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

[Sebastien Besson (Staff)]

Hi Konrad

thanks for sharing a representative example.

First of all, despite their extension, both the 8 and 16 bit raw images are not OME-TIFF but simple
multi-page TIFF files.

It should be possible to combining these stacks into a multi-channel image. This is a typical part of the
curation effort we sometimes do for IDR datasets. The attached picture describes an example of
combining all 12 of them into a rich multi-channel image rendered by OMERO.iviewer.

Obviously a better option would be that the acquisition software exporting the data in a representation that
captures the multi-channel aspect as well as any relevant acquisition metadata. Let us know if
there is a way we can help supporting this goal.

Best,
Sebastien
[cid:61362AE7-7049-44BE-A943-DD6B0A393FAF]
On 31 Oct 2018, at 13:51, Kölble, Konrad <Konrad.Koelble at uk-erlangen.de<mailto:Konrad.Koelble at uk-erlangen.de>> wrote:

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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