multiscales_strict Examples#
This document contains JSON examples for multiscales_strict metadata layouts.
multiscales_transformations#
1{
2 "zarr_format": 3,
3 "node_type": "group",
4 "attributes": {
5 "ome": {
6 "version": "0.6.dev3",
7 "multiscales": [
8 {
9 "coordinateSystems": [
10 {
11 "name": "physical",
12 "axes": [
13 {
14 "name": "y",
15 "type": "space",
16 "unit": "micrometer"
17 },
18 {
19 "name": "x",
20 "type": "space",
21 "unit": "micrometer"
22 }
23 ]
24 },
25 {
26 "name": "intrinsic",
27 "axes": [
28 {
29 "name": "y",
30 "type": "space",
31 "unit": "micrometer"
32 },
33 {
34 "name": "x",
35 "type": "space",
36 "unit": "micrometer"
37 }
38 ]
39 }
40 ],
41 "datasets": [
42 {
43 "path": "s0",
44 "coordinateTransformations": [
45 {
46 "scale": [1, 1],
47 "type": "scale",
48 "input": "s0",
49 "output": "intrinsic"
50 }
51 ]
52 }
53 ],
54 "coordinateTransformations": [
55 {
56 "scale": [10, 10],
57 "type": "scale",
58 "input": "intrinsic",
59 "output": "physical"
60 }
61 ],
62 "name": "image_with_coordinateTransformations",
63 "type": "foo",
64 "metadata": {
65 "key": "value"
66 }
67 }
68 ]
69 }
70 }
71}
multiscales_example#
1{
2 "zarr_format": 3,
3 "node_type": "group",
4 "attributes": {
5 "ome": {
6 "version": "0.6.dev3",
7 "multiscales": [
8 {
9 "name": "example",
10 "coordinateSystems": [
11 {
12 "name": "intrinsic",
13 "axes": [
14 { "name": "t", "type": "time", "unit": "millisecond" },
15 { "name": "c", "type": "channel" },
16 { "name": "z", "type": "space", "unit": "micrometer" },
17 { "name": "y", "type": "space", "unit": "micrometer" },
18 { "name": "x", "type": "space", "unit": "micrometer" }
19 ]
20 }
21 ],
22 "datasets": [
23 {
24 "path": "s0",
25 "coordinateTransformations": [
26 {
27 // the voxel size for the first scale level (0.5 micrometer)
28 // and the time unit (0.1 milliseconds), which is the same for each scale level
29 "type": "scale",
30 "scale": [0.1, 1.0, 0.5, 0.5, 0.5],
31 "input": "s0",
32 "output": "intrinsic"
33 }
34 ]
35 },
36 {
37 "path": "s1",
38 "coordinateTransformations": [
39 {
40 // the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
41 // and the time unit (0.1 milliseconds), which is the same for each scale level
42 "type": "scale",
43 "scale": [0.1, 1.0, 1.0, 1.0, 1.0],
44 "input": "s1",
45 "output": "intrinsic"
46 }
47 ]
48 },
49 {
50 "path": "s2",
51 "coordinateTransformations": [
52 {
53 // the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer)
54 // and the time unit (0.1 milliseconds), which is the same for each scale level
55 "type": "scale",
56 "scale": [0.1, 1.0, 2.0, 2.0, 2.0],
57 "input": "s2",
58 "output": "intrinsic"
59 }
60 ]
61 }
62 ],
63 "type": "gaussian",
64 "metadata": {
65 "description": "the fields in metadata depend on the downscaling implementation. Here, the parameters passed to the skimage function are given",
66 "method": "skimage.transform.pyramid_gaussian",
67 "version": "0.16.1",
68 "args": "[true]",
69 "kwargs": { "multichannel": true }
70 }
71 }
72 ]
73 }
74 }
75}
multiscales_example_relative#
1{
2 "multiscales": [
3 {
4 "version": "0.6.dev3",
5 "name": "example",
6 "coordinateSystems" : [
7 {
8 "name" : "world",
9 "axes": {
10 "t": {"type": "time", "unit": "millisecond"},
11 "c": {"type": "channel"},
12 "z": {"type": "space", "unit": "micrometer"},
13 "y": {"type": "space", "unit": "micrometer"},
14 "x": {"type": "space", "unit": "micrometer"}
15 }
16 },
17 {
18 "name" : "intrinsic",
19 "axes": [
20 {"name": "t", "type": "time", "unit": "millisecond"},
21 {"name": "c", "type": "channel"},
22 {"name": "z", "type": "space", "unit": "micrometer"},
23 {"name": "y", "type": "space", "unit": "micrometer"},
24 {"name": "x", "type": "space", "unit": "micrometer"}
25 ]
26 }
27 ],
28 "datasets": [
29 {
30 "path": "s0",
31 // the transformation of other arrays are
32 // defined relative to this, the highest resolution, array
33 "coordinateTransformations": [{
34 "type": "scale",
35 "scale": [1, 1, 1, 1, 1],
36 "input": "s0",
37 "output": "intrinsic"
38 }]
39 },
40 {
41 "path": "s1",
42 "coordinateTransformations": [{
43 // the second scale level (downscaled by a factor of 2 relative to "s0" in zyx)
44 "type": "scale",
45 "scale": [1, 1, 2, 2, 2],
46 "input" : "s1",
47 "output" : "intrinsic"
48 }]
49 },
50 {
51 "path": "s2",
52 "coordinateTransformations": [{
53 // the third scale level (downscaled by a factor of 4 relative to "s0" in zyx)
54 "type": "scale",
55 "scale": [1, 1, 4, 4, 4],
56 "input" : "s2",
57 "output" : "intrinsic"
58 }]
59 }
60 ],
61 "coordinateTransformations": [
62 {
63 "name": "additional_translation",
64 "type": "translation",
65 "translation": [0, 0, 10, 20, 30],
66 "input": "intrinsic",
67 "output": "world"
68 }
69 ]
70 }
71 ]
72}