Generate modulo annotation for FLIM

[jburel]

Create an annotation for FLIM data when imported into OMERO
See ​https://www.openmicroscopy.org/site/support/file-formats/working-with-ome-xml/6d-7d-and-8d-storage

Currently we had it to channels, we may want to rethink that later.
Crucial for Imperial

[jburel]

Discussion during satellites meeting:

• keep storing in channels for std files and announce to the list that we will move it to t.
• Create an XML annotation (modulo) when the image is imported.

[jburel]

Referencing ticket #7855 has changed sprint.

[jburel]

Added support in B-F and insight to view the modulo T
The file annotation is currently only added when using the FLIMfit importer. We need to generate a annotation and link to the image in the OMERO.importer.

[jburel]

Roger: could you have a look at that one?

[rleigh]

Now that Melissa's work on Modulo support for CZI is merged, readers such as SDT and Lavision should be able to use the same approach as used for CZI.

[mlinkert]

Unless I misunderstand the issue, the SDT and Lavision (Imspector) readers already generate modulo annotations as appropriate - see ​https://github.com/openmicroscopy/bioformats/pull/644.

[rleigh]

If these readers are already generating correct modulo annotations, then I think I'm misunderstanding what I'm supposed to be doing for this ticket. Is the original bug resolved, or is there some additional work to do here? If so, what exactly needs doing? Thanks!

[jburel]

if the annotation with correct namespace is generated and correctly linked to the image when imported into OMERO, for all relevant formats, we should be set.

[pwalczysko]

Imported images from test_images_good/sdt folder using OMERO.insight-5.0.0-beta1-1586-c6ae640-ice33-b490-mac to Gretzky - crash after opening of the images happened (see ​https://trac.openmicroscopy.org.uk/ome/ticket/11713). The images had no Modulo Attachments after import (see screenshot).

[jburel]

from Ian, I just tried importing a couple of .sdt & 1 Imspector .msr files to Gretzky via insight ( 5.0.0-beta1-1586-c6ae640-ice33-b490-mac) & they seemed ti import ok & with lifetime encoded as T. However, there seemed to be no xmlAnnotation visible under "other" & ithe time-points were displayed as T which, I think means that insight couldn't find the annotation either.

[jburel]

Increasing the priority since Beta2 will be rolled out at imperial.

[jamoore]

PR opened, but still needs work: ​https://github.com/openmicroscopy/bioformats/pull/820

[jamoore]

With the latest commit on PR 820 (​https://github.com/joshmoore/bioformats/commit/b8c6415facc4871e403a6f14f39eedd31491762c) I get the following in my DB on import:

ome2=> select id, ns, textvalue from annotation order by id desc limit 1;
-[ RECORD 1 ]-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
id        | 1402
ns        | openmicroscopy.org/omero/dimension/modulo
textvalue | <Modulo namespace="http://www.openmicroscopy.org/Schemas/Additions/2011-09"><ModuloAlongT End="12304.687643793777" Start="0.0" Step="195.3125022824409" Type="lifetime" TypeDescription="TCSPC" Unit="ps"/></Modulo>

Closing for further discussion on the PR.