exampleJob.json

{
  "_comment_on_input": "Bucket and path in the bucket to the parent folder of your plates of images",
  "input_bucket": "SOURCE_BUCKET",
  "input_location": "projects/PROJECTNAME/BATCHNAME/images/",
  "path_to_metadata": "Images/Index.idx.xml",
  "_comment_on_output": "Bucket and path in the bucket to the parent folder of .ome.zarr file",
  "output_bucket": "DESTINATION_BUCKET",
  "output_location": "projects/PROJECTNAME/BATCHNAME/images_zarr/",
  "_comment_on_upload_flags": "Enter any flags you want passed to s3 for upload. Otherwise set to false.",
  "_comment_on_upload_flags2": "e.g. --acl bucket-owner-full-control",
  "upload_flags": false,
  "_comment_on_settings": "If you want to set any of the following parameters, enter a value. Otherwise set to false.",
  "resolutions": false,
  "tile_width": false,
  "tile_height": false,
  "target-min-size": false,
  "_comment_on_additional_flags": "Enter any additional flags you want passed to BioFormats2Raw. Otherwise set to false.",
  "_comment_on_additional_flags2": "e.g. --extra-readers com.glencoesoftware.bioformats2raw.MiraxReader",
  "additional_flags": false,
  "_comment_on_downsample_after": "true if you want to add an additional downsampled resolution after .ome.zarr creation.",
  "_comment_on_downsample_only": "true if you want to download already-created .ome.zarr files and downsample them.",
  "downsample_after": false,
  "downsample_only": false,
  "downsample_scale": 8,
  "_comment_on_plates": "Each plate is an individual task and will be run in parallel",
  "plates": ["PLATEA","PLATEB","PLATEC","PLATED"]
}