bids-standard
Add 1PE to complement 2PE (microscopy)
https://blog.biodock.ai/one-vs-two-photon-microscopy/ seems to provide a nice comparison between one- and two-photon microscopy. Also https://www.gophotonics.com/community/what-are-single-photon-and-two-photon-excitation provides another comparison and uses "excitation" consistently between them.
Note that there is also already "FLUO" suffix for "Fluorescence microscopy" in general, of which both 1PE and 2PE and likely MPE (multi-photon) mechanisms are, so unclear when FLUO to be used, but I guess 2PE, MPE and now 1PE should be RECOMMENDED to be used in favor of FLUO as more specific
Some related references:
- https://github.com/bids-standard/bids-specification/pull/1632
ping @bids-standard/bep031 @bendichter
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- Who needs this?
- Is this an addition, or a refinement of
FLUO? - Is any metadata needed to make 1PE images usable?
- Are there any microscopy practitioners who support this?
@jcohenadad would you be willing to weigh in on this?
Okay, failing that, @yarikoptic I think it would be good to seek out some kind of consensus and not a bunch of non-practitioners who have commit privileges. IDK if posting to the bids-discussion list makes sense? Or perhaps OME lists?
@CodyCBakerPhD @bendichter , may be you could assist
- how much of one-photon imaging data do we have in dandi?
- do you see anything critical missing from https://bids-specification.readthedocs.io/en/stable/modality-specific-files/microscopy.html#microscopy-metadata-sidecar-json which would needs to be there for 1PE in addition to 2PE or FLUO?
@yarikoptic BIDS microscopy only applies to static images to my understanding. We may have a certain number of those scattered throughout (namely for anatomical markers) but the majority is time-dependent (videos)
There is a fair amount of metadata missing overall in BIDS to 'pull out' from NWB (field of view, coordinate systems, grid spacing, depths, optical channels)
From what I see the minimal amount to distinguish from 2P would be the excitation wavelengths (scalar per optic channel; technically the 'peak' of the excitation waveform). Some people even think the full waveform matters but can also usually be pulled from external sources if you specify the indicator
@yarikoptic BIDS microscopy only applies to static images to my understanding.
as I have mentioned in
- https://github.com/bids-standard/bids-specification/pull/1632#issuecomment-1769248031
there is nothing in BIDS microscopy restricting to anatomical, although indeed lacking desired temporal data formalized.
But overall questions mostly relevant to this particular PR: -given current listed support of 2PE and FLUO, would addition of 1PE be warranted for 1PE datasets (temporal data is not forbidden, thus IMHO permitted)?
- if not - would FLUO be appropriate for 1PE (but at the cost of loosing expresiveness)?
- Could there be FLUO which is not 1PE or 2PE?