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June 22, 2020

Detecting atherothrombosis using targeted MRI

Cardiovascular disease (CVD) is responsible for more than a quarter of all deaths in Australia and remains the global leading cause of death accounting for 17.9 million deaths per year. Of all CVDs, stroke and coronary artery disease account for the majority of deaths. A common underlying cause in these conditions in atherosclerosis, characterised by the build-up of abnormal deposits inside the arteries. Atherosclerotic plaques can rupture and cause thrombosis, or blood clots, resulting in stroke and myocardial infarction. Diagnostic strategies for the detection of thrombi are currently invasive and may not be sensitive to early biomarkers such as localised coagulation and inflammation.

A/Prof Ta, of Griffith University, has teamed up with researchers across Australia and internationally to develop a new form of MRI contrast agent. These ultra-small dual positive and negative contrast iron oxide nanoparticles (DCIONs) provide both T1-positive and T2-negative contrast effects, overcoming the limitations of single modality contrast agents. This duality is particularly important for imaging intravascular thromboses, as current single-contrast nanoparticles results in a black dye against a black artery. Further, the DCIONs are monodisperse, water-soluble, and biocompatible, of critical importance to biomedical applications.

In-vivo MRI of carotid artery thrombus (green arrows) detection after injection with a conjugated DCION. Image from Ta et al 2017.

Using non-invasive MRI at the NIF QLD Node, the application of a DCION conjugated to an enzyme found in activated platelets demonstrated accurate and sensitive detection of intravascular thrombosis. Work is continuing to further optimise the early detection of thrombi, expected to allow for earlier and more effective preventative treatments and improved clinical outcomes for patients at risk of stroke and myocardial infarction.

A/Prof Ta is enthusiastic about the future applications of DCIONs beyond thrombosis diagnoses, stating that “these nanoparticles have the potential to replace traditional gadolinium-based contrast agents due to their stronger T1 contrast effect. Existing alternatives cannot do what these nanoparticles can.”

If you have any concerns about heart disease or atherosclerosis, please talk to your GP and check this website.

June 18, 2020

Nighttime vision of the Australian Night Parrot

NIF Facility Fellow Dr Karine Mardon used CT to scan the intact skull of an exceedingly rare species, the Australian Night Parrot. These scans were compared to related parrots, finding that the night parrot may not be any better at seeing in the dark than other related species. Possibly a contributing factor to its rarity, these findings have implications for Night Parrot conservation efforts in the Australian outback.

Mysterious Australian Night Parrots in natural environment. Credit: Steve Murphy, Charles Darwin University.

Read more:

June 8, 2020

NIF Newsletter Jun 2020

Content

Research spotlights:

  • Stentrode for measuring cortical activity
  • MRTrix v.3 release
  • COVID-19 activities across NIF

Updates:

  • New NIF website, new equipment, job opportunites

Events:

  • ANZSNM online sessions
  • MBI Seminar Series
  • OHBM virtual meeting
  • University of Sydney Informatics Hub training
  • NEUBIAS Academy training
Read Online
June 2, 2020

Supporting Australia’s Healthcare and Research Ecosystem

The Australian Government’s National Collaborative Research Infrastructure Strategy (NCRIS) exists to enable national-scale research facilities, thereby facilitating Australian researchers to address critical national and global challenges effectively and efficiently. NCRIS projects provide equipment, resources, analysis tools and, importantly, expertise.

These facilities and services are providing essential resources for responding to Australian national crises, such as the COVID-19 pandemic. The NCRIS offerings pack outlines the facilities and services available to respond to Australia’s research needs during this pandemic.

As a biomedical imaging capability, NIF is well-positioned to support Australia’s Healthcare system during the COVID-19 pandemic. NIF sites across the country are involved in a variety of COVID-related activities to support Australia’s healthcare and research ecosystem.

The QLD Node (HIRF site) and The Florey Node at Heidelberg, co-located with hospital campuses, are providing clinical imaging support. This reduces patient risk by removing vulnerable groups from the hospital environment and frees up hospital equipment in case of an influx of respiratory patients.

The University of Melbourne Node is working closely with hospitals using the CT scanner to catalogue parts to be used for 3D printing – for example, parts of ventilators.

Similarly, the LARIF Node in South Australia has scaled up the 4DX technology from small animal work, successfully tested on a large animal. This offers a low-cost, easily manufactured ventilators for use with COVID-19 and ongoing use in less developed countries. An ethics application is in progress to enable production for human use.

In addition to directly working with healthcare providers, the NIF ecosystem is enabling research to support affected populations.

SAHMRI, housing the LARIF NIF node, is engaged in COVID vaccination studies in animal models. Also, the 4DX lung scanning technology is being used to investigate disease models for lung pathology.

At the University of Western Australia Node, researchers are utilising lung MRI to investigate the effect of ethanol inhalation on lipophilic viruses (including SARS-CoV-2). Through developing a deposition map for nebulised ethanol in the lungs, this study highlights a potentially inexpensive and readily available COVID-19 treatment. Find out more about this study by accessing the arXiv pre-print.

A research project is underway at the University of Sydney to bring supportive treatment to COVID patients in ICU. Researchers are testing the feasibility of implanting an Impella LVAD device via ultrasound guidance (2D and 3D intracardiac echocardiography). This work provides clinicians with more treatment options for high-risk patients without the need to transport through the hospital.

Finally, NIF radiochemistry capabilities are ready to provide clinical tracer supply as impacted by reduced import capability. The National Research Cyclotron Facility is available to supply clinical FDG to hospital sites to supplement disrupted supply chains.

Do you have a research project requiring the use of imaging facilities? COVID-related or otherwise, NIF is ready to facilitate your project with our network of instrumentation and expertise. Find out more by contacting us as admin@anif.org.au 

May 4, 2020

Stent-electrode array for cortical neural activity

Minimally invasive endovascular stent-electrode array for high-fidelity, chronic recordings of cortical neural activity

This news has been contributed by Assoc. Prof. Bradford Moffat of the Melbourne Brain Centre Imaging Unit, Department of Radiology and Medicine, The University of Melbourne, Parkville.

National Imaging Facility Fellow, Assoc. Prof. Bradford Moffat collaborated with Dr. Tom Oxley’s group at the University of Melbourne for this high profile publication[1] that appeared in the journal “Nature Biotechnology”.

High-fidelity intracranial electrode arrays for recording and stimulating brain activity have facilitated major advances in the treatment of neurological conditions over the past decade. Traditional arrays require direct implantation into the brain via open craniotomy, which can lead to inflammatory tissue responses, necessitating the development of minimally invasive approaches that avoid brain trauma. Here we demonstrate the feasibility of chronically recording brain activity from within a vein using a passive stent-electrode recording array (stentrode). We achieved implantation into a superficial cortical vein overlying the motor cortex via catheter angiography and demonstrate neural recordings in freely moving sheep for up to 190 d. Spectral content and bandwidth of vascular electrocorticography were comparable to those of recordings from epidural surface arrays. Venous internal lumen patency was maintained for the duration of implantation. Stentrodes may have wide-ranging applications as a neural interface for treatment of a range of neurological conditions. The following figures are representative images that appear in the article and were generated from data acquired on the 7T MRI scanner at the University of Melbourne node of NIF.

Figure 1: Superficial cortical venous variability in humans and a sheep model; from [1]
Figure 2: Vascular electrocorticography: somatosensory evoked potentials; from [1]

This technology has been licensed by Synchron and is in currently undergoing a first in man clinical trial (https://www.synchronmed.com/stentrode/). For further information, the interested reader is pointed to our full publication which can be accessed at (http://dx.doi.org/10.1038/nbt.3428).

References

  1. Oxley, T.J., N.L. Opie, S.E. John, G.S. Rind, S.M. Ronayne, T.L. Wheeler, J.W. Judy, A.J. McDonald, A. Dornom, T.J.H. Lovell, C. Steward, D.J. Garrett, B.A. Moffat, E.H. Lui, N. Yassi, B.C.V. Campbell, Y.T. Wong, K.E. Fox, E.S. Nurse, I.E. Bennett, S.H. Bauquier, K.A. Liyanage, N.R. van der Nagel, P. Perucca, A. Ahnood, K.P. Gill, B. Yan, L. Churilov, C.R. French, P.M. Desmond, M.K. Horne, L. Kiers, S. Prawer, S.M. Davis, A.N. Burkitt, P.J. Mitchell, D.B. Grayden, C.N. May, and T.J. O’Brien. ‘Minimally invasive endovascular stent-electrode array for high-fidelity, chronic recordings of cortical neural activity’, Nat Biotech, 2016. 
April 28, 2020

MRtrix3

MRtrix3: Advanced tools for the analysis of diffusion MRI data

Diffusion-weighted MRI (dMRI) is a commonly-used medical imaging modality for the investigation of tissue microstructure, exploiting the local hindrance and restriction of water diffusion as indirect probes. The neuroimaging research community utilises this technology extensively for the study of brain white matter in particular, reconstructing structural connectivity pathways and analysing estimated tissue properties. To do so requires extensive complex computations, including image pre-processing, biophysical modelling, digital reconstruction of neuronal fibre trajectories, and tailored statistical analysis and visualisation tools. The quality and capabilities of neuroscience research utilising this technology – as well as other applications such as neurosurgical planning – rely on all utilised aspects of this pipeline being robust yet powerful.

The recently released MRtrix 3.0.0 is a free, open-source software package that incorporates various state-of-the-art technologies in the field of dMRI, combining high computational performance with a consistent, user-friendly interface. It is built principally around the “spherical deconvolution” model, which is regularly utilised in the field as the reference model for optimal resolution of the various complex fibre configurations found throughout the brain white matter. Additional tools are provided for both quantitative estimations of structural connectivity between brain grey matter regions, and data-driven hypothesis testing of quantitative white matter imaging metrics, in the presence of such tissue complexity.

Figure 1 – “MRView”, the MRtrix3 visualisation tool. Anatomical-contrast image is displayed in “volume render” mode, with additional “clip planes” exposing internal contents of this three-dimensional image. Orange and cyan highlights correspond to delineations of the left and right precentral gyri respectively, responsible for voluntary motor movement. Coloured lines are the reconstructed streamlines tractography trajectories connecting these two regions through the corpus callosum, the principal pathway for inter-hemispheric brain communication. The overlay window at bottom-right shows the “Fibre Orientation Distribution”: at the spatial location manually selected in the interactive viewer, this captures the orientations of underlying white matter fibre bundles as estimated by the spherical deconvolution model.

An international collaboration of researchers has recently published the implementation of MRtrix3 in the peer-reviewed journal, NeuroImage. Lead author Dr J-Donald Tournier and colleagues provide “a high-level overview of the features of the MRtrix3 framework and general-purpose image processing applications provided with the software”, highlighting the guiding principles of development including reproducible neuroscience and consistent documentation. This manuscript also details the underlying software framework and Application Programming Interface (API) of the MRtrix3 software to encourage utilisation of its library features by other neuroscience methods developers.

NIF Facility Fellow Dr Robert Smith, of the Florey Node, is one of two principal developers of this software package, with over 3,200 code commits and 220,000 lines of code contributed. His involvement with the software project began not long after the commencement of his PhD candidature in 2009, for which Dr Tournier was a supervisor. The two key technical developments resulting from his PhD – the “Anatomically-Constrained Tractography (ACT)” and “Spherical-deconvolution Informed Filtering of Tractograms (SIFT)” methods (each of which has over 250 citations on Google Scholar) were developed & distributed with the MRtrix3 package, improving the biological accuracy and quantitative properties of white matter connectivity experiments throughout the worldwide neuroscience community.

Figure 2 – MRtrix workshop held in Antwerp in 2019, bringing together 50 researchers to join the MRtrix3 community and improve their MRI analysis capabilities

The MRtrix3 community forum, where users of the software interact directly with developers and one another, currently has over 900 active users and over 1.5 million page views. The manuscript describing the previous version of this software (“MRtrix 0.2”), published in 2012, now has over 500 citations; while the MRtrix3 manuscript was published too recently to accumulate a large citation count, its long-term influence would be reasonably expected to exceed this. Google Scholar searches yield over 1500 hits for “mrtrix diffusion mri”, and over 450 hits for “mrtrix surgery”. Some of the capabilities included in MRtrix3 are incorporated in Siemens’ Track Density Imaging and tractography prototype, currently available for early testing at participating Siemens MRI research sites. The software is also utilised by many companies that specialise in providing third-party services for image processing and analysis. The development team additionally runs software workshops to teach usage of the software to the research community.

Figure 3 – A screenshot of the MRTrix3 community page

The tools provided within this software package can improve the accuracy and utility of diffusion MRI analysis in many contexts, both neuroscientific and clinical. This will, over time, include characterisation of various brain disorders, tracking the efficacy of potential treatments of such, neurosurgical planning, and diagnosis.

This story was contributed by Dr Robert Smith. For more information, please visit the MRtrix3 website, community forum, GitHub repository, or follow on Twitter.

Quick coding demo showing dwi2response with four different modes; debug, default, info, quiet
April 14, 2020

Resources for Working from Home

NIF Central has been working from home for over 3 weeks now, and we’re just starting to find our rhythm! From daily video catchups to messaging apps, we’re keeping in touch. But this is a marathon, not a sprint, and we are always looking for ways to improve! Here is a collection of resources that I’ve found useful.

There are upsides and downsides to working from home. This Conversation article, written before the crisis, overviews some of the research into working from home generally.

It’s important to learn from those of us who came before – researchers in isolated field studies and sailors, for example.  Some tips for coping with isolation during lockdown are outlined here. Of course, they didn’t have to worry about home-schooling and childcare. Representing a suite of new challenges,  this guide for WFH with kids may give parents and carers some tips.

Some academics swear by the Pomodoro Technique to get things done. This is a time management technique that exploits deadline anxiety to overcome procrastination – if you’re having difficulty getting anything done while you work from home, this may help! Trackers such as these are also a good way to ensure you’re not working all the time.

LinkedIn has provided 16 online courses for those looking to maximise efficiency, manage the transition to work from home, and manage teamwork. These are particularly good if you’re unable to process all the reading you’ve been doing lately, as they’re video delivered!

Let’s get real for a moment – you can be forgiven if you don’t find time to put any of these ideas into practice! Even finding the energy to consume the resources provided might be enough to put you over the edge. So, I’m going to share these articles, in particular, to outline why your productivity might be down (and why that’s okay) and some steps you can take for your mental health and long-term productivity.

Are you relying on social media to get your social fix? Here are some hashtags on Twitter that you might like to follow:

#PhDChat – posts by or for PhD students

#ECRChat – posts by or for early career researchers

#AcademicChatter – posts by or for academics

#workingfromhome – posts about working from home

There are some good pieces of advice coming out on Twitter about managing your life when you work from home. See for example: Getting things done without going to the lab, WFH with kids,  and videoconference etiquette.

What hashtags and social media gurus are you following? Let us know! We’re here to help and enjoy hearing from you.

April 9, 2020

National Imaging Facility expands to include HIRF

The capacity to undertake research into dementia, mental illness, brain injury (e.g., stroke), and cancer in South-East Queensland has been greatly enhanced through the expanded human imaging capabilities of the National Imaging Facility (NIF).

The QLD Node now includes UQ CAI and HIRF

The NIF has formally expanded its Queensland Node, allowing for the translation of new imaging approaches into the clinical space.

The expansion brings together the capabilities of the Herston Imaging Research Facility (HIRF), based at Royal Brisbane and Women’s Hospital’s Herston Precinct and the University of Queensland’s Centre for Advanced Imaging (CAI) as a powerful joint node in Queensland.

The NIF Queensland Node Director, Prof Markus Barth, says, “the extension of the NIF Queensland Node will increase the medical imaging capabilities and improve translation from pre-clinical imaging to patient populations.”

HIRF is a research facility, primely positioned to conduct imaging research and clinical trials in patient populations.

Prof Michael O’Sullivan, Director of HIRF, adds, “Most of all, this (expansion) is excellent news for patients. Part of NIF’s mission is to move advanced imaging closer to the translational interface. At HIRF, our focus is to use advanced imaging to help tackle major health challenges that we find in our local population.”

HIRF was established as an alliance between Metro North Hospital and Health Services, QIMR Berghofer Medical Research Institute, Queensland University of Technology, and the University of Queensland.

HIRF contributes three cutting-edge research scanners, based at a hospital site, to the NIF network.

This expansion dramatically increases the capacity of Queensland’s clinical research portfolio through multimodal imaging – magnetic resonance imaging (MRI), positron emission tomography (PET), and computed tomography (CT) scanning modalities.

Its position on Herston Campus provides not only access to large patient cohorts but certified radiochemistry facilities for a broad range of PET radiotracers.

Prof Graham Galloway, NIF CEO, says, “NIF commends the Queensland Node for this collaborative partnership of campuses across multiple institutions to deliver a comprehensive and coordinated imaging capability to researchers, not only in Queensland, but nationally and internationally.”

For more information about the NIF, please contact:

NIF CEO, Prof Graham Galloway – g.galloway@uq.edu.au

NIF Engagement Manager, Dr Noni Creasey – r.creasey@uq.edu.au

NIF would like to thank the Queensland Government for their support at the Queensland Node.

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