team, availability is limited and subject to scheduling. Please enquire early if you’re interested in these services.

    Contact us via [email protected] to discuss.

  • Can you provide training for a microscope in my facility?

    Our training is for users of our facility. We are unable to provide off-site training for equipment located outside of CMCA at this time. However, we occasionally run workshops on microscopy and image processing basics, which may be of interest for new users of optical microscopy techniques. Contact us to find out more or sign up to the WA Optical Microscopy mailing list to receive latest news about local training courses & other events.

  • What kind of training do you provide?

    Our team provides comprehensive training for new users of the facility. We offer training tailored to your specific needs, from basic microscopy operation to advanced techniques. We also provide refresher training for users who may need to revisit their skills. Our aim is to ensure researchers using our facility have the expertise and confidence to work independently.

  • Can industry users access your facilities?

    Absolutely! We work with industry and government partners across various sectors. Whether you're exploring product development or require advanced imaging for analysis, we can support your research needs. Contact us via [email protected] to discuss.

  • How much does instrument access cost?

    Charge out rates depend on the type of equipment and the scope of use. Contact us directly for a customised quote based on your project needs.

  • Can you help with data analysis?

    We provide access to some complete analysis software suites on our analysis computers, and basic training to get you started. We can also provide advice on other analysis options, e.g. how to access High Performance Computing (HPC) facilities. We encourage you to discuss your data analysis requirements with us, and we’ll do our best to guide you in the right direction.

  • What are your operating hours?

    Our standard operating hours are Monday-Friday, 9am-5pm, but access to the equipment may be available outside these hours by prior arrangement for experienced users.

Platform experts

Dr Liisa Hirvonen
Optical Platform Leader, Centre for Microscopy Characterisation and Analysis

Alysia Hubbard
Research Officer, Centre for Microscopy Characterisation and Analysis

Dr Finn McCluggage
Research Officer, Centre for Microscopy Characterisation and Analysis

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