From cc4437fa9fcdc2af4fd7cf620c477381d6a009b7 Mon Sep 17 00:00:00 2001 From: William Moore Date: Mon, 12 Jan 2026 14:38:34 +0000 Subject: [PATCH 1/3] use s0 paths for scale paths in index.md --- index.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/index.md b/index.md index 842f5fdf..7268cfa0 100644 --- a/index.md +++ b/index.md @@ -73,7 +73,7 @@ Note that the number of dimensions is variable between 2 and 5 and that axis nam │ # Group level attributes are stored in the `zarr.json` file and include │ # "multiscales" and "omero" (see below). │ - ├── 0 # Each multiscale level is stored as a separate Zarr array, + ├── s0 # Each multiscale level is stored as a separate Zarr array, │ ... # which is a folder containing chunk files which compose the array. ├── n # The name of the array is arbitrary with the ordering defined by │ │ # by the "multiscales" metadata, but is often a sequence starting at 0. @@ -98,7 +98,7 @@ Note that the number of dimensions is variable between 2 and 5 and that axis nam ├── zarr.json # Zarr Group which is both a multiscaled image as well as a labeled image. │ # Metadata of the related image and as well as display information under the "image-label" key. │ - ├── 0 # Each multiscale level is stored as a separate Zarr array, as above, but only integer values + ├── s0 # Each multiscale level is stored as a separate Zarr array, as above, but only integer values └── ... # are supported. ``` @@ -130,7 +130,7 @@ A well group SHOULD NOT be present if there are no images in the well. │ │ ├── 0 # First field of view of well A1 │ │ │ │ │ │ │ ├── zarr.json # Implements "multiscales", "omero" - │ │ │ ├── 0 # Resolution levels + │ │ │ ├── s0 # Resolution levels │ │ │ ├── ... │ │ │ └── labels # Labels (optional) │ │ └── ... # Other fields of view @@ -498,12 +498,12 @@ store.zarr # Root folder of the zarr store │ ├── volume │ ├── zarr.json # group level attributes (multiscales) -│ └── 0 # a group containing the 0th scale +│ └── s0 # a group containing the 0th scale │ └── image # a zarr array │ └── zarr.json # physical coordinate system and transformations here └── crop ├── zarr.json # group level attributes (multiscales) - └── 0 # a group containing the 0th scale + └── s0 # a group containing the 0th scale └── image # a zarr array └── zarr.json # physical coordinate system and transformations here From adbdb091a1f64c43d21a177480d6c15cf0f28029 Mon Sep 17 00:00:00 2001 From: William Moore Date: Mon, 12 Jan 2026 14:39:11 +0000 Subject: [PATCH 2/3] use s0 paths for scale paths in examples json --- examples/multiscales_strict/multiscales_example.json | 12 ++++++------ .../multiscales_transformations.json | 4 ++-- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/examples/multiscales_strict/multiscales_example.json b/examples/multiscales_strict/multiscales_example.json index b874f281..9fa8e1c4 100644 --- a/examples/multiscales_strict/multiscales_example.json +++ b/examples/multiscales_strict/multiscales_example.json @@ -21,40 +21,40 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { // the voxel size for the first scale level (0.5 micrometer) // and the time unit (0.1 milliseconds), which is the same for each scale level "type": "scale", "scale": [0.1, 1.0, 0.5, 0.5, 0.5], - "input": "0", + "input": "s0", "output": "intrinsic" } ] }, { - "path": "1", + "path": "s1", "coordinateTransformations": [ { // the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer) // and the time unit (0.1 milliseconds), which is the same for each scale level "type": "scale", "scale": [0.1, 1.0, 1.0, 1.0, 1.0], - "input": "1", + "input": "s1", "output": "intrinsic" } ] }, { - "path": "2", + "path": "s2", "coordinateTransformations": [ { // the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer) // and the time unit (0.1 milliseconds), which is the same for each scale level "type": "scale", "scale": [0.1, 1.0, 2.0, 2.0, 2.0], - "input": "2", + "input": "s2", "output": "intrinsic" } ] diff --git a/examples/multiscales_strict/multiscales_transformations.json b/examples/multiscales_strict/multiscales_transformations.json index 46e60a4c..338faab8 100644 --- a/examples/multiscales_strict/multiscales_transformations.json +++ b/examples/multiscales_strict/multiscales_transformations.json @@ -40,12 +40,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] From 6dccc1de9a0315eff05eb8bac7c86a105e0ffefd Mon Sep 17 00:00:00 2001 From: William Moore Date: Mon, 12 Jan 2026 14:39:56 +0000 Subject: [PATCH 3/3] use s0 paths for scale paths in most tests json --- tests/image_suite.json | 88 +++++++++++++++++------------------ tests/strict_image_suite.json | 28 +++++------ 2 files changed, 58 insertions(+), 58 deletions(-) diff --git a/tests/image_suite.json b/tests/image_suite.json index 71d099ef..cd008382 100644 --- a/tests/image_suite.json +++ b/tests/image_suite.json @@ -36,12 +36,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [0.13, 0.13], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -83,11 +83,11 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1, 1], - "input": "0", + "input": "s0", "output": "intrinsic", "type": "scale" } @@ -128,11 +128,11 @@ "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [0.13, 0.13], - "input": "0", + "input": "s0", "output": "intrinsic", "type": "scale" } @@ -229,11 +229,11 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1, 1], - "input": "0", + "input": "s0", "output": "intrinsic", "type": "scale" } @@ -274,12 +274,12 @@ "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -316,12 +316,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -360,12 +360,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], "type": "translation", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -404,12 +404,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "translation": [1, 1], "type": "translation", - "input": "0", + "input": "s0", "output": "intrinsice" } ] @@ -462,12 +462,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1, 1, 1, 1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -506,12 +506,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -565,12 +565,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [0.13, 0.13], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -604,12 +604,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -650,12 +650,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -738,12 +738,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -788,7 +788,7 @@ ], "datasets": [ { - "path": "0" + "path": "s0" } ] } @@ -870,12 +870,12 @@ { "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -914,12 +914,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -958,18 +958,18 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" }, { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -992,12 +992,12 @@ "axes": [], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -1042,12 +1042,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1, 1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -1097,12 +1097,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] @@ -1159,7 +1159,7 @@ , "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [] } ] @@ -1200,7 +1200,7 @@ { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "intrinsic" } ] diff --git a/tests/strict_image_suite.json b/tests/strict_image_suite.json index e0a335c5..edf1346f 100644 --- a/tests/strict_image_suite.json +++ b/tests/strict_image_suite.json @@ -76,34 +76,34 @@ , "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "type": "scale", "scale": [1.0, 1.0, 0.5, 0.5, 0.5], - "input": "0", + "input": "s0", "output": "intrinsic" } ] }, { - "path": "1", + "path": "s1", "coordinateTransformations": [ { "type": "scale", "scale": [1.0, 1.0, 1.0, 1.0, 1.0], - "input": "1", + "input": "s1", "output": "intrinsic" } ] }, { - "path": "2", + "path": "s2", "coordinateTransformations": [ { "type": "scale", "scale": [1.0, 1.0, 2.0, 2.0, 2.0], - "input": "2", + "input": "s2", "output": "intrinsic" } ] @@ -175,12 +175,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "physical" } ] @@ -289,12 +289,12 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], "type": "scale", - "input": "0", + "input": "s0", "output": "physical" } ] @@ -379,23 +379,23 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1, 0.5, 0.13, 0.13], "type": "scale", - "input": "0", + "input": "s0", "output": "physical" } ] }, { - "path": "1", + "path": "s1", "coordinateTransformations": [ { "scale": [1, 1, 1, 0.26, 0.26], "type": "scale", - "input": "1", + "input": "s1", "output": "physical" } ]