NeuroMorpho.Org

NeuroMorpho.Org#

NeuroMorpho.Org is the largest public repository of digitally reconstructed neurons — over 250,000 cells from hundreds of labs. braincell ships a full client that searches, downloads, caches, and parses these reconstructions into ready-to-use morphologies.

The client requires the IO extra:

pip install -U braincell[io]

One-liner: load a neuron by id#

The simplest path is to load a neuron directly by its NeuroMorpho id. The file is downloaded once and cached locally, so subsequent calls are instant:

import braincell

morpho = braincell.Morphology.from_neuromorpho(12345)

Equivalently, via the IO module entry point:

import braincell.io as io

morpho = io.load_neuromorpho(12345)

# also get the validation report
morpho, report = io.load_neuromorpho(12345, return_report=True)

Note

The argument is the integer neuron id from NeuroMorpho.Org (the number in a neuron’s URL), not its name.

Searching the repository#

To find neurons matching criteria, use the NeuroMorphoClient:

from braincell.io import NeuroMorphoClient

client = NeuroMorphoClient()

# iterate search results (species, brain region, cell type, …)
for neuron in client.iter_search(species="mouse", brain_region="neocortex"):
    print(neuron.neuron_id, neuron.neuron_name)

# describe a single neuron
detail = client.get_neuron(12345)

# download its reconstruction file(s)
record = client.download(12345)

Search and query construction are typed through NeuroMorphoQuery and return rich models (NeuroMorphoNeuron, NeuroMorphoMeasurement, NeuroMorphoSearchPage).

Downloading without parsing#

To fetch raw files (standard and/or original SWC) without immediately building a morphology:

import braincell.io as io

record = io.fetch_neuromorpho(12345, mode="both")   # 'standard' | 'original' | 'both'
print(record)   # NeuroMorphoDownloadRecord: what was written where

Caching#

Downloads are cached under a user cache directory (braincell.io.DEFAULT_USER_CACHE_DIR) and managed by NeuroMorphoCache. You can point any entry point at a custom location with cache_dir=..., and inspect cache state through the client’s get_cache_status.

Command-line interface#

The client is also exposed as a CLI, braincell-neuromorpho, for searching and downloading from a shell:

braincell-neuromorpho --help

See also#