Skip to main content

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);

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

ndx-ecog-0.1.1.tar.gz (14.7 kB view hashes)

Uploaded Source

Built Distribution

ndx_ecog-0.1.1-py2.py3-none-any.whl (6.1 kB view hashes)

Uploaded Python 2 Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page