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‎_version.py‎

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__version__ = '0.6.dev2'
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__version__ = '0.4.1'

‎citing.md‎

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[Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.](https://ngff.openmicroscopy.org/0.4)
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J. Moore, *et al*. Open Microscopy Environment Consortium, 8 February 2022.
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This edition of the specification is [https://ngff.openmicroscopy.org/{{version}}](https://ngff.openmicroscopy.org/{{version}}]).
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The latest edition is publicly available {cite}`ngff_spec_latest`.
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This edition of the specification is [https://ngff.openmicroscopy.org/0.4/](https://ngff.openmicroscopy.org/0.4/]).
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The latest edition is available at [https://ngff.openmicroscopy.org/latest/](https://ngff.openmicroscopy.org/latest/).
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[(doi:10.5281/zenodo.4282107)](https://doi.org/10.5281/zenodo.4282107)
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```{bibliography}
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:style: unsrt

‎examples/bf2raw/image.json‎

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{
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"zarr_format": 3,
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"node_type": "group",
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"attributes": {
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"ome": {
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"version": "0.6.dev2",
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"bioformats2raw.layout": 3
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}
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}
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}
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"bioformats2raw.layout" : 3
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}

‎examples/bf2raw/plate.json‎

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{
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"zarr_format": 3,
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"node_type": "group",
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"attributes": {
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"ome": {
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"version": "0.6.dev2",
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"bioformats2raw.layout": 3,
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"plate": {
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"columns": [
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{
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"name": "1"
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}
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],
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"name": "Plate Name 0",
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"wells": [
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{
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"path": "A/1",
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"rowIndex": 0,
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"columnIndex": 0
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}
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],
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"field_count": 1,
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"rows": [
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{
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"name": "A"
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}
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],
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"acquisitions": [
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{
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"id": 0
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}
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]
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}
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}
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"bioformats2raw.layout" : 3,
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"plate" : {
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"columns" : [ {
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"name" : "1"
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} ],
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"name" : "Plate Name 0",
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"wells" : [ {
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"path" : "A/1",
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"rowIndex" : 0,
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"columnIndex" : 0
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} ],
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"field_count" : 1,
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"rows" : [ {
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"name" : "A"
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} ],
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"acquisitions" : [ {
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"id" : 0
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} ],
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"version" : "0.4"
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}
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}

‎examples/coordinate_systems/.config.json‎

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‎examples/coordinate_systems/arrayCoordSys.json‎

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‎examples/label_strict/colors_properties.json‎

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{
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"zarr_format": 3,
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"node_type": "group",
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"attributes": {
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"ome": {
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"version": "0.6.dev2",
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"image-label": {
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"colors": [
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{
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"label-value": 0,
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"rgba": [0, 0, 128, 128]
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},
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{
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"label-value": 1,
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"rgba": [0, 128, 0, 128]
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}
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],
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"properties": [
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{
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"label-value": 0,
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"area (pixels)": 1200,
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"class": "intercellular space"
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},
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{
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"label-value": 1,
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"area (pixels)": 1650,
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"class": "cell",
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"cell type": "neuron"
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}
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],
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"source": {
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"image": "../../"
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}
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"image-label": {
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"version": "0.4",
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"colors": [
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{
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"label-value": 1,
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"rgba": [255, 255, 255, 255]
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},
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{
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"label-value": 4,
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"rgba": [0, 255, 255, 128]
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}
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],
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"properties": [
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{
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"label-value": 1,
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"area (pixels)": 1200,
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"class": "foo"
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},
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{
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"label-value": 4,
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"area (pixels)": 1650
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}
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],
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"source": {
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"image": "../../"
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}
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}
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}

‎examples/multiscales_strict/multiscales_example.json‎

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{
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"zarr_format": 3,
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"node_type": "group",
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"attributes": {
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"ome": {
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"version": "0.6.dev2",
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"multiscales": [
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"multiscales": [
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{
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"name": "example",
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"coordinateSystems": [
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{
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"name": "intrinsic",
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"axes": [
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{ "name": "t", "type": "time", "unit": "millisecond" },
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{ "name": "c", "type": "channel" },
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{ "name": "z", "type": "space", "unit": "micrometer" },
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{ "name": "y", "type": "space", "unit": "micrometer" },
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{ "name": "x", "type": "space", "unit": "micrometer" }
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]
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}
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],
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"datasets": [
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{
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"path": "0",
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"coordinateTransformations": [
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"version": "0.4",
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"name": "example",
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"axes": [
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{"name": "t", "type": "time", "unit": "millisecond"},
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{"name": "c", "type": "channel"},
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{"name": "z", "type": "space", "unit": "micrometer"},
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{"name": "y", "type": "space", "unit": "micrometer"},
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{"name": "x", "type": "space", "unit": "micrometer"}
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],
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"datasets": [
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{
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// the voxel size for the first scale level (0.5 micrometer)
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// and the time unit (0.1 milliseconds), which is the same for each scale level
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"type": "scale",
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"scale": [0.1, 1.0, 0.5, 0.5, 0.5],
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"input": "0",
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"output": "intrinsic"
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}
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]
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},
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{
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"path": "1",
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"coordinateTransformations": [
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"path": "0",
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"coordinateTransformations": [{
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// the voxel size for the first scale level (0.5 micrometer)
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"type": "scale",
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"scale": [1.0, 1.0, 0.5, 0.5, 0.5]
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}]
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},
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{
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// the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
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// and the time unit (0.1 milliseconds), which is the same for each scale level
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"type": "scale",
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"scale": [0.1, 1.0, 1.0, 1.0, 1.0],
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"input": "1",
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"output": "intrinsic"
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}
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]
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},
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{
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"path": "2",
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"coordinateTransformations": [
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"path": "1",
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"coordinateTransformations": [{
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// the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
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"type": "scale",
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"scale": [1.0, 1.0, 1.0, 1.0, 1.0]
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}]
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},
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{
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// the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer)
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// and the time unit (0.1 milliseconds), which is the same for each scale level
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"type": "scale",
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"scale": [0.1, 1.0, 2.0, 2.0, 2.0],
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"input": "2",
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"output": "intrinsic"
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"path": "2",
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"coordinateTransformations": [{
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// the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer)
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"type": "scale",
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"scale": [1.0, 1.0, 2.0, 2.0, 2.0]
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}]
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}
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]
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],
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"coordinateTransformations": [{
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// the time unit (0.1 milliseconds), which is the same for each scale level
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"type": "scale",
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"scale": [0.1, 1.0, 1.0, 1.0, 1.0]
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}],
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"type": "gaussian",
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"metadata": {
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"description": "the fields in metadata depend on the downscaling implementation. Here, the parameters passed to the skimage function are given",
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"method": "skimage.transform.pyramid_gaussian",
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"version": "0.16.1",
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"args": "[true]",
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"kwargs": {"multichannel": true}
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}
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],
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"type": "gaussian",
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"metadata": {
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"description": "the fields in metadata depend on the downscaling implementation. Here, the parameters passed to the skimage function are given",
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"method": "skimage.transform.pyramid_gaussian",
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"version": "0.16.1",
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"args": "[true]",
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"kwargs": { "multichannel": true }
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}
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}
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]
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}
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}
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]
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}

‎examples/multiscales_strict/multiscales_example_relative.json‎

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