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multiscales_strict

This document contains JSON examples for multiscales_strict metadata layouts.

multiscales_transformations

multiscales_transformations.json
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{
  "zarr_format": 3,
  "node_type": "group",
  "attributes": {
    "ome": {
      "version": "0.5",
      "multiscales": [
        {
          "coordinateSystems": [
            {
              "name": "intrinsic",
              "axes": [
                {
                  "name": "y",
                  "type": "space",
                  "unit": "micrometer"
                },
                {
                  "name": "x",
                  "type": "space",
                  "unit": "micrometer"
                }
              ]
            }
          ],
          "datasets": [
            {
              "path": "s0",
              "coordinateTransformations": [
                {
                  "scale": [1, 1],
                  "type": "scale",
                  "input": "s0",
                  "output": "intrinsic"
                }
              ]
            }
          ],
          "name": "image_with_multiscaleTransformations",
          "type": "foo",
          "metadata": {
            "key": "value"
          }
        }
      ]
    }
  }
}

multiscales_example

multiscales_example.json
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{
  "zarr_format": 3,
  "node_type": "group",
  "attributes": {
    "ome": {
      "version": "0.6dev2",
      "multiscales": [
        {
          "name": "physical",
          "coordinateSystems": [
            {
              "name": "physical",
              "axes": [
                { "name": "t", "type": "time", "unit": "millisecond" },
                { "name": "c", "type": "channel" },
                { "name": "z", "type": "space", "unit": "micrometer" },
                { "name": "y", "type": "space", "unit": "micrometer" },
                { "name": "x", "type": "space", "unit": "micrometer" }
              ]
            }
          ],
          "datasets": [
            {
              "path": "s0",
              "coordinateTransformations": [
                {
                  // the voxel size for the first scale level (0.5 micrometer)
                  // the time unit (0.1 milliseconds), which is the same for each scale level
                  "type": "scale",
                  "scale": [0.1, 1.0, 0.5, 0.5, 0.5],
                  "input": "s0",
                  "output": "physical"
                }
              ]
            },
            {
              "path": "s1",
              "coordinateTransformations": [
                {
                  // the voxel size for the second scale level (1 micrometer)
                  // the time unit (0.1 milliseconds), which is the same for each scale level
                  "type": "scale",
                  "scale": [0.1, 1.0, 1.0, 1.0, 1.0],
                  "input": "s1",
                  "output": "physical"
                }
              ]
            },
            {
              "path": "s2",
              "coordinateTransformations": [
                {
                  // the voxel size for the third scale level (2 micrometer)
                  // the time unit (0.1 milliseconds), which is the same for each scale level
                  "type": "scale",
                  "scale": [0.1, 1.0, 2.0, 2.0, 2.0],
                  "input": "s2",
                  "output": "physical"
                }
            ]
            }
          ],
          "type": "gaussian",
          "metadata": {
            "description": "the fields in metadata depend on the downscaling implementation. Here, the parameters passed to the skimage function are given",
            "method": "skimage.transform.pyramid_gaussian",
            "version": "0.16.1",
            "args": "[true]",
            "kwargs": { "multichannel": true }
          }
        }
      ]
    }
  }
}

multiscales_example_relative

multiscales_example_relative.json
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{
    "multiscales": [
        {
            "version": "0.5-dev",
            "name": "example",
            "coordinateSystems" : [
                {
                    "name" : "exampleCoordinateSystem",
                    "axes": [
                        {"name": "t", "type": "time", "unit": "millisecond"},
                        {"name": "c", "type": "channel"},
                        {"name": "z", "type": "space", "unit": "micrometer"},
                        {"name": "y", "type": "space", "unit": "micrometer"},
                        {"name": "x", "type": "space", "unit": "micrometer"}
                    ]
                },
                {
                    "name" : "array_0",
                    "axes": [
                        {"name": "t", "type": "time", "unit": "millisecond"},
                        {"name": "c", "type": "channel"},
                        {"name": "z", "type": "space", "unit": "micrometer"},
                        {"name": "y", "type": "space", "unit": "micrometer"},
                        {"name": "x", "type": "space", "unit": "micrometer"}
                    ]
                }
            ],
            "datasets": [
                {
                    "path": "s0",
                    // the transformation of other arrays are defined relative to this, the highest resolution, array
                    "coordinateTransformations": [{
                        "type": "identity",
                        "input": "s0",
                        "output": "array_0"
                    }]
                },
                {
                    "path": "1",
                    "coordinateTransformations": [{
                        // the second scale level (downscaled by a factor of 2 relative to "0" in zyx)
                        "type": "scale",
                        "scale": [1, 1, 2, 2, 2],
                        "input" : "s1",
                        "output" : "array_0"
                    }]
                },
                {
                    "path": "s2",
                    "coordinateTransformations": [{
                        // the third scale level (downscaled by a factor of 4 relative to "0" in zyx)
                        "type": "scale",
                        "scale": [1, 1, 4, 4, 4],
                        "input" : "s2",
                        "output" : "array_0"
                    }]
                }
            ],
            "coordinateTransformations": [{
                // the time unit (0.1 milliseconds), the voxel size for all spatial axes of "0" (0.5 micrometers)
                "type": "scale",
                "scale": [0.1, 1.0, 0.5, 0.5, 0.5],
                "input" : "array_0",
                "output" : "exampleCoordinateSystem"
            }],
            "type": "gaussian",
            "metadata": {
                "description": "the fields in metadata depend on the downscaling implementation. Here, the parameters passed to the skimage function are given",
                "method": "skimage.transform.pyramid_gaussian",
                "version": "0.16.1",
                "args": "[true]",
                "kwargs": {"multichannel": true}
            }
        }
    ]
}