High-accuracy electrode implantation in deep brain structures using multi-camera neuronavigation in non-human primates

This adjoining data includes the surgical planning, post-operative localization, and electrophysiological neural recordings of three macaque monkeys (macaca fasicularis) associated with the article entitled “High-accuracy electrode implantation in deep brain structures using multi-camera neuronavigation in non-human primates”. Seven DBS electrode implantations were performed across the three animals (Monkey E, Monkey O, Monkey K) to target either the hippocampus (HC), or the parahippocampal gyrus (PHG) and entorhinal cortex (EC). Note that in Monkey K, we explanted the first HC electrode and reimplanted another one. The surgical planning (marking of entry points and targets) was performed after co-registering the MRI and pre-operative CT. Post-operatively, CT was acquired again, which enabled to assess electrode localization. For each animal, the individual surgical planning file is presented as a medical research bundle (.mrb) file, which can be opened with using 3D Slicer v5.8.1 (https://www.slicer.org/). For Monkey K, histological slices registered to the MRI data are also included. Surgical planning and electrode localization Each .mrb file (MonkeyE_Planning_Implantation.mrb, MonkeyK_Planning_Implantation.mrb, and MonkeyO_Planning_Implantation.mrb) is structured as follows: Volumes: MRI T1: isotropic 0.5 mm resolution, denoised Brain extracted from T1 CT pre-operative: isotropic 0.15 mm, denoised post-operative: isotropic 0.15 mm, denoised Segmentations Brain mask Brain Areas HC EC PHG (parahippocampal gyrus), only for Monkey E Pre-operative skull Post-operative electrodes (extracted from post-operative CT) Planned trajectories HC: Hippocampus, target marked on T1 MRI, entry point on skull EC: Entorhinal cortex, , target marked on T1 MRI, entry point on skull Post-operative electrode contacts HC contacts: 8 points marked as sphere on post-operative CT PHG contact: 8 points marked as sphere on post-operative CT Histology Slice registration An additional .mrb file (MonkeyK_Histology_Slice_Registration.mrb) shows the histology slice registration to MRI. The structure of the file is as follows: Volumes : MRI: T1: isotropic 0.5 mm resolution, denoised, copied from MonkeyK_Planning_Implantation.mrb Brain extracted: from T1 copied from MonkeyK_Planning_Implantation.mrb Original histology slices: 25 slices with resolution (0.0046 x 0.0043 mm) sliced at 0.6mm apart Cropped Aligned Slices: four slices (slice 14, slice 16, slice 18 and slice 20) were registered to MRI with anterior-posterior (AP) value shown for corresponding slice. Electrode implantations (copied from MonkeyK_Planning_Implantation.mrb): HC First Implant HC First Implant Planned: the planned trajectory for HC implantation, which was later explanted HC First Implant Electrode Segmented: Electrode segmented from post-op CT HC First Implant Contacts: 8 points marked as sphere on post-operative CT HC Reimplantation HC Reimplant Planned: the planned trajectory for HC reimplantation HC Reimplanted Electrode Segmented: reimplanted electrode segmented from post-op CT HC Reimplantation Contacts: 8 points marked as sphere on post-operative CT PHG Implant PHG Planned: the planned trajectory for PHG implantation PHG Electrode Segmented: Electrode segmented from post-op CT PHG Contacts: 8 points marked as sphere on post-operative CT Electrophysiology Stimulation-indued afterdischarges were recorded during short, stand-alone sessions. For these sessions, we provide the unprocessed raw data in the original Blackrock native formats (.nsx and .ccf). Sleep recordings were extracted from behavioral sessions. These data have been processed to isolate the relevant segment, and we provide only a snippet corresponding to the sleep episode. The Zip file “Electrophysiology” contains the Python scripts and datasets required to reproduce Figures 9 and 10 from the article: These scripts were tested with the following Python version and packages: Python 3.12.3 (conda-forge build) numpy 1.26.4 pandas 2.2.3 File organization: The folder “Electrophysiology/Code” contains the scripts used to generate Figures 9 and 10. Each script calls a corresponding dataset stored in “Electrophysiology/Data”: Figure 9, panel A Run: 'plot_Monkey_E_Sleep.py' Dataset: 'Data/Monkey_E_Sleep.mat' Figure 9, panel B Run: 'plot_Monkey_E_Afterdischarges.py' Dataset: 'Data/Monkey_E_Afterdischarges' Figure 10, panel A Run: 'plot_Monkey_O_Sleep.py' Dataset: 'Data/Monkey_O_Sleep.mat' Figure 10, panel B Run: 'plot_Monkey_O_Afterdischarges.py' Dataset: 'Data/Monkey_O_Afterdischarges' Note: The folder 'Utilitaries' contains supporting functions and toolboxes shared across scripts: 'Function_load_plot.py': common functions (re-referencing, filtering, etc.) 'PythonUtilitiesmain/': toolbox developed by BlackRock Neuroscience for loading neural data files recorded with their system. More details and usage examples are available in `Offline Utilities IFU.pdf` inside the folder.本配套数据集关联论文《基于多相机神经导航的非人灵长类动物深部脑结构电极高精度植入术》，包含3只食蟹猴（Macaca fasicularis）的手术规划、术后定位及神经电生理记录数据。 共为3只实验猴（猴E、猴O、猴K）实施7次深部脑刺激（Deep Brain Stimulation, DBS）电极植入术，靶点涵盖海马体（HC）、海马旁回（PHG）及内嗅皮层（EC）。需说明的是，猴K的首枚海马体电极已被取出并重新植入一枚新电极。手术规划（包括穿刺入点与靶点标记）基于MRI与术前CT的配准结果完成；术后再次采集CT影像，用于评估电极植入位置。 每只实验猴的手术规划文件以医学研究包（.mrb）格式存储，可通过3D Slicer v5.8.1软件打开（下载地址：https://www.slicer.org/）。针对猴K，本数据集还包含配准至MRI影像的组织学切片数据。 ### 手术规划与电极定位 以下为三个手术规划文件（"MonkeyE_Planning_Implantation.mrb"、"MonkeyK_Planning_Implantation.mrb"及"MonkeyO_Planning_Implantation.mrb"）的结构： #### 影像序列 - MRI - T1加权像：各向同性分辨率0.5mm，已降噪处理 - 脑区提取结果：从T1加权像中提取的脑区 - CT影像 - 术前CT：各向同性分辨率0.15mm，已降噪处理 - 术后CT：各向同性分辨率0.15mm，已降噪处理 #### 分割结果 - 脑区掩码 - 脑区标注 - 海马体（HC） - 内嗅皮层（EC） - 海马旁回（PHG，仅猴E包含该标注） - 术前颅骨模型 - 术后电极：从术后CT影像中分割得到的电极模型 #### 规划穿刺轨迹 - 海马体轨迹：靶点标注于T1 MRI影像，穿刺入点位于颅骨表面 - 内嗅皮层轨迹：靶点标注于T1 MRI影像，穿刺入点位于颅骨表面 #### 术后电极触点 - 海马体电极触点：术后CT影像中标记有8个球形触点 - 海马旁回电极触点：术后CT影像中标记有8个球形触点 ### 组织学切片配准 额外附带的"MonkeyK_Histology_Slice_Registration.mrb"文件展示了组织学切片与MRI影像的配准过程，该文件结构如下： #### 影像序列 - MRI - T1加权像：各向同性分辨率0.5mm，已降噪处理，数据来源于"MonkeyK_Planning_Implantation.mrb" - 脑区提取结果：从T1加权像中提取的脑区，数据来源于"MonkeyK_Planning_Implantation.mrb" - 原始组织学切片：共25张，分辨率为0.0046×0.0043mm，切片间距0.6mm - 裁剪配准切片：选取其中4张（第14、16、18、20张）与MRI影像完成配准，每张切片标注有前后位（AP）坐标值 #### 电极植入模型（数据来源于"MonkeyK_Planning_Implantation.mrb"） 1. 首次海马体植入 - 规划轨迹：首次海马体电极植入的预设穿刺路径，该电极后续被取出 - 分割电极：从术后CT影像中分割得到的首枚植入电极 - 电极触点：术后CT影像中标记有8个球形触点 2. 海马体二次植入 - 规划轨迹：二次海马体电极植入的预设穿刺路径 - 分割电极：从术后CT影像中分割得到的二次植入电极 - 电极触点：术后CT影像中标记有8个球形触点 3. 海马旁回植入 - 规划轨迹：海马旁回电极植入的预设穿刺路径 - 分割电极：从术后CT影像中分割得到的植入电极 - 电极触点：术后CT影像中标记有8个球形触点 ### 电生理数据 在短期独立实验中记录了刺激诱导的后放电现象，该部分原始未处理数据以BlackRock公司原生格式（.nsx和.ccf）存储。 睡眠记录数据提取自行为学实验，该部分数据已完成相关片段的分离处理，仅提供与睡眠时段对应的片段数据。 压缩包"Electrophysiology"包含用于复现论文中图9与图10的Python脚本及数据集： 下述Python环境与依赖包已完成脚本测试： - Python 3.12.3（conda-forge编译版本） - numpy 1.26.4 - pandas 2.2.3 #### 文件组织结构 - "Electrophysiology/Code"文件夹存储用于生成图9与图10的Python脚本，每个脚本调用存储于"Electrophysiology/Data"中的对应数据集： - 图9A：运行脚本`plot_Monkey_E_Sleep.py`，对应数据集`Data/Monkey_E_Sleep.mat` - 图9B：运行脚本`plot_Monkey_E_Afterdischarges.py`，对应数据集`Data/Monkey_E_Afterdischarges` - 图10A：运行脚本`plot_Monkey_O_Sleep.py`，对应数据集`Data/Monkey_O_Sleep.mat` - 图10B：运行脚本`plot_Monkey_O_Afterdischarges.py`，对应数据集`Data/Monkey_O_Afterdischarges` ### 补充说明 "Utilitaries"文件夹存储所有脚本共用的辅助函数与工具包： - `Function_load_plot.py`：包含通用处理函数（如重参考、滤波等） - `PythonUtilitiesmain/`：BlackRock Neuroscience公司开发的工具包，用于读取其采集系统记录的神经数据文件。详细说明与使用示例可参阅文件夹内的`Offline Utilities IFU.pdf`文档。