Fix invalid Shape.TheC value

[melissalinkert]

Noticed while testing glencoesoftware/ome-omero-roitool#38:

• open any OMERO image in QuPath using this extension
• draw a simple shape
• send annotations back to OMERO
• try to export the annotation with ome-omero-roitool, get an exception because Shape.TheC is -1

ome-omero-roitool will get a companion PR shortly, but this should at least prevent the extension from sending an invalid value. Repeating the same steps as above with this change and a different image should successfully export the ROI to OME-XML.

[sbesson]

Confirmed as part of the testing of glencoesoftware/ome-omero-roitool#38 that the current release of the QuPath OMERO extension sets theC to -1 for each Shape exported to OMERO. With this PR included, theC is set to 0 and the ROIs can be exported as OME-XML using the current HEAD of ome-omero-roitool.

Is setting this value unconditionally to the first channel the expected beahvior? An alternative default would be not to set TheC which means the ROI would be applied to all channels.

[melissalinkert]

With defb154, The* should not be set when exporting from QuPath to OMERO. Using Integer instead of int means the values will only be serialized to JSON if not null. Since nothing in the ROI export logic changes the plane indexes, these values should always be null and thus no longer set in OMERO. ome-omero-roitool should be able to export ROIs without The* set.

[sbesson]

With the last commit, using a multi-channel multi-Z fluorescence images hosted on OMERO and exporting annotations created from QuPath, I get the following behavior

All theC, theZ and theT properties are now unset and the ROIs will be interpreted as applying to all planes.

A possible follow-up would be to look into populating the TheZ value in QuPath and translate it accordingly when exporting to OMERO. My understanding is that the Z/T index was not properly populated prior to this PR so this is not a regression. It would be useful to have a second opinion from @muhanadz or anyone involved in the QuPath workflow.