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

[Jean-Marie Burel (Staff)]

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 on behalf of
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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