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NeurodataWithoutBorders / nwb-schema

Data format specification schema for the NWB neurophysiology data format
http://nwb-schema.readthedocs.io
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DRAFT: Add OnePhotonSeries neurodata_type #283

Closed rly closed 2 years ago

rly commented 5 years ago

Similar to TwoPhotonSeries but for handling one photon calcium imaging data from the Miniscope.

Details and differences with TwoPhotonSeries need to be fleshed out.

bendichter commented 5 years ago

It should at least have a link to a Device

rly commented 5 years ago

Proposed solution: add optional link to Device in ImageSeries. add OnePhotonSeries with related metadata. Make an extension for OnePhotonSeries and we could fast track it into the core.

bendichter commented 4 years ago

From talking with @chrapkiewicz, we have some more specific metadata requirements:

OnePhotonSeries need to link to two different types of devices: Objective Lens and Camera. Objective Lens can be the same as in 2p. It either needs to be specified with a model number (which fully defines it) or with:

Unlike 2p, OnePhotonSeries would also need an associated camera. Again, this could be mostly specific by a model number, but in the absence of a model number these futures would be needed:

then there are two settings you might need to store:

finally, you should indicate power, which is generally <5 mW. Alternatively, you might want to store intensity, which is units mW/mm^2, but it sounds like power is more common

chrapkiewicz commented 4 years ago

Looks good to me. There are probably slightly different metadata for miniscopes and 1p microscopes for head-fixed experiments. In the latter case if that's a commercial body, the model should be known and what users are changing are: filters (excitation, emission, dichroic) and objective. A camera is easily upgradable and defines image properties and should be reported too.

For custom microscope really the only extra part that needs to be reported is just a tube lens defined by a focal length (float) typically between 90 and 200 mm and a model.