Re: Request for information on the Innervation pattern of Local Interneurons

[Dr Gregory Jefferis]

Dear Prateek,

The neuprint API provides information about glomerular innervation.

You can access this as follows using the R neuprintr API

library(neuprintr)
library(dplyr)
# make sure we connect to hemibrain dataset
hbconn=neuprint_login(dataset='hemibrain:v1.2.1')
ln2pmeta=neuprint_get_meta("/type:lLN2P_[abc]", conn=hbconn)
roi.innerv=neuprint_get_roiInfo(ln2pmeta$bodyid, conn = hbconn)

# make a nice label for each LN
ln2pmeta <- ln2pmeta %>%
  group_by(type) %>%
  mutate(label=paste(type, 1:n())) %>%
  ungroup()

roi.innerv.mat <- roi.innerv %>%
  select(starts_with('AL-')) %>%
  # change downstream to upstream for inputs
  select(ends_with("(R).downstream")) %>%
  # extract glomerulus from column names
  rename_with(~sub("AL-([^(]+)\\(.*","\\1", .x)) %>%
  replace(is.na(.), 0L) %>%
  data.matrix()
rownames(roi.innerv.mat) <- ln2pmeta$label
heatmap(roi.innerv.mat, scale = 'col', Colv = NA)

I would recommend this approach for convenience. However the built-in glomerulus ROIs are slightly different from those used in the paper for analysis. For that we used the AL-PN meshes distributed with the paper together with the XYZ locations for synapses. You could contact Sri (cced) if you want more information.

Best wishes,

Greg Jefferis.

On 9 Aug 2023, at 10:42, PRATEEK YADAV wrote:

Dear Dr. Gregory Jefferis,

I hope this email finds you well. I recently had the opportunity to read
your excellent research paper titled "Information flow, cell types and
stereotypy in a full olfactory connectome".

I am writing to inquire about the methodology employed in determining the
glomerular innervation pattern of individual local interneurons as
presented in your paper. The detailed data regarding this aspect would
greatly contribute to my understanding of neuronal connectivity in the
context of the fly olfactory system.

*Specifically, how was it determined which neuron innervates
which glomeruli? Because, in the hemibrain dataset, I could only find out
innervation of any glomerulus only indirectly, via the type of Projection
Neurons (uni or biglomerular) that LNs synapsed with. *

I couldn't find this info even in the publication by Chou et al: "Diversity
and wiring variability of olfactory local interneurons in the Drosophila
antennal lobe. Nature Neuroscience".

I would sincerely appreciate any guidance or insights you could provide. If
there are any supplementary materials or references that I might have
missed, I would be grateful for your direction.

Thank you very much for your consideration.

Warm Regards
Prateek Yadav
IPhD Student
IISER Tirupati, India

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Gregory Jefferis, PhD Tel: +44 1223 267048
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 0QH, UK

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://jefferislab.org
http://www.zoo.cam.ac.uk/research/groups/connectomics