Simulations of cochlear nucleus bushy cells reconstructed from serial blockface electron microscopy (V1.3)

Globular bushy cells (GBCs) of the cochlear nucleus play central roles in the temporal processing of sound. Despite investigation over many decades, fundamental questions remain about their dendrite structure, afferent innervation, and integration of synaptic inputs. Here, we use volume electron microscopy (EM) of the mouse cochlear nucleus to construct synaptic maps that precisely specify convergence ratios and synaptic weights for auditory- nerve innervation and accurate surface areas of all postsynaptic compartments. Detailed biophysically-based compartmental models can help develop hypotheses regarding how GBCs integrate inputs to yield their recorded responses to sound. We established a pipeline to export a precise reconstruction of auditory nerve axons and their endbulb terminals together with high-resolution dendrite, soma, and axon reconstructions into biophysically-detailed compartmental models that could be activated by a standard cochlear transduction model. With these constr..., 1. Description of methods used for collection/generation of data: Reconstructions were made in syGlass (IstoVisio, Morgantown, WV) as SWC files (Cannon et al., 1988), and converted to the HOC format for use in NEURON for simulations. The SWC files were traced by hand from semi-automated mesh and annotated reconstructions of the cell membranes (soma, dendrites, axons).
2. Methods for processing the data: The SWC files were converted to the HOC format for use in NEURON for simulations. The repository of the code for running the simulations is at https://github.com/pbmanis/VCNModel (release version 1.0.0), and is based on the cnmodel package (https://github.com/cnmodel/cnmodel; Manis and Campagnola, 2018). 3. Instrument- or software-specific information needed to interpret the data: Python 3.8 or later. The complete set of package requirements and a script to build the required environment can be found in requirements.txt at the github repository listed in (2), The programs that generated these files and that generate plots for the figures in the paper are at the github repository listed in Methods.
The simulation data and a reference table is provided as files and compressed archives (zip files), which will need to be unzipped into the appropriate target directories. The files should be placed in a folder (named something like \"BU_simulation_data\"). The compressed archives named \"Impedance Calculations\" and \"VCN_nn\" should placed in a subdirectory called \"Simulations\", and uncompressed there. The compressed file \"IntermediateAnalyses\" should be placed under the top directory (e.g., \"BU_simulation_data\"), and uncompressed there. Refer to the instructions in the github archive VCNModel. Paths to data will need to be edited in the file \"wheres_my_data.toml\".
The uncompressed data set is approximately 180 GB.Â

耳蜗核的球形毛细胞（Globular bushy cells, GBCs）在声音的时间加工中发挥核心作用。尽管已开展数十年的相关研究，但关于其树突结构、传入神经支配以及突触输入整合的基础问题仍有待解答。本研究通过对小鼠耳蜗核进行体积电子显微镜（volume electron microscopy, EM）成像，构建了突触图谱，可精准确定听神经支配的会聚比例与突触权重，并准确标注所有突触后结构的表面积。基于详细生物物理特性的隔室模型有助于提出假说，阐释GBCs如何整合输入信号以产生已记录到的声音响应。我们建立了一套流程，可将听神经轴突及其终球突触末梢的精准重建，与高分辨率的树突、胞体和轴突重建相结合，导入可通过标准耳蜗转导模型激活的高细节生物物理隔室模型中。

1. 数据收集与生成方法：重建工作在syGlass（IstoVisio公司，西弗吉尼亚州摩根敦）中完成，导出为SWC格式文件（Cannon等，1988），并转换为HOC格式以用于NEURON仿真。SWC文件通过半自动网格与手动追踪获得，并对细胞膜（胞体、树突、轴突）的重建进行注释。
2. 数据处理方法：SWC文件被转换为HOC格式以用于NEURON仿真。运行仿真的代码仓库位于https://github.com/pbmanis/VCNModel（发布版本1.0.0），其基于cnmodel工具包（https://github.com/cnmodel/cnmodel; Manis与Campagnola，2018）。
3. 数据解读所需的仪器或软件相关信息：Python 3.8及以上版本。完整的依赖包列表与环境构建脚本可在上述方法中提及的GitHub仓库的requirements.txt文件中获取。生成本数据集与论文中图版绘图的程序，同样位于方法部分提及的GitHub仓库中。
仿真数据与参考表格以文件及压缩归档（zip压缩包）形式提供，需解压至对应目标目录。文件应放置在名为"BU_simulation_data"的文件夹中。名为"Impedance Calculations"与"VCN_nn"的压缩归档应放入名为"Simulations"的子目录并在此处解压。名为"IntermediateAnalyses"的压缩文件应置于根目录（例如"BU_simulation_data"）并在此处解压。具体操作请参考GitHub仓库VCNModel中的说明。需在"wheres_my_data.toml"文件中编辑数据路径。未压缩的数据集总大小约为180 GB。