Overview Experiments Cells SDK Transgenic Characterization Documentation Help
Allen Software Development Kit

The AllenSDK is a Python package that facilitates downloading and manipulating Allen Institute data sets. Using the AllenSDK, Allen Brain Observatory experimental data can be retrieved in the Neurodata Without Borders (NWB) file format. The AllenSDK enables deep, custom data analysis by providing utilities for accessing experimental metadata, extracting cell fluorescence traces, and more. It also contains the codebase used to process, quantify, and visualize the data available in Allen Brain Observatory data portal. This includes scripts for:

  • neuropil subtraction
  • dF/F computation
  • stimulus-specific tuning analysis

Get started here with the AllenSDK. Users are strongly encouraged to walk through the main Jupyter Notebook for an overview of the available functionality. For example:

Accessing Current Cell Filters via the AllenSDK

The AllenSDK can access the current set of filtered cells using the BrainObservatoryCache class. The code below will apply the current filter set. Please note that if you have an existing manifest file, you will want to customize the manifest_file argument below. For more information on manifests, please look at this jupyter notebook.

from allensdk.core.brain_observatory_cache import BrainObservatoryCache
import json
filter_json = """

filters = json.loads(filter_json)
boc = BrainObservatoryCache(manifest_file="brain_observatory/manifest.json")
cells = boc.get_cell_specimens(filters=filters)