Plot injection sites

Visualize where viral injections were placed, either one region at a time or combined.

Injection sites in antero-medial visual cortex (VISam), shown across coronal slices.

Python:

# Plot each region's injections separately
bsv.plot_multi_region_injections(
    experiment_imgs, '/path/to/allenCCF',
    ['VISp', 'VISl', 'VISal'],
    10, 15, 'coronal', True, 2, 'global',
    color, 'injectionIntensity')

# Or show all regions overlaid
bsv.plot_injections_combined(
    experiment_imgs, '/path/to/allenCCF',
    input_regions, color)

MATLAB:

% One region at a time
for iRegion = 1:length(inputRegions)
    bsv.plotConnectivity(experimentImgs, allenAtlasPath, inputRegions(iRegion), ...
        10, 15, 'coronal', true, 2, 'global', color, 'injectionIntensity')
end

% Combined
bsv.plotInjectionsCombined(experimentImgs, allenAtlasPath, inputRegions, color)