diff --git a/latest/index.bs b/latest/index.bs index e82eee26..1895fafc 100644 --- a/latest/index.bs +++ b/latest/index.bs @@ -108,7 +108,7 @@ Images {#image-layout} The following layout describes the expected Zarr hierarchy for images with multiple levels of resolutions and optionally associated labels. -``` +
 .                             # Root folder, potentially in S3,
 │                             # with a flat list of images by image ID.
 │
@@ -153,7 +153,9 @@ multiple levels of resolutions and optionally associated labels.
                 ├── 0         # Each multiscale level is stored as a separate Zarr array, as above, but only integer values
                 │   ...       # are supported.
                 └── n
-```
+
+ + High-content screening {#hcs-layout} ------------------------------------ @@ -170,7 +172,7 @@ dataset. Three groups must be defined above the images: [plate specification](#plate-md) -``` +
 .                             # Root folder, potentially in S3,
 │
 └── 5966.zarr                 # One plate (id=5966) converted to Zarr
@@ -197,7 +199,7 @@ dataset. Three groups must be defined above the images:
     │   └── 12
     ├── ...                   # Rows
     └── H
-```
+
Metadata {#metadata} ==================== @@ -344,10 +346,10 @@ should ignore all except the _last_ entry. Some implementations may represent overlapping labels by using a specially assigned value, for example the highest integer available in the pixel range. -The `properties` key defines a list of JSON objects which also describes the unique -label values. Each entry in the list MUST contain the key "label-value" with the -pixel value for that label. Additionally, an arbitrary number of key-value pairs -MAY be present for each label value denoting associated metadata. Not all label +The `properties` key defines a list of JSON objects which also describes the unique +label values. Each entry in the list MUST contain the key "label-value" with the +pixel value for that label. Additionally, an arbitrary number of key-value pairs +MAY be present for each label value denoting associated metadata. Not all label values must share the same key-value pairs within the properties list. The `source` key is an optional dictionary which contains information on the @@ -428,7 +430,7 @@ custom attributes of the plate group under the `plate` key.
version
A string defining the version of the specification.
wells
-
A list of JSON objects defining the wells of the plate. Each well object +
A list of JSON objects defining the wells of the plate. Each well object MUST contain a `path` key identifying the path to the well subgroup.
@@ -507,8 +509,8 @@ well group.
images
A list of JSON objects defining the fields of views for a given well. Each object MUST contain a `path` key identifying the path to the - field of view. If multiple acquisitions were performed in the plate, it - SHOULD contain an `acquisition` key identifying the id of the + field of view. If multiple acquisitions were performed in the plate, it + SHOULD contain an `acquisition` key identifying the id of the acquisition which must match one of acquisition JSON objects defined in the plate metadata.
version