The workflow seems to work properly, but the current output image pyramid data shows quantization issues. It looks like the Zeiss .czi file (included in the upload) stores its image as UInt16, but the ome.tiff file has a UInt8 image. This implies that some error was made in translation from the .czi to the .ome.tiff . My understanding is that that translation was done using the Zeiss Zen (black) software, circa 2014. This issue should not be closed until a correctly translated dataset is passed through the pipeline. See https://github.com/hubmapconsortium/ingest-pipeline/issues/348
The workflow seems to work properly, but the current output image pyramid data shows quantization issues. It looks like the Zeiss .czi file (included in the upload) stores its image as UInt16, but the ome.tiff file has a UInt8 image. This implies that some error was made in translation from the .czi to the .ome.tiff . My understanding is that that translation was done using the Zeiss Zen (black) software, circa 2014. This issue should not be closed until a correctly translated dataset is passed through the pipeline. See https://github.com/hubmapconsortium/ingest-pipeline/issues/348