CAPABILITIES

The Imaging CoE combines world class expertise with capabilities across all the key imaging workflow elements – sample preparation and optimisation, data acquisition, data analysis and visualisation. Our data acquisition techniques span a wide range of length scales from the macroscopic whole animal or whole tissue imaging down to atomic scale imaging.

Core Capability:

Imaging technologies & expertise across multiple length and time scales

X-Ray Free Electron Laser (XFEL) Nano Crystallography

Synchrotron Macromolecular Crystallograph

Cryo – Electron Microscopy

Single Molecule Localisation Microscopy

Super-Resolution Microscopy

Adaptive Micro endoscopy

Confocal Microscopy

Two-photon Microscopy

Fluorescence Microscopy

Imaging Centre physicists are actively engaged in the use of new large international X-ray Free Electron Laser facilities (XFEL) at Standford (LCLS), Japan (SACLA) and Germany (European XFEL). These combine large scale accelerator technology with sophisticated detector systems and huge computer farms for data collection and handling.

Light sources: XFEL sources are able to produce incredibly bright pulses of X-rays with wavelengths ranging from 1keV-10keV and with pulse durations ranging from a few femtoseconds to 100 femtoseconds. These light sources are tunable, can be operated in two colour mode and have a repetition rate ranging from a few Hz to a few kHz. These light sources are unique because that offer the possibility of capturing chemical and biological processes in a snapshot revealing critical information about dynamical processes.

In particular these facilities have been developed to realise the long-held ambition of imaging the structures of biomolecules in close to their native state without the need to form crystalline samples.

Detectors: Enormous investment has gone into the development of detection systems which are able to capture and read out the scattered signal generated by diffraction experiments using XFEL sources. The detectors are constructed from panels that are configured in such a way to maximise their ability to record scattered photons while allowing unscattered photons to pass through a central hole. The unscattered photons can be recycled in further experiments directly downstream.

Data collection and handling: Each femtosecond pulse scatters photons into a large detector array and at atomic resolution over a large angle. Each pulse, therefore, consists of an array of data involving several mega-words of information. Experiments typically run for more than a day and generate many terabytes of data. In order to maintain the flow of information from the detectors large processing farms are attached to these facilities to collect, store and process the data. Then use of an XFEL more closely resembles experiments in particle or astrophysics than conventional laboratory-based imaging techniques.

The Centre’s researchers have access to X-ray Free Electron Laser beamlines at the European XFEL through our Centre partners, the Deutsches Elektronen Synchrotron (DESY), and the Linac Coherent Light Source facility (LCLS) at Stanford University. The ultrahigh energy, femtosecond pulses of X-rays generated at these facilities could potentially be a revolutionary technique for protein crystallography by enabling structure determination of very small crystals.

The Centre’s researchers are heavy users of the Australian Synchrotron at ANSTO, particularly the Macromolecular Crystallography (MX) beamlines, which are a crucial and routine instrument used to determine structures of microcrystals. The Centre’s formal partnership with the Australian Synchrotron allows us to embed researchers at the Synchrotron itself. This enables us deeper insight into the design and operations of these instruments as well as provide the Synchrotron with closer access to key users and their research outputs and needs.

Centre CIs Jamie Rossjohn and James Whisstock were part of a team of scientists who won a $2M grant to upgrade and install a new state-of-the-art detector on the MX beamline that enabled faster and higher resolution image acquisition.

The Clive and Vera Ramaciotti Centre for Structural Cryo-Electron Microscopy at Monash University was launched in February 2015. This facility enables researchers to access word-class biological electron microscopy facilities and expertise in a burgeoning field that has been declared Method of the year 2015 by Nature Methods.

In 2015 also, a unique $5M electron microscope was launched at Monash University, Clayton campus. Transforming the way we view the human immune system and advance Australian research towards better treatment for diseases from cancer and malaria to diabetes, rheumatism and multiple sclerosis.

The Ramaciotti Centre and the FEI Titan Krios Cryo-Electron Microscope are central to the work of the Imaging CoE, of which Monash University is a lead partner.

Single Molecule Science – the ability to observe and track individual molecules and monitor molecular interactions in living cells – heralds a revolution in biology. It’s a collaboration between biologists, physicists and engineers that feeds off the capacity of new microscopes and other technology to identify single molecules and analyse their behaviour in intact samples. It has emerged from developing, using and combining technologies such as single-molecule fluorescence and super resolution microscopy, atomic force microscopy, optical and magnetic tweezers, new sensors and more sophisticated computing and mathematical techniques. Single Molecule Science presents us with a new way of understanding life processes from the bottom up, following the paths and changes of many different molecules as they move through the cell, form complexes with other molecules, and influence cell function.

Data collection and handling: Researchers are developing novel algorithms that will extend the Centre’s capabilities in quantitative super-resolution imaging. Some of the tools under development are: molecular counting, stoichiometric analysis, cluster analysis, filament tracking, mapping dynamic molecular interactions, 3D membrane topography analysis, 3D organelle and cell morphology analysis. For example, the questions with respect to the 3D membrane topography analysis relate to how extra optics can be used to establish 3D maps of the cell membrane at nanometre resolution. The aim is to create a membrane landscape in order to view whether or not this will correlate to protein function and to see if the distribution of TCRs is correlated with the surface topology of the membrane. The research will also solve fundamental questions in signal transduction such as signal integration and signal amplification.

Through working on both hardware and software solutions we hope to optimise and develop novel single molecule and super-resolution fluorescence microscopy approaches.

Advanced hardware: Imaging CoE single molecule scientists focus on transforming medicine by providing a molecular perspective on complex biological systems and processes, encompassing biophysics, biochemistry and cell biology as well as nanotechnology and nanofabrication. They are building cutting-edge instruments by gaining access to pre-commercial equipment and designing and building new microscopes. There are currently over ten different microscopes in operation in the Single Molecule Science Lab at UNSW node.

Each microscope contributes to the goals of the Centre by being optimised for different applications: speed, resolution, imaging depth, multi-colour imaging.

Enabling/Auxiliary Capabilities:

The Monash Antibody Technologies Facility (MATF) is a world-class antibody facility servicing Monash University and the broader scientific community.

MATF provides services for antibody production, assay development, robotics, high throughput screening and antibody characterisation. It uses state-of-the-art equipment to support researchers not only from Monash University, the Imaging CoE but elsewhere in Victoria, Australia and worldwide.

The platform primary focus is on generating high-affinity monoclonal antibodies through advanced discovery techniques and antibody engineering.

The Monash Protein Production Unit (PPU)  offers expertise in protein expression, purification and optimisation using the latest high-throughput platforms.

The PPU has the capacity to express and purify large numbers of recombinant proteins for a variety of research purposes in a high-throughput manner. Our platform offers expertise in optimising the expression and purification of recombinant proteins (E.coli, yeast, insect cell and mammalian).

Macromolecular crystallography provides unparalleled details of the 3D structures of biological macromolecules and provides the basis for the rational design of therapeutics.

The Monash Macromolecular Crystallisation Facility (MMCF) delivers access to a fully automated platform for the high-throughput crystallisation of biological macromolecules. The use of robotics allows for miniaturisation of crystallisation experiments, which enables screening of a wide range of conditions with/from limited sample volumes.

The Monash Immersive Visualisation Platform (MIVP) operates Monash University’s advanced, immersive and large scale visualisation facilities, ranging from the ultrascale CAVE2TM down to personal head-mounted virtual reality (VR) devices like Oculus Rift.

 

  • The Multi-modal Australian Sciences Imaging and Visualisation Environment (MASSIVE) and the Victorian Life Sciences Computation Initiative (VLSCI) are the Centre’s primary partners for high-performance computing for computational imaging, data processing and visualisation. Access to these high-performance supercomputing clusters is crucial as our imaging datasets continue to grow rapidly and can generate up to terabytes of data per day.
  • MASSIVE
  • VLSCI