Neuromorpho¶

Neuromorpho is a searchable online repository for neuron morphologies. At the time of writing it contains over 168k neurons from 91 different species. While the website features a comprehensive search and some neat stats, it can be useful to download these data to run your own analyses or compare to other data sets.

For that purpose, navis provides an interface to neuromorpho that wraps some of their API.

# Import navis
import navis

# Import the actual neuromorpho interface
import navis.interfaces.neuromorpho as nm

First we can use navis.interfaces.neuromorpho.get_neuron_fields() to figure out what we can search for:

fields = nm.get_neuron_fields()
fields[:10]

['neuron_id',
 'neuron_name',
 'archive',
 'age_scale',
 'gender',
 'reference_pmid',
 'reference_doi',
 'note',
 'age_classification',
 'brain_region']

Next, we will use navis.interfaces.neuromorpho.get_available_field_values() to get an idea of the possible values for a given field:

species = nm.get_available_field_values('species')
species[:10]

['mouse',
 'rat',
 'drosophila melanogaster',
 'human',
 'zebrafish',
 'monkey',
 'chimpanzee',
 'Xenopus laevis',
 'Semipalmated sandpiper',
 'C. elegans']

Let’s find a couple human neurons, shall we?

# Note that we're only fetching the first couple results
info = nm.find_neurons(species='human', page_limit=10)
info.head()

	neuron_id	neuron_name	archive	age_scale	gender	age_classification	brain_region	cell_type	species	...	slicing_thickness	min_age	max_age	min_weight	max_weight	png_url	reference_pmid	reference_doi	physical_Integrity	_links
0	102399	H17-03-010-11-13-01_656411100_m	Allen Cell Types	Year	Female	adult	[neocortex, occipital, middle temporal gyrus]	[interneuron, Aspiny]	human	...	350	38.0	38.0	Not Reported	Not Reported	http://neuromorpho.org/images/imageFiles/Allen...	[27810003]	[10.1016/j.neuron.2016.10.019]	Dendrites Complete, Axon Incomplete	{'self': {'href': 'http://neuromorpho.org/api/...
1	102400	H17-03-010-11-13-06_651089035_m	Allen Cell Types	Year	Female	adult	[neocortex, occipital, middle temporal gyrus]	[principal cell, Spiny]	human	...	350	38.0	38.0	Not Reported	Not Reported	http://neuromorpho.org/images/imageFiles/Allen...	[27810003]	[10.1016/j.neuron.2016.10.019]	Dendrites Complete, Axon Incomplete	{'self': {'href': 'http://neuromorpho.org/api/...
2	102401	H17-03-011-11-04-05_650978964_m	Allen Cell Types	Year	Male	adult	[neocortex, occipital, middle temporal gyrus]	[principal cell, Spiny]	human	...	350	30.0	30.0	Not Reported	Not Reported	http://neuromorpho.org/images/imageFiles/Allen...	[27810003]	[10.1016/j.neuron.2016.10.019]	Dendrites & Axon Moderate	{'self': {'href': 'http://neuromorpho.org/api/...
3	102402	H17-03-011-11-09-04_648981937_m	Allen Cell Types	Year	Male	adult	[neocortex, occipital, middle temporal gyrus]	[principal cell, Spiny]	human	...	350	30.0	30.0	Not Reported	Not Reported	http://neuromorpho.org/images/imageFiles/Allen...	[27810003]	[10.1016/j.neuron.2016.10.019]	Dendrites & Axon Moderate	{'self': {'href': 'http://neuromorpho.org/api/...
4	102403	H17-06-005-12-15-01_605485782_m	Allen Cell Types	Year	Male	adult	[neocortex, occipital, middle temporal gyrus]	[interneuron, Aspiny]	human	...	350	38.0	38.0	Not Reported	Not Reported	http://neuromorpho.org/images/imageFiles/Allen...	[27810003]	[10.1016/j.neuron.2016.10.019]	Dendrites & Axon Complete	{'self': {'href': 'http://neuromorpho.org/api/...

5 rows × 45 columns

Now on to fetching some actual neurons! The way you typically want to do this is by passing the info for your neurons of interest to navis.interfaces.neuromorpho.get_neuron():

neurons = nm.get_neuron(info)
neurons

102701 generated an exception: 404 Client Error: Not Found for url: http://neuromorpho.org/dableFiles/ortega/CNG%20version/WT6_02.CNG.swc
102706 generated an exception: 404 Client Error: Not Found for url: http://neuromorpho.org/dableFiles/ortega/CNG%20version/WT4_02.CNG.swc
102709 generated an exception: 404 Client Error: Not Found for url: http://neuromorpho.org/dableFiles/ortega/CNG%20version/WT9_02.CNG.swc
102719 generated an exception: 404 Client Error: Not Found for url: http://neuromorpho.org/dableFiles/ortega/CNG%20version/WT7_02.CNG.swc
102726 generated an exception: 404 Client Error: Not Found for url: http://neuromorpho.org/dableFiles/ortega/CNG%20version/WT5_02.CNG.swc
102728 generated an exception: 404 Client Error: Not Found for url: http://neuromorpho.org/dableFiles/ortega/CNG%20version/WT8_02.CNG.swc

<class 'navis.core.neuronlist.NeuronList'> containing 494 neurons (26.0MiB)

	type	name	id	n_nodes	n_connectors	n_branches	n_leafs	cable_length	soma	units
0	navis.TreeNeuron	H17-03-010-11-13-01_656411100_m	102399	1498	None	15	20	1684.614746	[1, 2, 3]	1 dimensionless
1	navis.TreeNeuron	H17-03-010-11-13-06_651089035_m	102400	10451	None	69	81	13138.289062	[1, 2, 3]	1 dimensionless
...	...	...	...	...	...	...	...	...	...	...
492	navis.TreeNeuron	H9-MECP2-T158M-T158M-CREB-17	103393	137	None	14	20	326.003082	[1, 2, 3]	1 dimensionless
493	navis.TreeNeuron	H9-MECP2-T158M-T158M-CREB-38	103394	172	None	43	52	324.924866	[1, 2, 3]	1 dimensionless

As you can see some of these neurons are missing an SWC. That happens occasionally.

Let’s plot some of these!

import matplotlib.pyplot as plt
import seaborn as sns

fig, axes = plt.subplots(1, 10, figsize=(15, 5))

for n, c, ax in zip(neurons, sns.color_palette('muted', len(axes)), axes):
    _ = navis.plot2d(n, method='2d', ax=ax, c=c)
    ax.set_aspect('equal')
    ax.set_axis_off()

That’s all for now!