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Task #9843 (new)

Opened 7 years ago

Last modified 3 years ago

BUG: Insight/OMERO imageJ metadata discrepancies

Reported by: rkferguson Owned by:
Priority: minor Milestone: Metadata
Component: General Version: 4.4.9
Keywords: n.a. Cc: mlinkert, jburel, nikolaus.ehrenfeuchter@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

Report from Basel:

When an image is opened in OMERO and then opened in ImageJ/fiji via the plugin there is a loss in the image metadata when viewing the image metadata in imagej/fiji.

Screenshot attached shows comparison of metadata and scientist report above where they identified the loss of channel names.
Original data file attached.

Attachments (2)

viewing_metadata_via_imagej_plugin.png (462.4 KB) - added by rkferguson 7 years ago.
230_11_R3D_D3D_PRJ.dv (2.0 MB) - added by rkferguson 7 years ago.

Change History (9)

Changed 7 years ago by rkferguson

Changed 7 years ago by rkferguson

comment:1 Changed 7 years ago by jburel

  • Sprint changed from 2012-11-20 (2) to 2012-12-18 (3)

Moved from sprint 2012-11-20 (2)

comment:2 Changed 7 years ago by jburel

  • Cc jburel added
  • Component changed from Insight to General
  • Owner jburel deleted
  • Sprint 2012-12-18 (3) deleted

comment:3 Changed 6 years ago by mlinkert

The user should be able to see the channel names and wavelengths if the "Display OME-XML metadata" option is checked in the "Bio-Formats Import Options" window when opening in ImageJ/Fiji.

Adding the channel names to the "Image Info" window is possible, but I'd rather not end up having to put all of the metadata there. Including the channel names in that window amounts to updating the original metadata for OmeroReader?.

Gus, if you think that checking the "Display OME-XML metadata" option is enough, then please close this ticket; otherwise, please assign to me and I'll open a PR to update the reader.

comment:4 Changed 6 years ago by rkferguson

Melissa, I don't have the practical experience of working with real data or the understanding of Bioformats/ImageJ use to be able to sensibly decide this issue.
Below is Scott's reply to your comment.
I think you should make an executive decision on whether to leave it or change the reader and I will then pass that on to Scott.

From: Scott Loynton <s.loynton@…>

Subject: Re: Fwd: [OME] #9843: BUG: Insight/OMERO imageJ metadata discrepancies

Date: 13 March 2013 10:47:21 GMT

Looking into the problem it is more specifically when you are working between OMERO and ImageJ/Fiji.

So in the scenario I have the user wants to open their image from OMERO into ImageJ/Fiji. When you do this in OMERO via the right click "open with" the image is opened in ImageJ/Fiji but working this way you do not get access to the Bio-Formats import options, so the tick box to select "display OME-XML metadata" is not shown or accessible. This is where the perceived breakdown is that you would require access to this metadata in your analysis tool.

I have looked into a work around but it would mean either exporting your image as a OME-TIFF and opening in ImageJ/Fiji, but this way you do not have all the original metadata as you would in the raw data. So the alternative is to download the raw data from OMERO and work on a separate image to the one that has already been imported into OMERO.

There is the option to display metadata when in ImageJ/Fiji via image> properties shows a limited amount of metadata. So I would in principle agree with Melissia that "display OME-XML metadata" is enough but it would mean having access to the Bio-Formats import options when you open an image in OMERO.

Otherwise I would argue more for a generic set of metadata in the option image> properties if you need any input on what this might be I have had some discussion about some of the microscope image acquisition software.

comment:5 Changed 6 years ago by jburel

Mix of issues here:

  • Open with uses the OME-TIFF but could open the origin format if available. (also need an option there when open in imageJ see sussex note)
  • The OME-TIFF created needs to have more of the metadata (schema branch)
  • Metadata option display availability.

We can certainly improve the workflow in insight.

comment:6 Changed 6 years ago by jburel

  • Cc nikolaus.ehrenfeuchter@… added
  • Version set to 4.4.9

comment:7 Changed 3 years ago by jamoore

  • Milestone changed from 5.x to Metadata
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