Advanced Microscopy Centre Techniques

Fluorescence Microscopy

Fluorescence microscopy is a workhorse technique for localizing cellular components. The Axio Imager Alpha and Beta Microscopes give researchers advanced widefield fluorescence capabilities including Z-stacks, tiling, and ApoTome imaging. The Metafer Alpha and Beta microscopes help researchers to automate imaging and analysis of metaphase chromosomes and interphase nuclei.

Live Cell Imaging

Viewing cells in their living state provides a wealth of information not available from fixed specimens. Live cell imaging involves the collection of images at successive time intervals under conditions that support cell culture. Four of our microscopes support live cell imaging: Cell Observer Widefield for transmitted light and fluorescence, Cell Observer SD and Cell Voyager for spinning-disk confocal, and LSM 880 Airyscan for confocal and super-resolution imaging.

Confocal Microscopy

Confocal microscopy enables researchers to visualize cellular structures in three dimensions. Our laser-scanning confocal microscope, LSM 880 Airyscan, has seven laser lines, selectable emission range and spectral unmixing capabilities. The Cell Observer SD and Cell Voyager microscopes support multichannel confocal imaging of live cells using spinning disk technology.

Super-Resolution Microscopy

Visualising separate objects smaller than the theoretical limit of optical resolution is called super-resolution.

Our in-house built Super-Resolution Microscope enables researchers to resolve structures of less than 50 nm in fixed samples using a single molecule localisation approach. With the LSM 880 Airyscan, standard fluorescent samples and live cells can be imaged with as low as 120 nm resolution.

Lightsheet Imaging and Stereomicroscopy

Lightsheet imaging is an optical microscopy technique in which a thin section of a sample is illuminated with a thin sheet of light, resulting in robust, fast and gentle three-dimensional imaging of large specimens. When combined with a tissue clearing sample preparation technique, large tissue samples or whole-mount embryos up to 5 mm thick can be imaged using the Lightsheet Z.1 microscope. Optically sectioning fluorescent samples using Lightsheet microscopy can replace traditional serial sectioning in a fraction of the time while retaining the overall three-dimensional structure of the sample. Using a more traditional microscopy technique, the SteREO Lumar.V12 Fluorescence Stereomicroscope enables imaging large samples such as embryos, zebrafish and whole tissues.

Image Analysis

Key to getting the most out of microscope images is a well thought out strategy to analyse and extract meaningful data. The best time to determine the analysis approach is before starting the experiment. We can advise on image analysis approaches and help with image analysis software available at the facility, which allow image viewing, image processing and deconvolution, and two- or three-dimensional quantitative analyses. Software packages include SVI Huygens, Bitplane Imaris, Zeiss ZEN, FIJI/ImageJ, Cell Profiler and Metasystems running on seven dedicated image analysis computers.

Advanced Microscopy Centre Instruments

Image Analysis Workstations

Imaging from ATAC’s microscope systems is supported by six powerful computer workstations with software packages for digital image analysis. These computers allow researchers to extract quantitative data from microscope images, allowing them to test hypotheses and propel their research forward.

Zeiss Lightsheet Z.1 Microscope

The Zeiss Lightsheet Z.1 is a fluorescent microscope designed to image larger specimens ranging in size from 0.5 mm to 5 mm. Specimens are embedded in agarose, suspended vertically and are able to be rotated 360 degrees, allowing the entire specimen to be imaged from different views before being digitally reconstructed. A specialized objective lens and sample chamber are available for samples that have been cleared using certain tissue clearing techniques, including SCALE. The Lightsheet Z.1 is accompanied by a specialised image analysis workstation.

dSTORM Super-Resolution Microscope

The CMRI dSTORM Super-Resolution microscope is specialized for single molecule localization super-resolution imaging. Used in this way, the microscope can achieve a resolution below 50 nm. Built in-house, the microscope uses 638 nm and 532 nm lasers as light sources and can be adjusted for TIRF or ‘quasi-TIRF’ illumination. Protocols and training for super-resolution imaging are available. Due to the design and construction of the microscope, advanced safety training is essential.

Zeiss SteREO Lumar.V12 Fluorescence Stereomicroscope

The Zeiss SteREO Lumar.V12 stereomicroscope is capable of high-resolution three-dimensional imaging over a large field of view. This makes it the ideal system for imaging larger samples such as embryos, zebrafish and whole tissues. It has brightfield reflected and transmitted light capabilities, as well as a range of filters (DAPI, GFP, YFP, RFP) allowing fluorescence imaging. The Zeiss SteREO Lumar.V12 stereomicroscope is a fully motorised with a magnification range from 9.6x to 120x and is capable of multichannel acquisition, Z-stacks, time lapse and tiling experiments.

Yokogawa CV1000 Cell Voyager Microscope

The Yokogawa Cell Voyager microscope is a spinning disk confocal microscope specialized for long-term live cell imaging. The Cell Voyager enables three-dimensional imaging of fluorescently-labelled live cells. The box design maximizes thermal stability of live cell cultures while hardware autofocus can compensate for thermal drift. Features include confocal imaging of fluorescent signals, Z-stacking, time-lapse and brightfield imaging. Two types of sample chambers for live cells as well as a sample holder for fixed samples are available.

Zeiss LSM 880 Airyscan Laser Scanning Confocal Microscope

Laser scanning confocal microscopy is an essential method in cell biology research for its ability to optically section and reconstruct cellular samples in three dimensions. The LSM 880 at ATAC is the first of its kind installed in Australia. Equipped with the Zeiss Airyscan detector, this microscope allows us to visualize intracellular structures in higher resolution, up to the super-resolution level.

Zeiss Cell Observer SD Spinning Disk Confocal Microscope

Live cell imaging will enable us to establish a new paradigm for telomere research because of its capacity to visualise dynamic telomere functions in normal and cancer cells. The Cell Observer SD microscope lets us reconstruct structures inside living cells in three dimensions over time and can capture rapid cellular events occurring at a time scale of milliseconds.

Zeiss Axio Observer Widefield Live Cell Microscope

Visualizing living cells offers a dimension to experiments that fixed (preserved) specimens can’t provide. By imaging live cells over the course of hours or days, this microscope enables studying the effects of abnormal telomeres on the cell cycle, cell lifespan and genome integrity. Cells can be imaged unlabelled or tagged with fluorescent proteins.

Zeiss Axio Imager Z2 with ApoTome.2 Widefield Upright Microscopes

The two Axio Imager upright fluorescence microscopes are the ‘workhorses’ of ATAC, allowing researchers to capture images of a wide range of fluorescently-labelled cell samples. The ApoTome.2 instrument allows the reconstruction of images in three dimensions with enhanced resolution and contrast.

MetaSystems Metafer Chromosomal Analysis Microscopes

CMRI researchers pioneered the use of automated metaphase chromosome imaging in telomere research using the Metafer automated fluorescence microscopy system. ATAC’s two Metafer systems accelerate research by automating fluorescence microscopy of cancer and normal cells, enabling imaging in a few hours cell that would otherwise have taken weeks to complete.

The Australian Cancer Research Foundation Telomere Analysis Centre (ATAC) was opened in 2015 as Australia’s first centre dedicated to supporting research into the cellular functions of telomeres.

Telomeres, nucleoprotein structures that protect chromosome ends, have emerging roles in cancer risk and oncogenesis, and the telomere maintenance mechanisms that are activated in almost all cancers are prime targets for the development of new cancer diagnostics and therapeutics.

The primary scientific focus of ATAC is centred on the study of telomeres and their roles in cell proliferation, cancer and ageing, with the secondary focus to support a broad range of medical and biological research projects. ATAC was developed by Kids Cancer Alliance telomere research leaders from Children's Medical Research Institute, Sydney Children's Hospital Network, and Children's Cancer Institute. The centre was established with the support of the Australian Cancer Research Foundation (ACRF) and the Ian Potter Foundation. ACRF granted $2 million to Children’s Medical Research Institute (CMRI) to fund equipment for the centre, which is located in a purpose-built facility within CMRI's building expansion at Westmead.

Read the ATAC 2020 Annual Report: Download PDF

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