DOI: 10.5281/zenodo.18393123
title: Transient morphogenetic constraints organize self-assembling axon neighborhoods for robust yet flexible wiring

description: Transient morphogenetic constraints organize self-assembling axon neighborhoods for robust yet flexible wiring

Overview

This repository provides data supporting the study of constrained stochastic assembly in the C. elegans nerve ring. It includes embryonic morphogenetic imaging, curated EM-derived neurite contact and spatial domain datasets, and agent-based innervation simulation outputs and intermediate processed data used in all analyses. Source code for agent-based simulations and figure generation is maintained in a companion GitHub repository (https://github.com/cabrittin/constrained-innervation-abm/), with versioned releases archived for reproducibility. Documentation specifies data formats, software dependencies, and instructions for reproducing the analyses and simulations.

Data Organization (Conceptual Structure)

Conceptually, the datasets are organized into the following categories:- Embryonic imaging data used to identify rosettes, corridor cells and pioneer axon trajectories.   - EM-derived neurite contact, spatial domain datasets and neighborhood metrics.  - Agent-based simulation outputs  

Due to file size constraints, datasets are provided as individually downloadable files and compressed archives rather than a nested directory structure.

File Manifest



exemplar_embryo_rosette_corridor_id.tar.bz2: Exemplar embryo used to identify rosettes and corridor cells; includes raw embryo image and associated AceTree lineage file

embryo_340.tar.bz2: TrakEM2 reconstruction* of 340 mp4 embryo. Supports Fig. 3A. 

embryo_365.tar.bz2: TrakEM2 reconstruction* of 365 mp4 embryo. Support Fig. 4A,D

movie_s1.mp4: Select frames form embryo_340 highlighting early SIAD outgrowh (SubL rosette) along corridor cells (IL1Vm and IL2V) towards the ProxL rosette. 

movie_s2.mp4: Select frames from embryo_365 highlighting early pioneer outgrowth. Pointer tracks the SIAD proscesses, culminating at the Dorsal rosette (RMED and ALA). 

movie_s3.mp4: Flythrough of L4 EM. Pioneer axons have opaque colors. Axons are colored by adult spatial domain assignment. The underlying TrakEM2 data can be dowloaded from https://doi.org/10.5281/zenodo.4763083. 

abm_sim_model54.tar.bz2: ABM simulations for local self-organizing model 54; raw simulation data used for Fig. 5E-M and Fig. S9

abm_sim_model58.tar.bz2: ABM simulations for local self-organizing model 58; raw simulation data used for Fig. 6A,B,C,F,G,H; Fig. 7A-E; Fig. S9

abm_sim_model65.tar.bz2: ABM simulations for local self-organizing model 65; raw simulation data used for Fig. 7F 

abm_sim_pi_models.tar.bz2: ABM simulations for positionally informed models 66, 67, 68; ABM simulations for positionally informed negative control; raw simulation data used for Fig. S7B

table_s5.xlsx: Table S5: Agent based models for simulating axon patterning. Parameters and simulation results for local self-organizing and (negative results for) positionally informed models. This is the complete table, a smaller version of the table was provided with initial submission. 


Notes: 

* TrakEM2 reconstructions are provided as is. Requires Fiji TrakEM2 to view. Only a small subset of cell necessary to support conclusions in the manuscript as provided. Reconstructions for any specific cell should not be assumed to be complete (e.g. only every nth segment may actually be reconstructed). Do not read anything into color choices, these were arbitrary choices to aid reconstruction. If you add to or improve the reconsructions, consider sharing with us. 

Code Availability

Source code for agent-based simulations, data processing, and figure generation is hosted in a companion GitHub repository:

GitHub: https://github.com/cabrittin/constrained-innervation-abm/

Versioned releases of the codebase are archived via Zenodo for long-term reproducibility.

Reproducibility

Documentation in the GitHub repository specifies:- Software dependencies- Execution instructions- Scripts to reproduce figures and analyses

Processed datasets in this repository correspond to the analyses reported in the manuscript.

Citation

Citation for this dataset will be updated upon manuscript publication.

Zenodo DOI: 10.5281/zenodo.18704853

License

Data are released under the CC-BY 4.0 License, unless otherwise noted.Code is released under the MIT License (see GitHub repository).

Contact

For questions, contact:Christopher Brittin (corresponding author)