with the upcoming NGFF implementation, not clear to me yet the exact locations where and how (positional) metadata should be stored are not clear to me yet.
The MoBIE view would always be the topmost layer containing everything necessary to define how data is visualized. Scaling to physical space should reside as close to the data blob as possible. But where exactly and what about other transformations?
What I've encountered so far:
"classic" BDV (hdf5, n5):
here the partition is rather clear. Metadata resides in the XML while storage related parameters reside in the data containers.
In cases such as registrations/transformations that have been done in BigWarp/BDV-PG and store related transformations in the XML, these should be extracted from there.
My approach when importing such data into MoBIE is to strip all additional metadata beyond the pixel scaling (to physical space) and write it into the MoBIE views.
"NGFF", "advanced" formats:
I've recently come across a new N5 implementation from Janelia that stores positional metadata (scaling, origin offset) in the JSON parameter files inside the N5 container. (see /g/emcf/schorb/data/sbemtestexport/aligned/20211117)
Now the question is, how can we make this metadata available in MoBIE? Also, I think we would like to keep backwards-compatibility with "classic" BDV formats.
I would suggest a step-wise import:
Extract the metadata from the N5 and write it into the XML (enabling to open the dataset in BDV).
when importing this source into MoBIE we strip the metadata from the XML and put it into MoBIE views.
Hi,
with the upcoming NGFF implementation, not clear to me yet the exact locations where and how (positional) metadata should be stored are not clear to me yet. The MoBIE view would always be the topmost layer containing everything necessary to define how data is visualized. Scaling to physical space should reside as close to the data blob as possible. But where exactly and what about other transformations?
What I've encountered so far:
"classic" BDV (hdf5, n5): here the partition is rather clear. Metadata resides in the XML while storage related parameters reside in the data containers. In cases such as registrations/transformations that have been done in BigWarp/BDV-PG and store related transformations in the XML, these should be extracted from there. My approach when importing such data into MoBIE is to strip all additional metadata beyond the pixel scaling (to physical space) and write it into the MoBIE views.
"NGFF", "advanced" formats: I've recently come across a new N5 implementation from Janelia that stores positional metadata (scaling, origin offset) in the JSON parameter files inside the N5 container. (see
/g/emcf/schorb/data/sbemtestexport/aligned/20211117)Now the question is, how can we make this metadata available in MoBIE? Also, I think we would like to keep backwards-compatibility with "classic" BDV formats.
I would suggest a step-wise import:
What are your thoughts?