Open JoeZiminski opened 11 months ago
Hi Joe,
I think your question is really related to the BIDS specifications themselves, and therefore, I would re-post it there: https://github.com/bids-standard/bids-specification/issues (and I'll answer there with what I know ;) )
Cheers,
Sylvain
FWIW, an example of BIDS dataset with micr
stained data https://dandiarchive.org/dandiset/000108/draft/files?location=sub-MITU01%2Fses-20210521h17m17s06%2Fmicr it has only post-mortem/no func
though. Indeed feels odd to place mix functional and anatomical data within the same micr/
- for MRI indeed there is a clear separation but I don't think it was envisioned for micr
. I guess (?) it would be a different session though and likely a different suffix (2PE
vs SPIM
)? But indeed in any case sounds more of a generic BIDS question, not for this BEP
FWIK, there was no functional data around when the BEP microscopy was put together and when it was integrated officially in the BIDS specs... so it's lacking, and @JoeZiminski , your post reflects this... the official specs for microscopy are here now: https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/10-microscopy.html, and correspond to what @yarikoptic explains: different suffixes are used for func (e.g 2PE) and anat (e.g CONF) data types; but indeed, this seperation between func and anat (using suffixes) is not consistent with how it's done for MRI (with different "BIDS modalities" sitting in different directories)...
@JoeZiminski this indeed an inconsistency between modalities
my suggestion to help keep them separate would be to use different session folders
ses-histology/micr/sub-*png
ses-funcimg/micr/sub-*2PE.png
Hi Everyone,
We have a question about microscopy data, apologies if this is the wrong place for this discussion (if so it would be much appreciated if someone could point us to the correct place).
We are currently thinking about how to store microscopy data of histological type (i.e. post-mortem) and what we call 'functional' imaging, such as 2-photon with calcium indicators. Currently we have the data-type names
histology
andfuncimg
although we would like to movehistology
tomicr
to align with BEP031. However, in this case it is not entirely clear what data should go undermicr
, from reading the specification, any 2-photon data should be stored inmicr
. However, it seems unintuitive to mix both functional imaging and post-mortem histology within the same data-type. Similarly this would not reflect the distinction made in neuroimaging BIDS, that hasanat
andfunc
to distinguish between anatomical and functional imaging.Does anyone have any further insight as to this question? We are considering using
micr
for histology andfuncimg
for functional microscopy. However, this naming is somewhat confusing (asfuncimg
is a form of microscopy), and we do not want to break BIDS compatibility if indeedmicr
is intended to contain functional microscopy.Thanks! Joe (from the SWC Neuroinformatics Unit working on NeuroBlueprint)