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revert changes to latest and put them instead in 0.5-dev1
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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. |
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{ | ||
"schema": "schemas/bf2raw.schema" | ||
} |
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{ | ||
"bioformats2raw.layout" : 3 | ||
} |
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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" | ||
} | ||
} |
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{ | ||
"schema": "schemas/strict_label.schema" | ||
} |
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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": "../../" | ||
} | ||
} | ||
} |
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{ | ||
"schema": "schemas/strict_image.schema" | ||
} |
54 changes: 54 additions & 0 deletions
54
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} | ||
} | ||
} | ||
] | ||
} |
47 changes: 47 additions & 0 deletions
47
0.5-dev1/examples/multiscales_strict/multiscales_transformations.json
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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" | ||
} | ||
} | ||
] | ||
} |
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{ | ||
"schema": "schemas/ome.schema" | ||
} |
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{ | ||
"series" : [ "0", "1" ] | ||
} |
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{ | ||
"schema": "schemas/strict_plate.schema" | ||
} |
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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 | ||
} | ||
] | ||
} | ||
} |
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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 | ||
} | ||
] | ||
} | ||
} |
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{ | ||
"schema": "schemas/strict_well.schema" | ||
} |
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@@ -0,0 +1,15 @@ | ||
{ | ||
"well": { | ||
"images": [ | ||
{ | ||
"acquisition": 0, | ||
"path": "0" | ||
}, | ||
{ | ||
"acquisition": 3, | ||
"path": "1" | ||
} | ||
], | ||
"version": "0.5-dev" | ||
} | ||
} |
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