From 3441103c326921b144ef108906668315efbf3132 Mon Sep 17 00:00:00 2001 From: jmoore Date: Wed, 19 Aug 2020 15:24:46 +0200 Subject: [PATCH 1/3] multiscale, labeled images layout change --- spec.md | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/spec.md b/spec.md index 7eaec5f..1d9e87c 100644 --- a/spec.md +++ b/spec.md @@ -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 ``` @@ -128,6 +133,10 @@ 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 @@ -166,7 +175,8 @@ If included it must include a key `array` whose value that is either: | 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 | From 59eea6d6abe41de0ea1b04989fdcd1e427a89ab9 Mon Sep 17 00:00:00 2001 From: jmoore Date: Wed, 19 Aug 2020 17:40:16 +0200 Subject: [PATCH 2/3] Add version for the omero metadata --- spec.md | 1 + 1 file changed, 1 insertion(+) diff --git a/spec.md b/spec.md index 1d9e87c..7a087bf 100644 --- a/spec.md +++ b/spec.md @@ -92,6 +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, From da260f26b78960c4b3d32b4753c50ec7618bf758 Mon Sep 17 00:00:00 2001 From: jmoore Date: Wed, 19 Aug 2020 17:54:35 +0200 Subject: [PATCH 3/3] Point image.array to a zgroup (needs renaming) see: https://github.com/ome/omero-cli-zarr/pull/19 --- spec.md | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/spec.md b/spec.md index 7a087bf..67e6817 100644 --- a/spec.md +++ b/spec.md @@ -155,7 +155,7 @@ 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": { @@ -163,14 +163,6 @@ If included it must include a key `array` whose value that is either: } } ``` -- 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" - } - } - ```