How to find BodyID for each exact neuron within a driver?

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miri...@gmail.com

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Feb 24, 2021, 9:23:36 AM2/24/21
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How to find BodyID for each exact neuron within a driver?

For example, the R23E10-GAL4 driver has (I think) 24 neurons.  When I view this on Neuronbridge thousands of single-neuron images appear with which to compare to the driver image (all with their own individual bodyID).  
Is there a way to know the EXACT body ID of the neurons within this driver or is it just a case to scrolling through the thousands of Neuronbridge images to find a best fit? This seems to be a very unreliable method and don't feel that i'd be able to trust my results if I did this.

jefferis

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Feb 24, 2021, 12:23:30 PM2/24/21
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Dear miridyson, 

Thanks for your interest in VFB.

Do you want to find the exact hemibrain bodyid for the neurons in R23E10? Unfortunately that is not really a question with a direct answer. First you need to decide which class of neurons you are interested in – likely the dFB neurons that are most strongly labelled – in R23E10.

What you can then hope to do is identify the specific dFB cell types defined by that driver line (e.g. based on morphological analysis of flip out data – assuming that the exact same set of neurons are labelled with a flipout reporter as with the original GFP reporter). Then using quantitative comparisons of the morphology, you can try to cross match those cell type(s) with cell types defined in the hemibrain EM dataset. You should not typically expect a 1 to 1 correspondence for every neuron in an image of R23E10 with hemibrain reconstructions. Indeed the total number of cells may also be slightly different. 

Incidentally, sorry you didn't get a spot on the workshop. We could have filled it three times over with relatively little advertising, so it seems there is unmet need. Anyway as a mini-connectomics workshop for you, please find attached a code example showing how you can whittle down candidate types. If you send me an email off list, I can send a link to a cloud instance that you can use to try out the code interactively without needing to install anything.

Best wishes,

Greg Jefferis.

Plot of mean neuron bridge score for sample R23E10 flip out data vs different hemibrain cell types occupying the PDL05 Cell body fibre tract.

r23matchingtypes.png
R23E10.zip

Greg Jefferis

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Feb 24, 2021, 1:03:40 PM2/24/21
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By the way you may also want to take a look at the worked examples that Alex Bates has put together here:

http://natverse.org/neuronbridger/

The function neuronbridge_search provides a way to fetch the hits for a given query id (including hemibrain neurons or GAL4 lines).

All the best,

Greg.

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