A Seminar to Remember!

By Warda Syeda

Last week, I attended an extremely informative introductory seminar by Dr Victoria Perreau about multiple Mouse and Human Brain Atlases and their associated suite of tools developed by Allen Institute for Brain Science – and it was awesome!

Dr Perreau is a leading researcher in the fields of bioinformatics and genomics. She is associated with the Florey Institute of Neuroscience and Mental Health and is also the Bioinformatics core coordinator, providing support and accessible expertise to neuroscientists in different areas of bioinformatics.  

This hour long seminar was a part of Neuroscience Seminar Series regularly held at Melbourne Brain Centre. At the start of the presentation, Dr Perreau introduced the online public resources of Allen Brain Institute and its brain atlas initiatives. 

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Allen Brain Atlases of Mouse and Human Brains are a unique online resource that allow scientists and researchers to view and search extensive gene expression data, neural connections, single cell characterisation and neuroanatomy - and there are over 40,000 genes in a mouse brain only!

During the seminar, Dr Perreau highlighted the fact that Allen Institute is a non-profit research organization dedicated to extending the frontiers of research and technology in bioscience. Their open science model allows them to share data, tools and knowledge with a global research community. They aim to promote easy and open access to scientific data as soon as it is useful to further our knowledge of biology - bioinformatics in particular. Under their brain atlas initiative, they have developed a huge repository of searchable brain atlases that can be accessed by their online data portal. These brain atlases include but are not limited to

  • Allen Mouse Brain Atlas
  • Allen Developing Mouse Brain Atlas
  • Allen Spinal Cord Atlas
  • Allen Mouse Brain Connectivity Atlas
  • Allen Human Brain Atlas
  • Allen Cell types

At the start of her talk, Dr Perreau introduced the basic concepts of annotated 3D reference space, anatomical slice directions, gene expressions, hybridization probes and gridding for 3D brains and grid data search services of Allen atlas. After covering the basics, Dr Perreau proceeded to explain the above-mentioned Atlases in detail.  

One of the most important contributions of Allen Brain Institute is the Anatomic Gene Expression Atlas (AGEA), which is used to quantitatively and interactively know where exactly a gene is expressed in the brain and how one particular gene correlates to other genes in specific regions of interest. Furthermore, it is also possible to carry out connectivity analysis between different regions of the brain based on gene expressions. 

Besides AGEA, the online data portal also offers high resolution developing and mature mouse and human brain atlases. These atlases are supported with a strong toolset to facilitate researchers in analysis. Recently, one of the Allen Brain Institute Atlases adorned the cover of nature magazine!

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(Image source: https://storify.com/2queues/join-our-technology-to-build)

Dr Perreau concluded by showcasing one of her worked examples of SLC1A gene expression in mouse brain. Overall, this neuroscience seminar was an excellent learning experience and I immensely enjoyed great visualisation of human and mouse brains.

If you are a neuroscience newbie struggling to tell the difference between Thalmus and Hippocampus or a researcher lost in intricacies of brain AND can fully relate to *the image* below, then head straight to http://alleninstitute.org. You can thank me later :D.

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DaRIS/Mediaflux at The Melbourne Brain Centre Imaging Unit

by Dr. Neil Killeen and Dr. Brad Moffat

The Melbourne Brain Centre Imaging Unit at Parkville (part of the National Imaging Facility) operates state of the art imaging systems in the form of Siemens PET/CT and 7-Tesla MR scanners. These systems image a diverse range of subject material including humans, anatomical samples and minerals. 

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Figure - A demonstration of the powerful static magnetic field in the 7T MR scanner (the metal bulldog clip is on the end of a chain).

A primary focus is on human neurological disease and the unit is closely engaged in clinical research projects that may lead to new therapies. The Unit places emphasis on being strongly engaged with the research community to enable the best use of its systems. A key part of this is an effective means of managing and delivering data to research teams.  

At the heart of the Unit’s data operations is the DaRIS (Distributed and Reflective Informatics System) data management capability.  DaRIS has been developed in collaboration with Arcitecta, Monash University and the University of Queensland.  DaRIS is a rich set of Mediaflux plugins (including a web-based portal).  It’s particular niche is for the handling of bio-medical imaging data for research projects, although it can be used more broadly.

DaRIS receives data directly from imaging scanners.  It operates in the dual role of providing the Unit with a comprehensive archive as well as providing researchers with convenient access to their data.  Distributed research teams access their data from DaRIS and deposit it in compute platforms or run integrated workflows to analyze it. 

The Imaging Unit’s DaRIS system utilises many of Mediaflux’s extensible framework characteristics with a DICOM engine that matches the DaRIS data model, a DICOM client for on-sending data to other DICOM servers, sinks to which (big) data can be deposited (e.g. scp and owncloud), and inter-operability with FileMakerPro servers (ensuring that critical meta-data are synchronized and accurate).  DaRIS also supports a RESTful API as well as the service interfaces.

The diagram shows the busy deployment at Parkville (there is a similar setup at Monash Biomedical Imaging [MBI]).  The instruments (MBC Imaging Unit, other NIF, Royal Children’s Hospital and MBI) can send data to the appropriate DaRIS system (e.g. Parkville for parkville precinct people and MBI for Monash precinct people). The deployment utilises other national infrastructure including RDSI storage, NeCTAR National Servers Program Virtual Machine, fast networks, HPC compute platforms, and ANDS for meta-data harvesting to RDA.

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DaRIS is deployed at a number of facilities and platforms around Australia (e.g. the National Imaging Facility). For more information, see the DaRIS wiki or find the code on github.

DaRIS is now available more broadly to the Victorian community via a central VicNode service. If you are interested in using this, or operating your own DaRIS, please contact VicNode (http://www.vicnode.org.au).

For more information about the Melbourne Brain Centre Imaging Unit  see http://www.neuroscience.unimelb.edu.au/content/melbourne-brain-centre-imaging-unit and also this newsletter article on the Unit - http://us7.campaign-archive2.com/?u=360e08c4bfc022c47854240f1&id=11d155162a

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