Marmoset Electrocorticography – Annotations of Electrodes

Authors: Ken Nakae¹, Misako Komatsu²*, Takaaki Kaneko^3,4,5, Junichi Hata^3,4,5, Hideyuki Okano^3,4, Shin Ishii¹, Tetsuo Yamamori²

1. Integrated Systems Biology Laboratory (Ishii Laboratory), Division of Systems Informatics, Department of Systems Science, Graduate School of Informatics, Kyoto University
2. Laboratory for Molecular Analysis of Higher Brain Function, RIKEN Center for Brain Science
3. Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science
4. Department of Physiology (Okano Lab), Keio University School of Medicine, Keio University School of Medicine
5. Central Institute for Experimental Animals

*corresponding author: Misako Komatsu (mskkomatsu@gmail.com)

DATASET DESCRIPTION

This dataset provides annotated electrode layouts for the animals that participated in ECoG experiments.

Method

The positions of electrodes of the electrocorticography (ECoG) for marmosets are normalized to the standard space, which is defined using the standard brain BMA 2019 Ex vivo.

This normalization consists of two steps:

1. electrode identification on the individual in vivo MRI (subject space)
2. registration to the averaged ex vivo MRI (standard space). Here, we explain these two steps.

1. Electrode identification on the subject space

We obtain a computed tomography (CT) scan image of individual marmoset after an electrode implantation, and an in vivo T2 weighted magnetic resonance imaging (MRI) for the same individual marmoset before surgery. The CT image is manually aligned to the in vivo MRI space by rigid transformation using AFNI software (Cox, 1996). The electrodes are manually segmented from the CT images using 3D Slicer (Fedorov et al., 2012) to eliminate non-electrode regions and numbering the electrodes.

2. Registration to the standard space

The in vivo individual MRI (subject space) is registered to the in vivo average MRI data of marmosets by free-form deformation using ANTs software (Avants et al, 2011). The in vivo averaged MRI data is also registered to the standard space defined by BMA 2019 Ex vivo using ANTs software. Then, we map the segmented electrode on the subject space to those on the standard space based on these registrations. Finally we determine a nearest voxel of each electrode on the standard brain using a nearest neighbor method, and annotate a cortical region of the voxel to the electrode.

Contents of Data

Each ElectrodesXx.zip archive contains ElectrodesXx.mat and ElectrodeIndexXx.csv files.

1. ElectrodesXx.mat

Information of the ECoG electrode locations on a 2D subject space.

• MRI: 2D view of the marmoset brain
• LINE: The outline of the marmoset brain
• X: X positions of the electrodes
• Y: Y positions of the electrodes

optionally:

• LX: X positions of the LEDs
• LY: Y positions of the LEDs
• IX: X positions of the virus injections
• IY: Y positions of the virus injections

2. ElectrodesIndexXx.csv

Information of the ECoG electrode on the standard space.

• Column 1: segment number
• Column 2: segment name
• Column 3: area number based on Hashikawa Atlas
• Column 4: area abbreviation
• Column 5: area name
• Column 6: hemisphere
• Column 7-9: RAS coordinates on the standard space

CITATION

Nakae, Ken; Komatsu, Misako; Kaneko, Takaaki; Hata, Junichi; Okano, Hideyuki; Ishii, Shin; Yamamori, Tetsuo : Brain/MINDS Marmoset Brain ECoG Annotations of Electrodes (DataID: 4958)

LICENSE

This work is licensed under a Creative Commons Attribution 4.0 International License.

CONTENT

Data Name	Data Type	Marmoset ID	Electrode Type
ElectrodesKr.zip	MAT, CSV	R02_9024_CM515M	R64+8bLED
ElectrodesMr.zip	MAT, CSV	R02_0003_CM943M	L96v1
ElectrodesOr.zip	MAT, CSV	R03_0035_CM814F	R96v1
ElectrodesPr.zip	MAT, CSV	R04_0070_CM962F	R64
ElectrodesJi.zip	MAT, CSV	R03_0024_CM622M	L96v2
ElectrodesQc.zip	MAT, CSV	R01_0074_CM1066F	R96v1
ElectrodesRc.zip	MAT, CSV	R03_0044_CM997M	R96v2
ElectrodesSs.zip	MAT, CSV	R03_0070_CM1002M	R96v2
ElectrodesNr.zip	MAT, CSV	R02_0043_CM1129F	L96v2
ElectrodesTk.zip	MAT, CSV	R03_0040_CM929M	L96v2+16bLED