This file defines shortcuts useful for storing experiment-level metadata. For more information about each field, and the organization of fields in the NWB file, please see the ‘general’ section in the NWB file format specification
"""
Copyright (c) 2015 Allen Institute, California Institute of Technology,
New York University School of Medicine, the Howard Hughes Medical
Institute, University of California, Berkeley, GE, the Kavli Foundation
and the International Neuroinformatics Coordinating Facility.
All rights reserved.
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"""
# metadata storage constants
# these are so users don't have to remember exact path to
# meatadata fields, and to avoid/detect typos
# all constants here are for storing data in the files top-level
# group 'general'
#
# some are string constants and others are functions that
# return strings. functions are used when there's a variable
# element in metadata storage path
DATA_COLLECTION = "data_collection"
EXPERIMENT_DESCRIPTION = "experiment_description"
EXPERIMENTER = "experimenter"
INSTITUTION = "institution"
LAB = "lab"
NOTES = "notes"
PROTOCOL = "protocol"
PHARMACOLOGY = "pharmacology"
RELATED_PUBLICATIONS = "related_publications"
SESSION_ID = "session_id"
SLICES = "slices"
STIMULUS = "stimulus"
SURGERY = "surgery"
VIRUS = "virus"
SUBJECT = "subject/description"
SUBJECT_ID = "subject/subject_id"
SPECIES = "subject/species"
GENOTYPE = "subject/genotype"
SEX = "subject/sex"
AGE = "subject/age"
WEIGHT = "subject/weight"
def DEVICE(name):
return "devices/" + name
########################################################################
# for extra-cellular ephys recordings
EXTRA_ELECTRODE_MAP = "extracellular_ephys/electrode_map"
EXTRA_ELECTRODE_GROUP = "extracellular_ephys/electrode_group"
EXTRA_IMPEDANCE = "extracellular_ephys/impedance"
EXTRA_FILTERING = "extracellular_ephys/filtering"
def EXTRA_CUSTOM(name):
return "extracellular_ephys/" + name
def EXTRA_SHANK_DESCRIPTION(shank):
return "extracellular_ephys/" + shank + "/description"
def EXTRA_SHANK_LOCATION(shank):
return "extracellular_ephys/" + shank + "/location"
def EXTRA_SHANK_DEVICE(shank):
return "extracellular_ephys/" + shank + "/device"
def EXTRA_SHANK_CUSTOM(shank, name):
return "extracellular_ephys/" + shank + "/" + name
########################################################################
# for intra-cellular ephys recordings
def INTRA_ELECTRODE_DESCRIPTION(name):
return "intracellular_ephys/" + name + "/description"
def INTRA_ELECTRODE_FILTERING(name):
return "intracellular_ephys/" + name + "/filtering"
def INTRA_ELECTRODE_DEVICE(name):
return "intracellular_ephys/" + name + "/device"
def INTRA_ELECTRODE_LOCATION(name):
return "intracellular_ephys/" + name + "/location"
def INTRA_ELECTRODE_RESISTANCE(name):
return "intracellular_ephys/" + name + "/resistance"
def INTRA_ELECTRODE_SLICE(name):
return "intracellular_ephys/" + name + "/slice"
def INTRA_ELECTRODE_SEAL(name):
return "intracellular_ephys/" + name + "/seal"
def INTRA_ELECTRODE_INIT_ACCESS_RESISTANCE(name):
return "intracellular_ephys/" + name + "/initial_access_resistance"
########################################################################
# for optophysiology imaging
def IMAGE_SITE_DESCRIPTION(site):
return "optophysiology/" + site + "/description"
def IMAGE_SITE_MANIFOLD(site):
return "optophysiology/" + site + "/manifold"
def IMAGE_SITE_INDICATOR(site):
return "optophysiology/" + site + "/indicator"
def IMAGE_SITE_EXCITATION_LAMBDA(site):
return "optophysiology/" + site + "/excitation_lambda"
def IMAGE_SITE_CHANNEL_LAMBDA(site, channel):
return "optophysiology/" + site + "/" + channel + "/emission_lambda"
def IMAGE_SITE_CHANNEL_DESCRIPTION(site, channel):
return "optophysiology/" + site + "/" + channel + "/description"
def IMAGE_SITE_IMAGING_RATE(site):
return "optophysiology/" + site + "/imaging_rate"
def IMAGE_SITE_LOCATION(site):
return "optophysiology/" + site + "/location"
def IMAGE_SITE_DEVICE(site):
return "optophysiology/" + site + "/device"
def IMAGE_SITE_CUSTOM(site, name):
return "optophysiology/" + site + "/" + name
########################################################################
# for optogentics
def OPTOGEN_SITE_DESCRIPTION(site):
return "optogenetics/" + site + "/description"
def OPTOGEN_SITE_DEVICE(site):
return "optogenetics/" + site + "/device"
def OPTOGEN_SITE_LAMBDA(site):
return "optogenetics/" + site + "/excitation_lambda"
def OPTOGEN_SITE_LOCATION(site):
return "optogenetics/" + site + "/location"
def OPTOGEN_SITE_CUSTOM(site, name):
return "optogenetics/" + site + "/" + name