Hi everyone,
I'm currently using the Allan Brain Atlas's Mouse Brain Connectivity tool (http://connectivity.brain-map.org/) to look at the connectivity between certain sensory and association brain regions. However, most of the literature on neural tracer studies uses different nomenclature for brain regions, and more specifically almost the entire literature uses different nomenclature than the Allan Brain's Mouse Brain Reference Atlas.
For example in the literature, the primary auditory cortex is often referred to as A1, the Auditory Core areas (A1 + AAF), Brodmann area 41, or Te1. Yet, the Mouse Brain Reference Atlas uses the name 'Auditory Areas', which they subdivide in the 'Dorsal auditory area', 'Primary auditory area', 'Posterior auditory area', 'Ventral auditory area'. In this case, I figure, 'Primary auditory area' is the region that I'm looking for, as it probably corresponds to A1 (and maybe AAF too?).
If this is the case then I can of course estimate for each brain region described in the literature its relative position to the primary sensory areas and then sort of guess in what Reference Atlas region it most likely is.. However, this seems rather imprecise, and also it will take a very long time.
So my question here is:
1) How can I find out what the regions of the Mouse Reference Atlas comprise of?
2) Is there potentially a mouse brain anatomy database, which allows you to quickly look up all/most of the different names used for certain brain regions?
3) Is there a database to identify homologues for brain regions across species?
Also, other tips to tackle this problem would be most welcome.
Best wishes and many thanks!
Jesse
Hi
I don't think there is a comprehensive single source for your topic. You should look for synonyms or abbreviations for the area you're studying. But data in the links below may help you.
1. Index of Abbreviations (In paxinos atlas the rat brain)
2. http://www.mbl.org/abbreviations/abbrev_frame.html
3. APPENDIX 2. NOMENCLATURE OF THE ALLEN REFERENCE ATLAS (in the link http://help.brain-map.org/download/attachments/2818169/AllenReferenceAtlas_v1_2008_102011.pdf?version=1)
Best wishes
For human brains, the hard work of comparing cytoarchitecture and myeloarchitecture-based maps in single subject cadaver brains has never been performed. Because only myeloarchitecture is visible in-vivo (best using quantitative T1 mapping), classification of cortical areas thus remains incomplete. Matching Brodmann areas to von Economou areas (both cytoarchitecture) is reasonably reliable, and the Jülich cytoarchitectural maps have built on these earlier studies. Chemoarchitecture, as developed by Zilles and colleagues, is well linked with such maps--although it is revealing further subdivisions of established cortical areas.
However, the areas painstakingly defined by Vogt and Vogt (1919) using myeloarchitecture have not yet been fully correlated with these maps. There is a crying need for this work to be done, which would at last enable unambiguous assignment of the specific functional range of regions of cortex to their specific neural organization. Modelling brain function without this capability will remain vague and speculative.
It will also be of enormous value to correlate myeloarchitecture and cytoarchitecture with gene expression, as the Allen Institute is starting to do.
Looking through the paper already mentionned above: http://help.brain-map.org/download/attachments/2818165/HBA_Ontology-and-Nomenclature.pdf?version=1&modificationDate=1382051847989
you will find this website: http://braininfo.rprc.washington.edu/
which might be of some help. Otherwise I think you are left with coming up with your own list of abbreviations and names for your favorite parts of cortex...
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