DRAFT: Add OnePhotonSeries neurodata_type

[rly]

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]

It should at least have a link to a Device

[rly]

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]

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:

• manufacturer: str
• magnification: float
• numerical aperture: float

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:

• quantum efficiency
• read noise (units: # electrons)
• pixels (I guess width and height would be best)

then there are two settings you might need to store:

• exposure time (this is often 1/frequency, but sometimes not)
• binning (combining pixels, could be 1,2,4 or 8)

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]

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.