Meaning of Sizes BF, DimOrder BF, DimOrder BF Array, DimOrder

[aliaksei-chareshneu]

Dear all,

Could you clarify a bit exact meaning of Sizes BF, DimOrder BF, DimOrder BF Array, DimOrder fields in metadata?

Thank you for any input.

[filippocastelli]

Hi, thank you for opening the issue. Sorry for the poor documentation of the project, some of the terminology is obscure and tied to the inital uses of this code as part of my previous research, this will need to be addressed in the future.

DimOrder BF should be the DimensionOrder field of the Pixels of the current image series, the values should reflect the ones in the OMEXML schema https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_DimensionOrder

DimOrder BF Array is just a reversed version of DimOrder BF, while DimOrder should be a copy of DimOrder BF Array.

Sizes BF is an array composed of

• TotalSeries which is the number of Image nodes in the OMEXML root
• SizeT, SizeZ, SizeC, SizeY, SizeX relative to the current image series, which are defined in the OMEXML schema https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_SizeT

I know this is very confusing, very obscure and specific to legacy applications, to be honest I don't even remember the reasons for this particular naming ( it probably made sense back then ). reader.metadata is just a summarization of the fields that are present in the OMEXML object, which you can read at reader.ox, all the names in reader.ox should be faithful to the OMEXML schema (if I did things right).

Again, sorry for the confusion

[aliaksei-chareshneu]

Thank you very much for the clarification. No worries, I understand that it is difficult to handle these. Thank you very much for developing this package!