Repository for ``Diverse and specialized connectivity facilitates multimodal roles in annotated connectomes'' by Moon, Ripoll-Sanchez, Vertes, Schafer & Ahnert.

About:

• This is the repo accompanying the preprint Moon et al., 2025, containing all scripts needed to generate the results.

Installation:

• Run pip install requirements.txt in your python environment of choice.
• Then run Jupyter notebooks to do analysis and generate figures into the figures folder.

Contents:

src

• \module\convect CONVECT, a CONnectivity VECTorisation analysis tool for annotated networks.
• ipynb Jupyter notebooks are in src
  • 01_vec_ent_nb.ipynb includes code for running the connectivity vectorisation, entropy calculations and the specialization-diversity calculations, then plotting distributions. We process these into connectivity vectors and specialization-diversity dataframes which are saved in generated data/*/processed subfolders. Creates figure 2 in Moon et al., 2025.
    • In addition to figures in the publication, we have plotly iframes for reference in figures/distributions_vis.
  • 02_null_models_nb.ipynb includes null models of the specialization-diversity entropic vector euclidean pairwise distances for cell types, serial homologues and left-right pairs. Creates figure 3 in Moon et al., 2025.
  • ZZ_supplementary.ipynb includes analysis for supplementary figures.

data

Please download from the Zenodo link above and save into the repository directory.

• celegans is a folder for celegans
  • /materials/072022_anatomical_class.csv is metadata from Ripoll-Sanchez et al., Neuron (2023).
  • /original/white_1986_whole.csv is an edge list from nemanode (Witvliet et al., Nature (2021), based on Varshney et al., PLOS Computational Biology (2011) and White et al., Philos Trans R Soc Lond B Biol Sci (1986)).
  • Cell_lists_herm.csv, Cell_lists_sexshared.csv, pharynx_ctypes.csv are neuron classifications from Cook et al., Nature (2019). These csvs are separated out from from the xlsx file SI 4 Cell lists.xlsx, available from wormwiring.
• 20241119_dm_data is the Drosophila VNC data pull of the Male Adult Nerve Cord (MANC) connectome and metadata pulled on 19/11/2024, Cheong et al., eLife (2024), available from neuprint.
  • manc_edges_20241119.csv is the edge list.
  • manc_meta_20241119.csv is the metadata.