From 1a7c38a175ca753311250e86b27b14137f6f41a9 Mon Sep 17 00:00:00 2001 From: Mark Kittisopikul Date: Wed, 30 Apr 2025 09:37:46 -0400 Subject: [PATCH 1/2] Use s prefix for multiscale example There is a tendency to replicate the examples exactly. Having multiscale paths only being a number can be easily confused with chunk paths. --- examples/multiscales_strict/multiscales_example.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/examples/multiscales_strict/multiscales_example.json b/examples/multiscales_strict/multiscales_example.json index 4b2c718a..f881689c 100644 --- a/examples/multiscales_strict/multiscales_example.json +++ b/examples/multiscales_strict/multiscales_example.json @@ -16,7 +16,7 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { // the voxel size for the first scale level (0.5 micrometer) @@ -26,7 +26,7 @@ ] }, { - "path": "1", + "path": "s1", "coordinateTransformations": [ { // the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer) @@ -36,7 +36,7 @@ ] }, { - "path": "2", + "path": "s2", "coordinateTransformations": [ { // the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer) From e7fff75aaa7ea511897d7f8783e5e5692db17a40 Mon Sep 17 00:00:00 2001 From: Mark Kittisopikul Date: Wed, 24 Sep 2025 15:44:30 -0400 Subject: [PATCH 2/2] Adapt index.bs and multiscales_transformations.json to use s prefix --- .../multiscales_transformations.json | 2 +- index.bs | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/examples/multiscales_strict/multiscales_transformations.json b/examples/multiscales_strict/multiscales_transformations.json index e4eb742a..cb38902d 100644 --- a/examples/multiscales_strict/multiscales_transformations.json +++ b/examples/multiscales_strict/multiscales_transformations.json @@ -20,7 +20,7 @@ ], "datasets": [ { - "path": "0", + "path": "s0", "coordinateTransformations": [ { "scale": [1, 1], diff --git a/index.bs b/index.bs index ffc7cf57..a7566149 100644 --- a/index.bs +++ b/index.bs @@ -79,10 +79,10 @@ 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. + ├── sn # The name of the array is arbitrary with the ordering defined by + │ │ # by the "multiscales" metadata, but is often a sequence starting at s0. │ │ │ ├── zarr.json # All image arrays must be up to 5-dimensional │ │ # with the axis of type time before type channel, before spatial axes. @@ -104,7 +104,7 @@ 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. @@ -143,7 +143,7 @@ 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