Find and fetch connectivity data

Query the Allen API for anterograde tracing experiments, then download and cache the projection density maps.

Python:

import bsv

# Find experiments with injections in visual cortex
experiment_ids = bsv.find_connectivity_experiments(
    ['VISp', 'VISl', 'VISal', 'VISam'],
    mouse_line='',           # '' = all lines, '0' = wild-type only
    primary_injection=True)  # only primary injection sites

# Download and cache projection data
experiment_imgs, injection_summary, _, _ = bsv.fetch_connectivity_data(
    experiment_ids,
    '/path/to/cache',        # local directory for cached files
    'my_query',              # cache name ('' = don't cache)
    'injectionIntensity',    # normalization: 'none' or 'injectionIntensity'
    False,                   # subtract contralateral hemisphere
    allen_atlas_path='/path/to/allenCCF')

MATLAB:

experimentIDs = bsv.findConnectivityExperiments({'VISp', 'VISl', 'VISal', 'VISam'}, '', true);

[experimentImgs, injectionSummary] = bsv.fetchConnectivityData(experimentIDs, ...
    saveLocation, 'my_query', 'injectionIntensity', false, '', allenAtlasPath);

Data is cached locally after the first download, so subsequent calls load from disk.