Specifying pixel size

For most tools, you must specify the pixel size of your data using command-line flags.

You can specify them directly

  • -x or --x-pixel-um Pixel spacing of the data in the first dimension, specified in um.

  • -y or --y-pixel-um Pixel spacing of the data in the second dimension, specified in um.

  • -z or --z-pixel-um Pixel spacing of the data in the third dimension, specified in um.

Or you can provide a supported metadata file

  • --metadata Metadata file containing pixel sizes (any format supported by micrometa can be used).

If both pixel sizes and metadata are provided, the command line arguments will take priority

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