brainmaps_api_fcn

Functions to set and get data via the Google Brainmaps API, e.g to

• download raw or segmentation image data,
• download surface meshes
• download skeletons created based on the segmentation
• retrieve or modify an agglomeration graph

API access

Authentication requires a client-secret.json from a Google project, that has the BrainMaps API enabled.

Installation

This has only been tested using Python 3.7.

using conda

Best work in a dedicated environment. Activate and install packages available to conda first.

conda install python-snappy networkx numpy requests

Then install the remaining requirements using pip

pip install -r requirements.txt

using pip

Then install the remaining requirements

pip install -r requirements.txt

Optional: for faster decompression, e.g. fordownloading subvolumes install python snappy

expand

Python-snappy requires the snappy c libraries to be installed.snappy.

Windows:
download binaries from [C. Gohlke](https://www.lfd.uci.edu/~gohlke/pythonlibs/#python-snappy) and install using [pip](https://pip.pypa.io/en/latest/user_guide/#installing-from-wheels)

Linux/MacOS:
```
APT: sudo apt-get install libsnappy-dev
RPM: sudo yum install libsnappy-devel
Brew: brew install snappy
```

Usage Example

Get segment id at a certain voxel position:

from brainmaps_api_fcn.subvolume_requests import SubvolumeRequest
svr = SubvolumeRequest(<path_to_client_secret>, volume_id)
arr = svr.get_subvolume([3014, 13292, 89], [1,1,1])

Download skeleton of a segment

from brainmaps_api_fcn.mesh_requests import Meshes
mr = Meshes(<path_to_client_secret>, volume_id)
segment_id = 55360714
skel_graph = mr.download_skeleton(segment_id)

Retrieve connected segments from an agglomeration graph

from brainmaps_api_fcn.equivalence_requests import EquivalenceRequests
er = EquivalenceRequests(<path_to_client_secret>, volume_id, change_stack_id)
segment_id = 55360714
edges = er.get_equivalence_list(segment_id)