Compare Uploaded Tracing with FlyLight Gal4 lines

[Isabel D'Alessandro]

I see that using NBLAST on-the-fly, you are able to compare a FlyCircuit clone against all FlyLight Gal4 lines with NBLAST. Is it possible to similarly compare an uploaded tracing (or something like a segment of a FlyCircuit neuron) against the Gal4 lines? Is this feature also available using nblast directly in R? In trying to look into this, I came across the following link which is supposed to contain the dotprops data for the GMR Gal4 lines. However, the link appears to be broken. 

http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/www/nblast_desktop/

Apologies if there is some documentation that I'm missing. 

Thanks for your help 

Isabel

[Greg Jefferis]

Dear Isabel,

On Friday, July 12, 2019 at 10:49:13 PM UTC+1, Isabel D'Alessandro wrote:

I see that using NBLAST on-the-fly, you are able to compare a FlyCircuit clone against all FlyLight Gal4 lines with NBLAST. Is it possible to similarly compare an uploaded tracing (or something like a segment of a FlyCircuit neuron) against the Gal4 lines? Is this feature also available using nblast directly in R?

As you guess, this is currently only possible in R.

 

In trying to look into this, I came across the following link which is supposed to contain the dotprops data for the GMR Gal4 lines. However, the link appears to be broken. 

http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/www/nblast_desktop/

The page has now been updated with corrected download instructions. If you search the forum you will see that Hideo Otsuna had a similar question a while back.

Best,

Greg.

[Isabel D'Alessandro]

Hi Greg, 

Great, thank you! One more quick question- which template brain do query neurons need to be registered to in order to perform an NBLAST search with this dataset? 

Thanks again,

Isabel

[Greg Jefferis]

Hi Isabel,

Sorry it seems like I missed your follow-up at the time. Info below for posterity.

Best,

Greg.

On Monday, July 15, 2019 at 5:33:09 PM UTC+1, Isabel D'Alessandro wrote:

 

Great, thank you! One more quick question- which template brain do query neurons need to be registered to in order to perform an NBLAST search with this dataset? 

We bridged that dataset into the same FCWB template brain space as the neurons. You can check this yourself by plotting some of the data.

library(flycircuit)

gmrdps<-read.neuronlistfh("http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/gmrdps/gmrdps.rds",

                          localdir=getOption('flycircuit.datadir'))

open3d()

plot3d(gmrdps[1:10])

library(nat.flybrains)

plot3d(FCWB)