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Minor text styling options #93

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Merged
jo-mueller merged 5 commits into from
Mar 3, 2026
Merged

Minor text styling options #93

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45e838c
spec: propper JSON terminology
jo-mueller Feb 25, 2026
f5d49b1
spec: better wording for wrapped transforms
jo-mueller Feb 25, 2026
0f869c7
spec: improve text styling
jo-mueller Mar 2, 2026
1d674af
Merge remote-tracking branch 'upstream/main' into minor-text-styling-…
jo-mueller Mar 2, 2026
e17e80d
Merge branch 'main' into minor-text-styling-options
jo-mueller Mar 2, 2026
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18 changes: 9 additions & 9 deletions index.md
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Original file line number Diff line number Diff line change
Expand Up @@ -153,7 +153,7 @@ those Zarr arrays SHOULD be stored in a Zarr group on the same level as images c
store.zarr # One scene dataset
│
├── zarr.json # coordinate transformations describing the relationship between two image coordinate systems
│ # are stored in the "scene" dictionary here.
│ # are stored in the "scene" object here.
│ # I.e., transformations between coordinate systems in the 'volume' and 'crop' multiscale images are stored here.
│
├── coordinateTransformations # transformations that use array storage for their parameters should go in a Zarr group named "coordinateTransformations".
Expand Down Expand Up @@ -514,8 +514,8 @@ Coordinate transformations can be stored in multiple places to reflect different
The output can be another coordinate system defined under `multiscales > coordinateSystems`.

- **Inside `scene > coordinateTransformations`**: Transformations between two or more images
MUST be stored in the attributes of a [`scene` dictionary](#scene-md) in a [scene Zarr group](#scene-format).
In this case, the `input` and `output` values are dictionaries
MUST be stored in the attributes of a [`scene` object](#scene-md) in a [scene Zarr group](#scene-format).
In this case, the `input` and `output` values are objects
that refer to coordinate systems in the same zarr.json or in the metadata of multiscale image subgroups.

This separation of transformations (inside `multiscales > datasets`, under `multiscales > coordinateTransformations` and under `scene > coordinateTransformations`) provides flexibility for different use cases while still maintaining a level of rigidity for implementations.
Expand Down Expand Up @@ -1141,8 +1141,8 @@ I.e. the y-displacement is first, because the y-axis is the first element of the
using lower dimensional transformations on subsets of dimensions.

**transformations**
: MUST be an array of wrapped transformations.
Each item MUST contain `input_axes`, `output_axes` and `transformation` fields.
: MUST be an array of objects where each object MUST contain
the fields `input_axes`, `output_axes` and `transformation`.
The values of `input_axes` and `output_axes` are arrays of integers.
The integer values in these arrays correspond to the axis indices in the `byDimension`'s or its parent's
`input` and `output` coordinate systems, respectively.
Expand Down Expand Up @@ -1505,7 +1505,7 @@ and MUST NOT be a duplicate of any other `name` in the `rows` array.
Care SHOULD be taken to avoid collisions on case-insensitive filesystems
(e.g. avoid using both `Aa` and `aA`).

The `plate` dictionary MUST contain a `wells` key
The `plate` object MUST contain a `wells` key
whose value MUST be a list of JSON objects defining the wells of the plate.
Each well object MUST contain a `path` key
whose value MUST be a string specifying the path to the well subgroup.
Expand Down Expand Up @@ -1579,7 +1579,7 @@ The first field is part of the first acquisition, and the second field is part o
For images that share a spatial relationship,
the `scene` metadata layout can be used to describe the relationship between images.

The `scene` dictionary MUST contain the field `coordinateTransformations`,
The `scene` object MUST contain the field `coordinateTransformations`,
whose value MUST be an array of valid [transformations](#trafo-types-md).
It MAY contain the field `coordinateSystems`,
whose values MUST be an array of valid [coordinate systems](#coordinate-systems-md).
Expand All @@ -1589,12 +1589,12 @@ which MUST contain the field `name` and MAY contain the field `path`.

**name**
Refers to the name of a `coordinateSystem` either in the multiscale image subgroup specified by the path,
or within the `scene` dictionary itself.
or within the `scene` object itself.

**path**
Refers to the path of a multiscale image subgroup in the Zarr hierarchy.

If `name` refers to a coordinate system in the `scene` dictionary,
If `name` refers to a coordinate system in the `scene` object,
the `path` value MAY be omitted or null.
If `name` refers to a coordinate system in the multiscale image subgroup specified by `path`,
both `path` and `name` MUST be provided.
Expand Down