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Tighten up some parts of the label specification #295

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Tighten up some parts of the label specification #295

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23 changes: 12 additions & 11 deletions 0.5/index.bs
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Expand Up @@ -390,19 +390,21 @@ It MUST also contain the fields "start" and "end", which are the start and end v
"labels" metadata {#labels-md}
------------------------------

In OME-Zarr, Zarr arrays representing pixel-annotation data are stored in a group called "labels". Some applications--notably image segmentation--produce
a new image that is in the same coordinate system as a corresponding multiscale image (usually having the same dimensions and coordinate transformations).
This new image is composed of integer values corresponding to certain labels with custom meanings. For example, pixels take the value 1 or 0
In OME-Zarr, Zarr arrays representing pixel-annotation data are stored in a Zarr group called "labels". Some applications--notably image segmentation--produce
a new image that is in the same coordinate system as a corresponding image.
This new image is composed of integer values corresponding to certain labels with custom meanings. For example, pixels can take the value 1 or 0
if the corresponding pixel in the original image represents cellular space or intercellular space, respectively.
Such an image is referred to in this specification as a 'label image'.

The "labels" group is nested within an image group, at the same level of the Zarr hierarchy as the resolution levels for the original image.
The "labels" group is not itself an image; it contains images. The pixels of the label images MUST be integer data types, i.e. one of
[`uint8`, `int8`, `uint16`, `int16`, `uint32`, `int32`, `uint64`, `int64`]. Intermediate groups between "labels" and the images within it are allowed,
but these MUST NOT contain metadata. Names of the images in the "labels" group are arbitrary.
The "labels" Zarr group is nested within an image Zarr group, at the same level as the resolution levels for the image.
The "labels" group contains other Zarr groups that contain image datasets with label data.
Every multiscales Zarr array within a labels Zarr group contains integers and MUST have a data type from the following list: [`uint8`, `int8`, `uint16`, `int16`, `uint32`, `int32`, `uint64`, `int64`].
Intermediate groups between "labels" and the images within it are allowed, but these MUST NOT contain any OME-Zarr metadata in the `zarr.json` file associated with the intermediate Zarr groups.
Names of the images in the "labels" group are arbitrary.

The OME-Zarr Metadata in the `zarr.json` file associated with the "labels" group MUST contain a JSON object with the key `labels`, whose value is a JSON array of paths to the
labeled multiscale image(s). All label images SHOULD be listed within this metadata file. For example:
labeled multiscale image(s).
All label images SHOULD be listed within this metadata file. For example:

```json
{
Expand All @@ -417,9 +419,8 @@ labeled multiscale image(s). All label images SHOULD be listed within this metad
}
}
```

The `zarr.json` file for the label image MUST implement the multiscales specification. Within the `multiscales` object, the JSON array
associated with the `datasets` key MUST have the same number of entries (scale levels) as the original unlabeled image.
Every path within the `labels` key MUST contain a Zarr group that implements the multiscales specification.
Within the `multiscales` object, the JSON array associated with the `datasets` key MUST have the same number of entries (scale levels) as the original unlabeled image.

In addition to the `multiscales` key, the OME-Zarr Metadata in this image-level `zarr.json` file SHOULD contain another key, `image-label`,
whose value is also a JSON object. The `image-label` object stores information about the display colors, source image, and optionally,
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