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mpi2 / PhenotypeData

Reorganisation, update, and extend code from PhenotypeArchive
Apache License 2.0
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Load nrrd images into omero #516

Open kbab opened 3 years ago

kbab commented 3 years ago

Omero IDs are missing for all nrrd images, resulting in missing thumbnails on mousephenotype.org (e.g. https://www.mousephenotype.org/data/imageComparator?&parameter_stable_id=IMPC_EYE_076_001&acc=MGI:1915826 ). nrrd images are currently not loaded into omero because our installation does not have the underlying java libraries to deal with compressed nrrd images.

The purpose here is to create uncompressed versions of these images (e.g. use SimpleITK in python to load, then re-save in uncompressed format) and load these uncompressed versions into omero.

kbab commented 2 years ago

There are two scripts that currently exclude the nrrd images. They are: PhenotypeData/external_tools/src/main/python/images/get_omero_ids_using_csv_file.py and PhenotypeData/external_tools/src/main/python/images/OmeroUploadUsingCsvFile.py