MicroManager: use PositionName key/value for storing the ImageName (rebased onto metadata54)

[sbesson]

This is the same as gh-3089 but rebased onto metadata54.

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See https://trello.com/c/5KT3Bvie/1-idr0040-aymoz-singlecell

Currently the Micro-Manager reader uses one of the TIFF filename for populating the ImageName metadata. For typical replica experiments across multiple positions (Pos0, Pos1,...), this results in duplicate image names. This commit now parses the PositionName key/value in the metadata JSON and use it if available to fill the ImageName.

This PR will probably affect the metadata of existing filesets, require a configuration change in which case it might be more suitable for a minor release increment.

/cc @dominikl

[sbesson]

--rebased-from #3089

[sbesson]

With this PR included, the updated image names for the Micro-Manager filesets was not preserved when importing the images into OMERO - see https://trello.com/c/5KT3Bvie/1-idr0040-aymoz-singlecell#comment-5a99443815517e95b51ccdc8. Here, the problem is related in the OMERO import process which overrides the name of the image to use either an externally specified value or a default value based on the filename of getCurrentFile(). This behavior and its problems had been already raised and described in greater details in ome/design#57.

In OMERO 5.3.0, part of this metadata loss has been fixed in the case of High-Content Screening datasets where the plate name is preserved and used. For non SPW data, the ImageName populated by Bio-Formats remains lost on import. To modify the behavior for Images, ome/openmicroscopy@94575d5 probably contains most of the required logic but the breaking impact requires discussion.

Immediately, populating the name column in bulk imports as was done in IDR/idr-metadata@8a5a7cd is our best option. Closing this PR against metadata54 but leaving the original PR opened against develop for consideration as the metadata improvement the Micro-Manager datasets remains a feature for the consumers of the Bio-Formats API.