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

[Kölble, Konrad]

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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