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Add fiber photometry metadata #3

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merged 3 commits into from
May 28, 2024
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alessandratrapani
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Added fiber photometry metadata, mainly devices. The setup is quite complicated.
Note that:

  • their photodetector is a CMOS sensor that is not described by a detected wavelength. I defined that as a simple Device, along with all the other components of the setup.
  • There is a dichroic mirror that has a dual-band transmission characteristic. I define two separate DichroicMirror devices and call them DichroicMirror3a and DichroicMirror3b and explicitly the single transmission band for each.
  • We need to ask if the OpticalFilter with CW 405 nm is also used to filter the 415 nm excitation.
  • The injection_location and injection_coordinates_in_mm are available, but they have not been reported for the specific indicator or opsin. I guess we will need to specify it subject by subject.

@alessandratrapani alessandratrapani self-assigned this May 8, 2024
@weiglszonja
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Thank you @alessandratrapani, this looks great. I'll also check the paper and come back with suggestions if any.
For now I would only have one question:

There is a dichroic mirror that has a dual-band transmission characteristic. I define two separate DichroicMirror devices and call them DichroicMirror3a and DichroicMirror3b and explicitly the single transmission band for each.

Would it make sense to add another type of Device in ndx-fiber-photometry that allows this dual-band specification?

@alessandratrapani
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Would it make sense to add another type of Device in ndx-fiber-photometry that allows this dual-band specification?

I thought about it but maybe it's better to modify the current one to take as many bandwidth as can be. In practice it would mean making the transmission band and reflection band fields a 2D array with shape (None, 2). Consequently the cut_on and cut_off wavelengths would be a 1D array the same length as the transmission band and reflection band

@weiglszonja weiglszonja merged commit 5bf20c2 into main May 28, 2024
@weiglszonja weiglszonja deleted the add_fiber_photometry_metadata branch May 28, 2024 11:58
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2 participants