Public data and code for connectomic analyses in Taisz, Galili et al. (2023)
To analyse connectomic data we relied on the natverse toolbox from our group: Bates et al. (2020).
https://natverse.org/
Datasets:
- FAFB – Zheng et al. (2018), Li et al. (2020), Dorkenwald et al. (2022) Manual tracings of FAFB neurons were deposited at https://catmaid-fafb.virtualflybrain.org/
We used the rcatmaid package to query data from CATMAID, and the fafbseg package to query data from FlyWire.
https://natverse.org/rcatmaid/
https://github.com/natverse/fafbseg
- hemibrain – Scheffer et al. (2020) The data is publically available at https://neuprint.janelia.org (hemibrain:v1.2.1).
We used the neuprintr package to query hemibrain data.
https://natverse.org/neuprintr/
Neuron identifiers (Skeleton IDs or bodyIDs) and the number of synaptic connections across cell types from both datasets can be found in Supplemental Tables 3 and 4. Our group identified neurons in the hemibrain prior to publication and contributed the annotation of all ORNs, PNs, and LH neurons in neuprint (Schlegel, Bates et al. 2021). Supplemental Table 5 shows specific analyses about third-order cell types of the cVA circuit related to Figure S6A.
All other data and analyses are available upon request. Lead contact: Greg Jefferis, https://github.com/jefferis
For generating image stacks from EM neurons for MIP search see the skeleton-to-MIP repository. https://github.com/jefferislab/skeleton-to-MIP