I have confocal images of immunostained adult Drosophila brains, and I want to find out more about the neurons that are labelled in my images. I am looking for an online tool where I could ideally select a small brain area and get links to published/database info about the function of specific neurons in that brain area. Could anyone please suggest the best way to do this? Thank you!
Virtual Fly Brain were certainly setting up to do something like that a couple of years ago. I've not looked into it too much since, but you can try it out with the link below
http://www.virtualflybrain.org/site/vfb_site/home.htm
Dear Olena,
As Lewis says, virtual fly brain (VFB) allows you to do this, so long as your starting point is a named neuropil region. There are sample queries linked from the home page
http://www.virtualflybrain.org/site/vfb_site/home.htm
To my knowledge VFB is the only public tool that will take you from a brain region to
In particular if you have confocal images in front of you and you want to find examples of neurons that might contribute to those expression patterns, right now your best best is the "neurons with some part in this region (clustered by shape)" search. There is an example on the home page: Find images of single neurons with some part in the ellipsoid body:
http://www.virtualflybrain.org/do/cluster_list.html?action=cluster_found&id=FBbt:00003678
Another database which you might like to look at is Kei Ito's Flybrain Neuron Database http://ndb.flybrain.org – this includes descriptions of neurons and links to the literature.
If you want to define your own arbitrary region of interest, there is presently no publicly available tool that will let you do this, although various groups such as Janelia Farm, Barry Dickson/VRVis (see brainbase.imp.ac.at) and my own group at the MRC LMB in Cambridge have internal tools or at least strategies for returning images matching criteria like this. However you will still have to revert back to VFB/Flybrain Neuron Database if you wanted to find out names and literature links for neurons.
Finally, you may find this hierarchical clustering of the flycircuit.tw dataset of interest
http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/clusters/
Best wishes,
Greg Jefferis.
(now one of 4 PIs for VFB)
Dear Greg,
Thank you for a lot of useful information! I have looked at the VFB, and I think the linkouts are to the literature where the neurons' anatomy was originally published, but not the neurons' function (please correct me if I'm wrong). Ideally, I was looking for a resource where, say, selecting ORNs would link to papers about the ORNs' responses to odorants, etc. Maybe VFB could incorporate this feature in the future? ;)
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