Quickstart

Install neuprint-python

If you’re using conda, use this command:

conda install -c flyem-forge neuprint-python

Otherwise, use pip:

pip install neuprint-python

Client and Authorization Token

All communication with the neuPrintHTTP server is done via a Client object.

To create a Client, you must provide three things:

  • The neuprint server address (e.g. neuprint.janelia.org)
  • Which dataset you’ll be fetching from (e.g. hemibrain:v1.2.1)
  • Your personal authentication token

To obtain your authorization token, follow these steps:

  1. Navigate your web browser to the neuprint server address.
  2. Log in.
  3. Using the account menu in the upper right-hand corner, select “Account” as shown in the screenshot below.
  4. Copy the entire auth token.
Auth Token menu screenshot

Create the Client

from neuprint import Client

c = Client('neuprint.janelia.org', dataset='hemibrain:v1.2.1', token='YOUR-TOKEN-HERE')
c.fetch_version()

Alternatively, you can set your token in the following environment variable, in which case the token parameter can be omitted:

$ export NEUPRINT_APPLICATION_CREDENTIALS=<my-token>

Execute a query

Use your Client to request data from neuprint.

The Client.fetch_custom() method will run an arbitrary cypher query against the database. For information about the neuprint data model, see the neuprint explorer web help.

Also, neuprint-python comes with convenience functions to implement common queries. See Queries.

In [1]: ## This query will return all neurons in the ROI ‘AB’
   ...: ## that have greater than 10 pre-synaptic sites.
   ...: ## Results are ordered by total synaptic sites (pre+post).
   ...: q = """\
   ...:     MATCH (n :Neuron {`AB(R)`: true})
   ...:     WHERE n.pre > 10
   ...:     RETURN n.bodyId AS bodyId, n.type as type, n.instance AS instance, n.pre AS numpre, n.post AS numpost
   ...:     ORDER BY n.pre + n.post DESC
   ...: """

In [2]: results = c.fetch_custom(q)

In [3]: print(f"Found {len(results)} results")
Found 177 results

In [4]: results.head()
Out[4]:
       bodyId    type                   instance  numpre  numpost
0  5813027016    FB4Y             FB4Y(EB/NO1)_R    1720     6508
1  1008378448    FB4Y             FB4Y(EB/NO1)_R    1791     6301
2  1513363614  LCNOpm        LCNOpm(LAL-NO3pm)_R     858     6501
3  5813057274    FB4Y             FB4Y(EB/NO1)_L    2001     5089
4  1131827390    FB4M  FB4M(PPM3-FB3/4-NO-DAN)_R    2614     4431

Next Steps

Try the interactive tutorial for a tour of basic features in neuprint-python.