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FTR: metadata useful for widefield data #110

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yarikoptic opened this issue Jan 12, 2022 · 3 comments
Open

FTR: metadata useful for widefield data #110

yarikoptic opened this issue Jan 12, 2022 · 3 comments

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@yarikoptic
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Channeling metadata @annechurchland (thank you!) has reported (during NWB Adoption session) to be useful for widefield data:

Metadata for widefield: 
Mouse
Light source, wavelength, intensity at sample
Optocal system (NA, resolution)
Camera
Focusing depth
Surgery (window or clear skull prep; qc)
Imaging speed
expression/indicator/injection(I guess that is included in mouse?)
width and height pixels,
magnification (same info as resolution I guess),
objective aperture,
wavelength need to be per channel,
light shielding (essential for rolling shutter - details on the shielding method are useful for reproducibility),
shutter mode (rolling/global),
cam exposure - not necessarily the same as frame rate,
illumination exposure - can be dictated by the common time of all lines,
exposure filter bandwidth,
exposure dichroic cutoff,
excitation dichroic cutoff,

whenever I have mentioned BEP031 (bids-standard/bids-specification#881)

@satra
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satra commented Jan 12, 2022

this should be in the bids json file associated with the data. i think a lot of these elements are already there. we can check what's missing.

see https://bids-specification--881.org.readthedocs.build/en/881/04-modality-specific-files/10-microscopy.html#microscopy-metadata-sidecar-json

the image acquisition section should have many of these elements.

there is additional metadata in the OME header itself, which should also be available in NGFF when that metadata is finalized.

@annechurchland
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annechurchland commented Jan 12, 2022 via email

@yarikoptic
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By the way, I moved to UCLA; this email is from my new address.

yeap, twitter keeps us updated, and github keeps us safe (no emails are exposed here AFAIK). Congrats on the move!

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