Downloading data

from morphapi.api.allenmorphology import AllenMorphology
​
​
am = AllenMorphology()
​
​
# Select mouse neurons in the primary visual cortex
neurons = am.neurons.loc[
    (am.neurons.species == "Mus musculus")
    & (am.neurons.structure_area_abbrev == "VISp")
]
​
# Download some of these neurons
neurons = am.download_neurons(neurons[:5].id.values)

from morphapi.api.neuromorphorg import NeuroMorpOrgAPI
​
api = NeuroMorpOrgAPI()
​
# ---------------------------- Downloading metadata --------------------------- #
# Get metadata for pyramidal neurons from the mouse cortex.
metadata, _ = api.get_neurons_metadata(
    size=10,  # Can get the metadata for up to 500 neurons at the time
    species="mouse",
    cell_type="pyramidal",
    brain_region="neocortex",
)
​
# To get a list of available query fields: print(api.fields)
# To get a list of valid values for a field: print(api.get_fields_values(field))
print("Neurons metadata:")
print(metadata[0])
​
# ---------------------------- Download morphology --------------------------- #
neurons = api.download_neurons(metadata[5])
​

from morphapi.api.mouselight import MouseLightAPI
​
​
# ---------------------------- Downloading neurons --------------------------- #
mlapi = MouseLightAPI()
​
# Fetch metadata for neurons with soma in the secondary motor cortex
neurons_metadata = mlapi.fetch_neurons_metadata(
    filterby="soma", filter_regions=["MOs"]
)
​
# Then we can download the files
neurons = mlapi.download_neurons(neurons_metadata[0])
​

from morphapi.api.mpin_celldb import MpinMorphologyAPI
​
​
api = MpinMorphologyAPI()
​
# ----------------------------- Download dataset ----------------------------- #
"""
    If it's the first time using this API, you'll have to download the dataset
    with all of the neurons' data.
"""
api.download_dataset()
# You can then inspect metadata about all neurons:
print(api.neurons_df.head())
​
​
# Get neurons for a given brain structure
neurons_ids = api.get_neurons_by_structure(837)
​
​
# and load the selected neurons
neurons = api.load_neurons(neurons_ids)
​