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photometry related: the name in LIGHT_SOURCE_MAP is experiment specific #886

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grg2rsr opened this issue Nov 21, 2024 · 0 comments
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@grg2rsr
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grg2rsr commented Nov 21, 2024

The light source map as it is hard coded right now contains experiment specific information

LIGHT_SOURCE_MAP = {
    'color': ['None', 'Violet', 'Blue', 'Green'],
    'wavelength': [0, 415, 470, 560],
    'name': ['None', 'Isosbestic', 'GCaMP', 'RCaMP'],
}

both color and wavelength are neurophotometrics FP3002 specific, but name is not. For example, the green blue excitation band at 470 nm might well be used to image dLight, the 560 channel might be used for tdTomato.

This could probably be moved to the experiment description file as such:

"""
neurophotometrics:
    fibers:
    - roi: G0
        location: VTA
    - roi: G1
        location: DR
    channel_names: Isosbestic, GCaMP, RCaMP
    collection: raw_photometry_data
    sync_label: bnc1out
    sync_channel: 1
    datetime: 2024-09-19T14:13:18.749259
sync:
    bpod
"""

it might be worth thinking about having channel_names a property of each fiber, as it could be possible that someone tries to image different sensors at different locations

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