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revert changes to latest and put them instead in 0.5-dev1
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d-v-b committed Jun 13, 2024
1 parent 48cf548 commit 583b2b2
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4 changes: 4 additions & 0 deletions 0.5-dev1/copyright.include
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Copyright © 2020-[YEAR]
<a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup>
(<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
OME trademark rules apply.
3 changes: 3 additions & 0 deletions 0.5-dev1/examples/bf2raw/.config.json
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{
"schema": "schemas/bf2raw.schema"
}
3 changes: 3 additions & 0 deletions 0.5-dev1/examples/bf2raw/image.json
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{
"bioformats2raw.layout" : 3
}
22 changes: 22 additions & 0 deletions 0.5-dev1/examples/bf2raw/plate.json
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{
"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"
}
}
3 changes: 3 additions & 0 deletions 0.5-dev1/examples/label_strict/.config.json
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{
"schema": "schemas/strict_label.schema"
}
31 changes: 31 additions & 0 deletions 0.5-dev1/examples/label_strict/colors_properties.json
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{
"image-label": {
"version": "0.5-dev",
"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": "../../"
}
}
}
3 changes: 3 additions & 0 deletions 0.5-dev1/examples/multiscales_strict/.config.json
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{
"schema": "schemas/strict_image.schema"
}
54 changes: 54 additions & 0 deletions 0.5-dev1/examples/multiscales_strict/multiscales_example.json
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{
"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": [
{
"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]
}]
},
{
"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]
}]
},
{
"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]
}]
}
],
"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}
}
}
]
}
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{
"multiscales": [
{
"axes": [
{
"name": "y",
"type": "space",
"unit": "micrometer"
},
{
"name": "x",
"type": "space",
"unit": "micrometer"
}
],
"datasets": [
{
"path": "0",
"coordinateTransformations": [
{
"scale": [
1,
1
],
"type": "scale"
}
]
}
],
"coordinateTransformations": [
{
"scale": [
10,
10
],
"type": "scale"
}
],
"version": "0.5-dev",
"name": "image_with_coordinateTransformations",
"type": "foo",
"metadata": {
"key": "value"
}
}
]
}
3 changes: 3 additions & 0 deletions 0.5-dev1/examples/ome/.config.json
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{
"schema": "schemas/ome.schema"
}
3 changes: 3 additions & 0 deletions 0.5-dev1/examples/ome/series-2.json
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{
"series" : [ "0", "1" ]
}
3 changes: 3 additions & 0 deletions 0.5-dev1/examples/plate_strict/.config.json
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{
"schema": "schemas/strict_plate.schema"
}
91 changes: 91 additions & 0 deletions 0.5-dev1/examples/plate_strict/plate_2wells.json
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{
"plate": {
"acquisitions": [
{
"id": 1,
"maximumfieldcount": 1,
"name": "single acquisition",
"starttime": 1343731272000
}
],
"columns": [
{
"name": "1"
},
{
"name": "2"
},
{
"name": "3"
},
{
"name": "4"
},
{
"name": "5"
},
{
"name": "6"
},
{
"name": "7"
},
{
"name": "8"
},
{
"name": "9"
},
{
"name": "10"
},
{
"name": "11"
},
{
"name": "12"
}
],
"field_count": 1,
"name": "sparse test",
"rows": [
{
"name": "A"
},
{
"name": "B"
},
{
"name": "C"
},
{
"name": "D"
},
{
"name": "E"
},
{
"name": "F"
},
{
"name": "G"
},
{
"name": "H"
}
],
"version": "0.5-dev",
"wells": [
{
"path": "C/5",
"rowIndex": 2,
"columnIndex": 4
},
{
"path": "D/7",
"rowIndex": 3,
"columnIndex": 6
}
]
}
}
72 changes: 72 additions & 0 deletions 0.5-dev1/examples/plate_strict/plate_6wells.json
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{
"plate": {
"acquisitions": [
{
"id": 1,
"maximumfieldcount": 2,
"name": "Meas_01(2012-07-31_10-41-12)",
"starttime": 1343731272000
},
{
"id": 2,
"maximumfieldcount": 2,
"name": "Meas_02(201207-31_11-56-41)",
"starttime": 1343735801000
}
],
"columns": [
{
"name": "1"
},
{
"name": "2"
},
{
"name": "3"
}
],
"field_count": 4,
"name": "test",
"rows": [
{
"name": "A"
},
{
"name": "B"
}
],
"version": "0.5-dev",
"wells": [
{
"path": "A/1",
"rowIndex": 0,
"columnIndex": 0
},
{
"path": "A/2",
"rowIndex": 0,
"columnIndex": 1
},
{
"path": "A/3",
"rowIndex": 0,
"columnIndex": 2
},
{
"path": "B/1",
"rowIndex": 1,
"columnIndex": 0
},
{
"path": "B/2",
"rowIndex": 1,
"columnIndex": 1
},
{
"path": "B/3",
"rowIndex": 1,
"columnIndex": 2
}
]
}
}
3 changes: 3 additions & 0 deletions 0.5-dev1/examples/well_strict/.config.json
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{
"schema": "schemas/strict_well.schema"
}
15 changes: 15 additions & 0 deletions 0.5-dev1/examples/well_strict/well_2fields.json
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{
"well": {
"images": [
{
"acquisition": 0,
"path": "0"
},
{
"acquisition": 3,
"path": "1"
}
],
"version": "0.5-dev"
}
}
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