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

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)# 瞬时形态发生约束调控自组装轴突群落，构建稳健且灵活的神经环路 ## 概述 本数据集仓库为秀丽隐杆线虫（C. elegans）神经环的约束型随机组装研究提供数据支撑。仓库包含胚胎形态发生成像数据、经整理的电子显微镜（Electron Microscopy，EM）来源的轴突接触与空间结构域数据集，以及所有分析中使用的基于智能体的神经支配模拟输出结果与中间处理数据。基于智能体的神经支配模拟与图表生成的源代码托管于配套的GitHub仓库（https://github.com/cabrittin/constrained-innervation-abm/），并通过版本化归档确保研究可复现。仓库文档详细说明了数据格式、软件依赖项，以及复现分析与模拟的操作指南。 ## 数据集组织（概念结构） 从概念层面，本数据集分为以下类别： - 用于识别玫瑰状结构（rosette）、通道细胞（corridor cell）与先驱轴突（pioneer axon）轨迹的胚胎成像数据 - 经电子显微镜（EM）整理的轴突接触、空间结构域数据集与群落评估指标 - 基于智能体的神经支配模拟输出结果 受限于文件体积，本数据集以独立可下载文件与压缩归档包的形式提供，而非嵌套目录结构。 ## 文件清单 exemplar_embryo_rosette_corridor_id.tar.bz2: 用于识别玫瑰状结构与通道细胞的典型胚胎样本，包含原始胚胎图像与关联的AceTree谱系文件 embryo_340.tar.bz2: 340号胚胎mp4影像的TrakEM2重建结果*，对应图3A embryo_365.tar.bz2: 365号胚胎mp4影像的TrakEM2重建结果*，对应图4A、4D movie_s1.mp4: 选取自embryo_340的影像帧，展示了沿通道细胞IL1Vm与IL2V向ProxL玫瑰状结构生长的早期SIAD突起（SubL玫瑰状结构） movie_s2.mp4: 选取自embryo_365的影像帧，展示了早期先驱轴突生长过程；箭头追踪SIAD突起的延伸路径，最终终止于背侧玫瑰状结构（RMED与ALA） movie_s3.mp4: L4期线虫电子显微镜影像的漫游视角视频。先驱轴突采用不透明颜色标识，其余轴突按成虫空间结构域分配着色。底层TrakEM2数据可从https://doi.org/10.5281/zenodo.4763083下载 abm_sim_model54.tar.bz2: 局部自组织模型54的基于智能体的神经支配模拟（Agent-Based Simulation，ABM）结果，为图5E-M与补充图S9提供原始模拟数据 abm_sim_model58.tar.bz2: 局部自组织模型58的ABM模拟结果，为图6A、6B、6C、6F、6G、6H、图7A-E与补充图S9提供原始模拟数据 abm_sim_model65.tar.bz2: 局部自组织模型65的ABM模拟结果，为图7F提供原始模拟数据 abm_sim_pi_models.tar.bz2: 位置信息辅助模型66、67、68以及位置信息辅助阴性对照的ABM模拟结果，为补充图S7B提供原始模拟数据 table_s5.xlsx: 补充表S5：用于模拟轴突模式形成的ABM模型，包含局部自组织模型与位置信息辅助模型（含阴性结果）的参数及模拟结果。本文件为完整版本，初始投稿时附带的为精简版本 ## 备注 * TrakEM2重建结果按现状提供，需使用Fiji TrakEM2软件查看。本数据集仅包含支撑论文结论所需的少量细胞数据，不得假定任一特定细胞的重建结果为完整（例如，仅对每n个节段进行了重建）。请勿对颜色标识赋予额外含义，其仅为辅助重建的随机选择。若您对重建结果进行补充或优化，欢迎与我们分享。 ## 代码可用性 基于智能体的神经支配模拟、数据处理与图表生成的源代码托管于配套GitHub仓库： GitHub: https://github.com/cabrittin/constrained-innervation-abm/ 代码库的版本化归档通过Zenodo存储，以保障长期可复现性。 ## 可复现性 GitHub仓库中的文档详细说明了以下内容： - 软件依赖项 - 执行指南 - 用于复现图表与分析的脚本 本仓库中的处理后数据集与论文中报告的分析结果完全对应。 ## 引用说明 本数据集的引用信息将在论文正式发表后更新。 Zenodo DOI: 10.5281/zenodo.18704853 ## 许可协议 除非另有说明，本数据集采用CC-BY 4.0协议发布。代码采用MIT协议发布（详见GitHub仓库）。 ## 联系方式 如有疑问，请联系：Christopher Brittin（克里斯托弗·布里廷，通讯作者）