brainmappy

Lightweight Python 3 package for fetching data via Google's brainmaps API.

Install

pip3 install git+git://github.com/schlegelp/brainmappy@master

Dependencies

Automatically installed with pip:

• google-api-python-client
• oauth2client
• numpy
• requests_futures
• tqdm

Brainmaps credentials

First, you need to need to be granted permission to use the API. The next steps depend on your level of access:

Developers

Developers can setup and enable the brainmaps API for projects through through Google's developer's console:

1. Go to Google developer's console.
2. Create a new project (top right) and activate the brainmaps API for this project via ENABLE APIS AND SERVICES on the dashboard.
3. Go to Credentials and generate an OAuth 2.0 client ID for the project.
4. Download client ID and client secret as client_secret.json

Users

As a user you will be able to use the brainmaps API but you need somebody with developer-level access to provide you with a client_secret.json.

Examples

First time authenticate:

import brainmappy as bm

# Authenticate and set these credentials as default
session = bm.acquire_credentials('client_secret.json',
                                 use_stored=False,
                                 make_global=True)

Credentials are stored, so from now on you can just run this:

session = bm.acquire_credentials()

Many functions require specifying a volume ID. You can pass this explicitly or define a single volume as default:

bm.set_global_volume('772153499790:fafb_v14:fafb_v14_16nm_v00c_split3xfill2')

Fetch list of all fragments constituting an object:

fragments = bm.get_fragments(21716312853)

Get mesh for given object:

verts, faces = bm.get_meshes_batch(21716312853)

Brainmaps Documentation

Documentation for the brainmaps API can be found here.