Annotations of Electrodes (DataID: 4958)

Authors: Ken Nakae1, Misako Komatsu2*, Takaaki Kaneko3,4,5, Junichi Hata3,4,5, Hideyuki Okano3,4, 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 (mkomatsu@brain.riken.jp)

DATASET DESCRIPTION

This page 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, in Brain/MINDS data portal.

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

 

1. Electrode identification on the subject space

test1

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

test2

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

ElectrodesXx.zip contains “ElectrodesXx.mat” and “ElectrodeIndexXx.csv”.

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
(If there are)
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

DOWNLOAD

Data Name Data Type Marmoset ID Electrode Type Preview Download
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

[Update history]
2021/09/21: The page was released