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mke...@ucla.edu
Oct 6, 2015, 4:09:48 PM10/6/15
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Hi,
I was wondering if it would be possible to search a trace (or a neuron ID from flycircuit) in registered Gal4s. Also, would it be possible to define a certain space in the brain and find all the registered Gal4s that have GFP expression there?
I'm also getting an error ('invalid neuron id') for IDs that I directly copy from flycircuit when I'm using NBLAST on the fly. I haven't tried this on the desktop version of but one example id is: Gad1-F-700090. Has anyone encountered this?
Thank you,
Greg Jefferis
Oct 6, 2015, 4:50:07 PM10/6/15
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Dear Mehmet,
Thanks for your interest in NBLAST and related tools.
On Tuesday, October 6, 2015 at 9:09:48 PM UTC+1, xxx wrote:
I was wondering if it would be possible to search a trace (or a neuron ID from flycircuit) in registered Gal4s. Also, would it be possible to define a certain space in the brain and find all the registered Gal4s that have GFP expression there?
This is obviously a major feature and something we are working on as a research project in my lab. However, I am afraid that we do not even have a prototype online for this at the moment. If you want to do searches against Gal4 lines, then presently you have to make a 3d mask and use that. There is already a thread on this user group with some rudimentary information about this (try looking for "mask search")
I'm also getting an error ('invalid neuron id') for IDs that I directly copy from flycircuit when I'm using NBLAST on the fly. I haven't tried this on the desktop version of but one example id is: Gad1-F-700090. Has anyone encountered this?
Unfortunately, that neuron is from the flycircuit v1.1 dataset. We do not have access to the original data. If you register with the site, you will be able to see download some registered data in the space of the flycircuit "typical_brain_female". Unfortunately we do not yet have a bridging registration for that template brain.
You can however look for neurons like that one. For example you can go to the superclusters page
drill down to supercluster II and then look for something similar. Perhaps this?
Best wishes,
Greg.
Greg Jefferis
Oct 6, 2015, 4:57:38 PM10/6/15
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On Tuesday, October 6, 2015 at 9:50:07 PM UTC+1, Greg Jefferis wrote:
Dear Mehmet,
drill down to supercluster II and then look for something similar. Perhaps this?
You can also try a search like this:
checking the use mean scores box. This will return the cell type for matches where known.
mke...@ucla.edu
Oct 6, 2015, 6:26:09 PM10/6/15
to nat-user
Dear Greg,
Thank you for the quick reply. I'll look into 3d masking and I'm excited about the feature your lab is working on.
Best,
Mehmet
Greg Jefferis
Dec 11, 2015, 10:41:36 AM12/11/15
to nat-user
Dear Mehmet,
I was wondering if it would be possible to search a trace (or a neuron ID from flycircuit) in registered Gal4s. Also, would it be possible to define a certain space in the brain and find all the registered Gal4s that have GFP expression there?
We have a prototype version of the functionality to search flycircuit ids against Gal4 lines. If you contact me directly, I can provide further details. We would be pleased to get feedback on our test version.
Best wishes,
Greg.
Greg Jefferis
Feb 3, 2016, 1:50:51 PM2/3/16
to nat-user
I was wondering if it would be possible to search a trace (or a neuron ID from flycircuit) in registered Gal4s. Also, would it be possible to define a certain space in the brain and find all the registered Gal4s that have GFP expression there?We have a prototype version of the functionality to search flycircuit ids against Gal4 lines. If you contact me directly, I can provide further details. We would be pleased to get feedback on our test version.
Further to this we now have a live online version of this Gal4 search available here:
Best wishes,
Greg.
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