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Wrong pixel values in ome.zarr made from ome.tiff #27

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pwalczysko opened this issue Apr 7, 2022 · 2 comments
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Wrong pixel values in ome.zarr made from ome.tiff #27

pwalczysko opened this issue Apr 7, 2022 · 2 comments

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@pwalczysko
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pwalczysko commented Apr 7, 2022 •
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  1. Convert the ...downloads.openmicroscopy.org/images/OME-TIFF/2016-06/binaryonly images into zarr using bf2raw version 0.4.0, using the command
  2. bioformats2raw binaryonly/multifile-Z1.ome.tiff multifile-Z1.ome.zarr
  3. Import the resulting multifile-Z1.ome.zarr folder to OMERO using the command (note the usage of the --depth 10)
  4. omero import --transfer=ln_s --skip=checksum --parallel-upload=10 --skip=minmax --depth 10 multifile-Z1.ome.zarr/
  5. Observe that the image in OMERO https://merge-ci.openmicroscopy.org/web/webclient/?show=image-228872 has all pixel values 0. This is not expected, as the original ome.tiff is looking as follows https://merge-ci.openmicroscopy.org/web/webclient/?show=image-228824 (user-8)
@sbesson
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sbesson commented May 16, 2022

Is this still the case or was it an intermediate result during the testing of #31 ?

@pwalczysko
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This is solved by the previous PR, sorry, did not close

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@sbesson @pwalczysko