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License: MIT License
If OpticalChannel
is defined in the imaging interface (BrezovecFunctionalGreenImagingInterface in this case), as follow:
channel_name = 'Green'
metadata["Ophys"]["OpticalChannel"][0].update(
name=channel_name,
emission_lambda=513.0,
description="Green channel of the microscope, 525/50 nm filter.",
)
When I run the conversion, it raises an error when validating an instance under the ophys schema:
ValidationError: Additional properties are not allowed ('OpticalChannel' was unexpected)
Failed validating 'additionalProperties' in schema['properties']['Ophys']:
NB: the way I am defining the OpticalChannel
is the same as for Device
, but for the Device it does not rise any error.
My guess is that in the BaseImagingExtractorInterface
, when Ophys metadata are initiated, only photon_series_type
, Device
and ImagingPlane
are defined.
https://github.com/catalystneuro/neuroconv/blob/567213d4b255a62d6b83e34e7a94929cf16c10b2/src/neuroconv/datainterfaces/ophys/baseimagingextractorinterface.py#L33C1-L42C12
This is to organize the conversion. Some general resources.
Fictrac:
https://github.com/rjdmoore/fictrac/tree/master
The paper:
https://www.biorxiv.org/content/10.1101/2022.03.20.485047v1
I will update as more information comes
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