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An NWB extension for storing the cortical surface of subjects in ECoG experiments

Project description

ndx-ecog Extension for NWB:N

Author: Ben Dichter

There are three data types, Surface, CorticalSurfaces, and ECoGSubject. CorticalSurfaces is simply a group (like a folder) to put Surface objects into. Surface holds surface mesh data (vertices and triangular faces) for sections of cortex. ECoGSubject is an extension of Subject that allows you to add the CorticalSurfaces object to /general/subject.

Usage

python

install:

pip install ndx_ecog

write:

import pynwb
from ndx_ecog import CorticalSurfaces, ECoGSubject

nwbfile = pynwb.NWBFile(...)

...

cortical_surfaces = CorticalSurfaces()
## loop me
    cortical_surfaces.create_surface(name=name, faces=faces, vertices=veritices)
##
nwbfile.subject = ECoGSubject(cortical_surfaces=cortical_surfaces)

You can optionally attach images of the subject's brain:

from pynwb.base import Images
from pynwb.image import GrayscaleImage

subject.images = Images(name='subject images', images=[GrayscaleImage('image1', data=image_data)])

read:

import nwbext_ecog
from pynwb import NWBHDF5IO
io = NWBHDF5IO('path_to_file.nwb','r')
nwb = io.read()
nwb.subject.cortical_surfaces

MATLAB

install:

generateExtension('/path/to/ndx-ecog/spec/ndx-ecog.namespace.yaml');

write:

cortical_surfaces = types.ecog.CorticalSurfaces;

%%% loop me
    surf = types.ecog.Surface('faces', faces, 'vertices', vertices);
    cortical_surfaces.surface.set(surface_name, surf);
%%%

file.subject = types.ecog.ECoGSubject(name, cortical_surfaces);

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