This document contains JSON examples for multiscales_strict metadata layouts.
multiscales_transformations¶
multiscales_transformations.json
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48{ "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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75{ "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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76{ "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} } } ] }