[ome-users] 12-channel Imaging Mass Cytometry -> OMERO

[Sebastien Besson (Staff)]

Dear Konrad,

following up on this thread, I happened to meet Roberto Spada last week. We went
together through an example of the workflow in order to export a multi-page OME-TIFF file
using the MCD Viewer. We were able to reproduce the behavior described by Jean-Marie
using ImageJ i.e. individual TIFF planes read correctly but the representation of the dataset
is incorrect as it fails to be detected as multi-channel.

From experience, the primary cause for similar behavior are invalid OME-TIFF files i.e. files
that are not compliant with the specification [1]. From the sample dataset shared by Konrad,
this is definitely the case as the file suffixed as `.ome.tiff` contains no OME metadata
in the ImageDescription tag of the first TIFF IFD. Bio-Formats simply falls back to reading
such files as regular multi-page TIFF files.

It looks like the way to fix this now lies within the proprietary software. As discussed with
Roberto, if technical people at Fluidigm want to get in touch with OME in order to resolve
this export issue, they should feel free to continue the discussion here or use any other public
support channel [2].

Best,
Sebastien

[1] https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/specification.html
[2] https://www.openmicroscopy.org/support/


On 7 Nov 2018, at 10:50, Jean-Marie Burel (Staff) <j.burel at dundee.ac.uk<mailto:j.burel at dundee.ac.uk>> wrote:

Hi Konrad

I tried the data into OMERO. The only one I can import is the OME-TIFF. I
have attached the screenshot Is it what you mean by ³blackboxes².
There is only one channel and not 7 as indicated in the summary.txt file.

I will check the MCD viewer when I have access to a window machine

Cheers

Jmarie




On 06/11/2018, 10:21, "ome-users on behalf of Kölble, Konrad"
<ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of
Konrad.Koelble at uk-erlangen.de<mailto:Konrad.Koelble at uk-erlangen.de>> wrote:

Hi,
the above remains unsolved; Sebastien Burel currently uses a "very
non-user friendly way [his words] to create OME metadata files combining
the planes from various TIFF files" and suggested to try Fluidigm's MCD
Viewer for export. Unfortunately its File-> Open followed by File->Export
`.ome.tiff` functionality creates output which blockboxes after OMERO
upload.
A sample 5-channel down-mix 20170713_spleen50_1_KK-select (together with
its parent 2017071313_spleen50_1.txt and an MCD Viewer 1.0 zip-archive)
can be found under

https://volafile.org/r/q6aqxn48

Any brainwaves?

Cheers
Konrad
________________________________________
Von: ome-users [ome-users-bounces at lists.openmicroscopy.org.uk]" im
Auftrag von "Kölble, Konrad [Konrad.Koelble at uk-erlangen.de]
Gesendet: Mittwoch, 31. Oktober 2018 14:51
An: ome-users at lists.openmicroscopy.org.uk
Betreff: [ome-users] 12-channel Imaging Mass Cytometry -> OMERO

Hi,
recently Fluidigm's Roberto Spada sent me a 12-marker human spleen FFPE
1mm2 section's Hyperion Imaging System dataset at the standard 1um2
resolution including

- an original raw 2017071313_spleen50_1.txt file
- MCD Viewer software which opens such *.txt files for analysis and
generation of original .ome.tiff or false color TIFF files
- original raw 16-bit and/or 32-bit .ome.tiff images

Has someone successfully managed to OMEROze pic & metadata output from
this interesting instrument
https://www.fluidigm.com/products/hyperion-imaging-system
for multichannel viewing?

You'll find the 2017071313_spleen50_1.txt, the MCD Viewer (incl. guide),
the 16bit tiff and the 32bit tiff images under
https://volafile.org/r/q1h07r5m

Cheers
Konrad
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