Incomplete metadata when using .lif files

[Holli25]

Hi Omero team,

I seem to run into a problem when handling ".lif" data from a Leica SP8 using Omero. Apparently only the metadata from one channel are read by Omero and I am missing informations about all other channels (like excitation wavelength, detector settings...).
This seems to be in connection with a problem in FIJI/Bio-Formats, as I have the same problem as described here: viewtopic.php?f=13&t=8430&p=18970&hilit=lif#p18963 as well (the same LUT for all channels; can be overcome by selecting "Colorized"). FIJI also does not read all the metadata and only shows the one from one channel.

Holli

[dgault]

Hi Holli,

Thank you for bringing this to our attention. What you are describing does sound similar to the previously reported issue as you mentioned, however in that particular case I had thought it was limited to the Bio-Formats plugin and had not noticed any issues with the metadata. The fact that you have noticed missing metadata suggests the issue may be related to the reader as opposed to plugin as previously thought.

If you had a suitable sample file which you were able to share for testing purposes that would be a great help. You can upload QA files to https://www.openmicroscopy.org/qa2/qa/upload/

David Gault

[Holli25]

Hello David,

Thank you for the fast answer! I uploaded a file to the page but am unsure, if this worked or not. Just tell me, if there is no file uploaded.

[dgault]

Thank you for uploading the sample file Holli, we received it Ok and I was able to test it this morning. I was able to reproduce the issues that had previously been reported in viewtopic.php?f=13&t=8430&p=18970&hilit=lif#p18963 with regards the channel display colours. Additionally as you had reported there appears to be metadata missing on the second channel.

I have updated the Trello card from the previous issue to make note of this new information and sample file. You can track the progress of the issue at https://trello.com/c/8BQ2ViRo/212-lif-c ... g-metadata

[Holli25]

Thank you very much!

[bjtho08]

What is the latest news on this issue?

I have noticed that OMERO does not correctly parse the original metadata when populating Microscope and Image metadata. All field values are shown as "other" or unset even though the values are present in the original metadata.
For example

Code: Select all

ATLConfocalSettingDefinition|MicroscopeModel   DMI6000B-CS
ATLConfocalSettingDefinition|ObjectiveName   HC PL IRAPO    40x/1.10 WATER

should have been parsed as the microscope model and objective name.

[rgozim]

Hi bjtho08,

To make it easier for us to find out what is causing the issue, could you upload the file you are having issues with to https://www.openmicroscopy.org/qa2/qa/upload/

Thanks,
Riad

[bjtho08]

Sorry for the delay. I was on vacation. I have uploaded an example now. Hope it can be of help to you

[dgault]

Thank you for submitting the new sample file, I was able to test and reproduce the metadata issues as you had described. I have updated the existing Trello card (https://trello.com/c/8BQ2ViRo/212-lif-c ... g-metadata) with the details of the new sample file and we will use this for further investigating a potential fix.

[bjtho08]

Thank you for taking the time to look through this issue. Do you know when we can expect the issue to be resolved? I can see that the issue is currently filed under "Investigating", but Trello does not reveal if there is any activity on the issue.