discrepant results accessing NBLAST via VFB site versus SI site

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Rachel Wilson

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Jul 19, 2016, 10:42:53 AM7/19/16
to nat-user
Thanks for this fantastic tool. We are now using NBLAST a lot to search and organize morphologies.
However, I've found discrepancies between the VFB and SI site.
Why are there discrepancies? Which version is more recent and/or more durable?

Gregory Jefferis

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Jul 20, 2016, 11:28:30 AM7/20/16
to Rachel Wilson, nat-user, Marta Costa
Dear Rachel,

Thanks for your interest. It’s great that you’re already finding the tools useful. Thanks also for writing to this list as you will probably not be the only person with these questions.

Indeed there are two separate sets of clusters and I agree this is not ideal. We decided to present only the central brain clusters in the SI (that is neurons with some arbours in the central brain, omitting those restricted to the optic lobe) because the results for the columnar regions of the optic lobe are not as good. However we had earlier released a full set of clusters to VFB and did not wish to remove those.

A few more specific comments inline.

On 19 Jul 2016, at 15:42, Rachel Wilson <rachel...@hms.harvard.edu> wrote:

Thanks for this fantastic tool. We are now using NBLAST a lot to search and organize morphologies.
However, I've found discrepancies between the VFB and SI site.
Why are there discrepancies? Which version is more recent and/or more durable?

These are not the same cluster. SI cluster 474 maps onto this cluster linked from VFB


The recipe is to take the exemplar of the SI cluster (the one with score 1.0 e.g. fru-F-700092 ) and then append that to the base url

Indeed.

Both clusters are durable in the sense that the URLs will continue to resolve even when we update the clusters that are returned by searching VFB.

@Marta, would you like to add anything.

Best,

Greg.



--
Gregory Jefferis, PhD
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 OQH, UK


Marta Costa

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Jul 20, 2016, 11:47:25 AM7/20/16
to nat-user
Hi Rachel,

It's great to know you find NBLAST useful.
The clusters on VFB include all of the FlyCircuit neurons, whereas the SI ones exclude the intrinsic optic lobe ones. So the cluster number and exemplar might be different between the sites. Though cluster composition itself might not differ that much.
We'll look into making that more explicit on both VFB and SI site. And I'll see if, for individual neuron pages on VFB like this (http://www.virtualflybrain.org/site/stacks/index.htm?id=VFB_00014678) we can add which cluster the neuron belongs to in the info section. That way you could search directly with a neuron identifier and check the cluster.

Best wishes,
Marta Costa
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