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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