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Changes to the spec and schemata for RFC-2 #242

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Changes to the spec and schemata for RFC-2 #242

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ff76581
Changes to the spec and schemata for RFC-2
normanrz May 30, 2024
81d8742
typo
normanrz Jun 2, 2024
00371a3
change version in link
normanrz Jun 28, 2024
ee4ce14
adapt spec to RFC-2 revision
normanrz Jul 2, 2024
f1bab0c
Update rfc/2/index.md
normanrz Jul 4, 2024
4e4bf5a
adds schema_url + changes the root object for the JSON schemas to 'at…
normanrz Sep 26, 2024
4df0940
rm schema_url
normanrz Sep 27, 2024
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8 changes: 6 additions & 2 deletions latest/examples/bf2raw/image.json
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
{
"bioformats2raw.layout" : 3
}
"zarr_format": 3,
"node_type": "group",
"attributes": {
"https://ngff.openmicroscopy.org/0.5": { "bioformats2raw.layout": 3 }
}
}
51 changes: 32 additions & 19 deletions latest/examples/bf2raw/plate.json
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@@ -1,22 +1,35 @@
{
"bioformats2raw.layout" : 3,
"plate" : {
"columns" : [ {
"name" : "1"
} ],
"name" : "Plate Name 0",
"wells" : [ {
"path" : "A/1",
"rowIndex" : 0,
"columnIndex" : 0
} ],
"field_count" : 1,
"rows" : [ {
"name" : "A"
} ],
"acquisitions" : [ {
"id" : 0
} ],
"version" : "0.4"
"zarr_format": 3,
"node_type": "group",
"attributes": {
"https://ngff.openmicroscopy.org/0.5": {
"bioformats2raw.layout": 3,
"plate": {
"columns": [
{
"name": "1"
}
],
"name": "Plate Name 0",
"wells": [
{
"path": "A/1",
"rowIndex": 0,
"columnIndex": 0
}
],
"field_count": 1,
"rows": [
{
"name": "A"
}
],
"acquisitions": [
{
"id": 0
}
]
}
}
}
}
57 changes: 31 additions & 26 deletions latest/examples/label_strict/colors_properties.json
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@@ -1,31 +1,36 @@
{
"image-label": {
"version": "0.5-dev",
"colors": [
{
"label-value": 0,
"rgba": [0, 0, 128, 128]
},
{
"label-value": 1,
"rgba": [0, 128, 0, 128]
"zarr_format": 3,
"node_type": "group",
"attributes": {
"https://ngff.openmicroscopy.org/0.5": {
"image-label": {
"colors": [
{
"label-value": 0,
"rgba": [0, 0, 128, 128]
},
{
"label-value": 1,
"rgba": [0, 128, 0, 128]
}
],
"properties": [
{
"label-value": 0,
"area (pixels)": 1200,
"class": "intercellular space"
},
{
"label-value": 1,
"area (pixels)": 1650,
"class": "cell",
"cell type": "neuron"
}
],
"source": {
"image": "../../"
}
}
],
"properties": [
{
"label-value": 0,
"area (pixels)": 1200,
"class": "intercellular space"
},
{
"label-value": 1,
"area (pixels)": 1650,
"class": "cell",
"cell type": "neuron"
}
],
"source": {
"image": "../../"
}
}
}
105 changes: 59 additions & 46 deletions latest/examples/multiscales_strict/multiscales_example.json
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@@ -1,54 +1,67 @@
{
"multiscales": [
"zarr_format": 3,
"node_type": "group",
"attributes": {
"https://ngff.openmicroscopy.org/0.5": {
"multiscales": [
{
"version": "0.5-dev",
"name": "example",
"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": [
"name": "example",
"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": "0",
"coordinateTransformations": [
{
"path": "0",
"coordinateTransformations": [{
// the voxel size for the first scale level (0.5 micrometer)
"type": "scale",
"scale": [1.0, 1.0, 0.5, 0.5, 0.5]
}]
},
// the voxel size for the first scale level (0.5 micrometer)
"type": "scale",
"scale": [1.0, 1.0, 0.5, 0.5, 0.5]
}
]
},
{
"path": "1",
"coordinateTransformations": [
{
"path": "1",
"coordinateTransformations": [{
// the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
"type": "scale",
"scale": [1.0, 1.0, 1.0, 1.0, 1.0]
}]
},
// the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
"type": "scale",
"scale": [1.0, 1.0, 1.0, 1.0, 1.0]
}
]
},
{
"path": "2",
"coordinateTransformations": [
{
"path": "2",
"coordinateTransformations": [{
// the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer)
"type": "scale",
"scale": [1.0, 1.0, 2.0, 2.0, 2.0]
}]
// the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer)
"type": "scale",
"scale": [1.0, 1.0, 2.0, 2.0, 2.0]
}
],
"coordinateTransformations": [{
// 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]
}],
"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}
]
}
],
"coordinateTransformations": [
{
// 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]
}
],
"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 }
}
}
]
}
]
}
}
}
81 changes: 40 additions & 41 deletions latest/examples/multiscales_strict/multiscales_transformations.json
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@@ -1,47 +1,46 @@
{
"multiscales": [
"zarr_format": 3,
"node_type": "group",
"attributes": {
"https://ngff.openmicroscopy.org/0.5": {
"multiscales": [
{
"axes": [
{
"name": "y",
"type": "space",
"unit": "micrometer"
},
{
"name": "x",
"type": "space",
"unit": "micrometer"
}
],
"datasets": [
{
"path": "0",
"coordinateTransformations": [
{
"scale": [
1,
1
],
"type": "scale"
}
]
}
],
"coordinateTransformations": [
"axes": [
{
"name": "y",
"type": "space",
"unit": "micrometer"
},
{
"name": "x",
"type": "space",
"unit": "micrometer"
}
],
"datasets": [
{
"path": "0",
"coordinateTransformations": [
{
"scale": [
10,
10
],
"type": "scale"
"scale": [1, 1],
"type": "scale"
}
],
"version": "0.5-dev",
"name": "image_with_coordinateTransformations",
"type": "foo",
"metadata": {
"key": "value"
]
}
],
"coordinateTransformations": [
{
"scale": [10, 10],
"type": "scale"
}
],
"name": "image_with_coordinateTransformations",
"type": "foo",
"metadata": {
"key": "value"
}
}
]
}
]
}
}
}
8 changes: 7 additions & 1 deletion latest/examples/ome/series-2.json
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Original file line number Diff line number Diff line change
@@ -1,3 +1,9 @@
{
"series" : [ "0", "1" ]
"zarr_format": 3,
"node_type": "group",
"attributes": {
"https://ngff.openmicroscopy.org/0.5": {
"series": ["0", "1"]
}
}
}
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