DOI: 10.5281/zenodo.17193906
title: High-accuracy electrode implantation in deep brain structures using multi-camera neuronavigation in non-human primates

description: 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.