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Labeled multiscales #70

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merged 3 commits into from
Sep 4, 2020
Merged

Labeled multiscales #70

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3441103
multiscale, labeled images layout change
joshmoore Aug 19, 2020
59eea6d
Add version for the omero metadata
joshmoore Aug 19, 2020
da260f2
Point image.array to a zgroup (needs renaming)
joshmoore Aug 19, 2020
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29 changes: 16 additions & 13 deletions spec.md
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Original file line number Diff line number Diff line change
Expand Up @@ -44,9 +44,14 @@ for public re-use.
│
└── original # Intermediate folders are permitted but not necessary
│ # and currently contain no extra metadata.
└── 0
├── .zarray # Each label itself is a 5D array matching the highest resolution
└── .zattrs # of the related image and has an extra key, "color", with display information.
│
└── 0 # Multiscale, labeled image. The name is unimportant but is registered in "labels".
├── .zgroup # Each labeled image is also a multiscaled image, and therefore a Zarr group.
├── .zattrs # Metadata of the related image and has an extra key, "color", with display information.
│
├── 0 # Each multiscale level is stored as a separate Zarr array, as above.
│ ...
└── n


```
Expand Down Expand Up @@ -87,6 +92,7 @@ can be found under the "omero" key in the group-level metadata:
```
"id": 1, # ID in OMERO
"name": "example.tif", # Name as shown in the UI
"version": "0.1", # Current version
"channels": [ # Array matching the c dimension size
{
"active": true,
Expand Down Expand Up @@ -128,6 +134,10 @@ the paths to label objects which can be found underneath the group:

Unlisted groups MAY be labels.

### "label""



### "color"

The `color` key defines an image that is "labeled", i.e. every unique value in the image
Expand All @@ -145,28 +155,21 @@ the value is an RGBA color (4 byte, `0-255` per channel) for representing the ob

The `image` key is an optional dictionary which contains information on the image the label is associated with.
If included it must include a key `array` whose value that is either:
- A relative path to a Zarr image array, for example:
- A relative path to a Zarr image group, for example:
```
{
"image": {
"array": "../../0"
}
}
```
- A URL to a Zarr image array (use this if the label is stored seperately from the image Zarr), for example:
```
{
"image": {
"array": "https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/0"
}
}
```



| Revision | Date | Description |
| ---------- | ------------ | ------------------------------------------ |
| 0.1.3 | 2020-08-18 | Rename masks as labels |
| 0.1.3-dev3 | in-progress | Convert labels to multiscales |
| 0.1.3-dev2 | 2020-08-18 | Rename masks as labels |
| 0.1.3-dev1 | 2020-07-07 | Add mask metadata |
| 0.1.2 | 2020-05-07 | Add description of "omero" metadata |
| 0.1.1 | 2020-05-06 | Add info on the ordering of resolutions |
Expand Down