WIP: 0.9.dev1

_version.py

@@ -1 +1 @@
-__version__ = '0.6rc0'
+__version__ = '0.9.dev1'

examples/bf2raw/image.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "bioformats2raw.layout": 3
     }
   }

examples/bf2raw/plate.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "bioformats2raw.layout": 3,
       "plate": {
         "columns": [

examples/label_strict/colors_properties.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "multiscales": [
         {
           "coordinateSystems": [

examples/multiscales_strict/multiscales_example.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "multiscales": [
         {
           "name": "example",

examples/multiscales_strict/multiscales_example_relative.json

@@ -1,7 +1,7 @@
 {
   "multiscales": [
     {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "name": "example",
       "coordinateSystems" : [
         {

examples/multiscales_strict/multiscales_reference_to_label.json

@@ -1,6 +1,6 @@
 {
   "ome": {
-    "version": "0.6rc0",
+    "version": "0.9.dev1",
     "multiscales": [
       {
         "name": "Image",

examples/multiscales_strict/multiscales_transformations.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "multiscales": [
         {
           "coordinateSystems": [

examples/ome/series-2.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "series": ["0", "1"]
     }
   }

examples/plate_strict/plate_2wells.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "plate": {
         "acquisitions": [
           {

examples/plate_strict/plate_6wells.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "plate": {
         "acquisitions": [
           {

examples/scene/scene_registration.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "scene": {
         "coordinateTransformations": [
           {

examples/scene/scene_stitching.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "scene": {
         "coordinateTransformations": [
           {

examples/subspace/subspacePermute.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "multiscales": [
         {
           "name": "multiscales",

examples/transformations/displacements/displacement_field.json

@@ -1,6 +1,6 @@
 {
   "ome": {
-    "version": "0.6rc0",
+    "version": "0.9.dev1",
     "name": "the_dfield",
     "multiscales": [
       {

examples/transformations/displacements/multiscales.json

@@ -1,6 +1,6 @@
 {
   "ome": {
-    "version": "0.6rc0",
+    "version": "0.9.dev1",
     "name": "some_image",
     "multiscales": [
       {

examples/well_strict/well_2fields.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "well": {
         "images": [
           {

examples/well_strict/well_4fields.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "well": {
         "images": [
           {

index.md

@@ -4,8 +4,8 @@ short_title: OME-Zarr
 authors: " "
 ---
 
-# Version 0.6rc0
-(ngff-spec:spec:0.6rc0)=
+# Version 0.9.dev1
+(ngff-spec:spec:0.9.dev1)=
 
 **Feedback:** [Forum](https://forum.image.sc/tag/ome-ngff), [Github](https://github.com/ome/ngff/issues)
 
@@ -18,19 +18,18 @@ authors: " "
 ## Abstract
 
 ```{warning}
-This is the release candidate for version 0.6rc0 of the ngff-specification.
-Upon release of 0.6, this warning will be removed and the version number in the document updated.
-
+This is a development version of the specification. It includes RFC-3 and RFC-4
+which have not yet been accepted.
 ```
 
 This document contains next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
 All specifications are submitted to the <https://image.sc> community for review.
 
 ## Status of This Document
 
-The working title version of this specification is 0.6rc0.
+The working title version of this specification is 0.9.dev1.
 Migration scripts will be provided between numbered versions.
-Data written with these latest changes (an "editor's draft") will not necessarily be supported.
+Data written with these latest changes will not necessarily be supported.
 
 The conventions and specifications defined in this document
 are designed to enable next-generation file formats to represent
@@ -66,7 +65,7 @@ but could equally be stored on a web server to be accessed via HTTP or in object
 ### Images
 
 The following layout describes the expected Zarr hierarchy for images with multiple levels of resolutions and optionally associated labels.
-Note that the number of dimensions is variable between 2 and 5 and that axis names are arbitrary, see [multiscales metadata](#multiscales-md) for details.
+Note that the number of dimensions is variable and that axis names are arbitrary, see [multiscales metadata](#multiscales-md) for details.
 
 ```text
 ├── 123.zarr                  # One OME-Zarr image (id=123).
@@ -84,8 +83,7 @@ Note that the number of dimensions is variable between 2 and 5 and that axis nam
     │   │                     # by the "multiscales" metadata, but is often a sequence starting at 0.
     │   │                     # All arrays must have the same datatype and number of dimensions.
     │   │
-    │   ├── zarr.json         # All image arrays must be up to 5-dimensional
-    │   │                     # with the axis of type time before type channel, before spatial axes.
+    │   ├── zarr.json
     │   │
     │   └─ ...                # Chunks are stored conforming to the Zarr array specification and
     │                         # metadata as specified in the array's `zarr.json`.
@@ -188,14 +186,14 @@ The OME-Zarr Metadata is stored in the various `zarr.json` files throughout the
 The OME-Zarr Metadata version MUST be consistent within a hierarchy.
 
 The group `attributes` MUST contain a key `ome`. The value of the `ome` key MUST be a JSON
-object that MUST contain a `version` key, the value of which MUST be a string specifying the version of the OME-Zarr specification defined by [this document](#ngff-spec:spec:0.6rc0).
+object that MUST contain a `version` key, the value of which MUST be a string specifying the version of the OME-Zarr specification defined by [this document](#ngff-spec:spec:0.9.dev1).
 
 ```jsonc
 {
   // ...
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       // ...
     }
   }
@@ -266,10 +264,56 @@ where each object describes a dimension (axis) and:
 - MAY contain the field `longName`.
   The value MUST be a string,
   and can provide a longer name or description of an axis and its properties.
+- MAY contain an "orientation" field, itself containing a "type" and a
+  "value". Currently, "type" may only be "anatomical", and "value" may
+  only be one from the list given in [list of possible anatomical
+  orientation values](orientation-values). A specific orientation value or
+  its inverse MUST NOT appear more than once in a given coordinate system.
 
 The values in the `name` fields MUST be unique within the same coordinate system.
 The length of "axes" MUST be equal to the number of dimensions of the arrays that contain the image data.
 
+```{note}
+:label: orientation-values
+
+When a spatial axis is aligned with a specific orientation, this can be
+indicated with the "orientation" field, which must have "type"
+"anatomical" (with further types to be added to the specification or as
+extensions in the future), and one of the values detailed below:
+
+**Common to both bipeds and quadrupeds:**
+- `left-to-right`
+- `right-to-left`
+- `proximal-to-distal`
+- `distal-to-proximal`
+
+**Primarily for bipeds (humans):**
+- `anterior-to-posterior` (front-to-back)
+- `posterior-to-anterior` (back-to-front)
+- `inferior-to-superior` (feet-to-head)
+- `superior-to-inferior` (head-to-feet)
+- `dorsal-to-palmar` (back of hand to palm)
+- `palmar-to-dorsal` (palm to back of hand)
+- `dorsal-to-plantar` (top of foot to sole)
+- `plantar-to-dorsal` (sole to top of foot)
+
+**Primarily for quadrupeds:**
+- `rostral-to-caudal` (nose/beak-to-tail, especially for nervous system)
+- `caudal-to-rostral` (tail-to-nose/beak, especially for nervous system)
+- `cranial-to-caudal` (head-to-tail)
+- `caudal-to-cranial` (tail-to-head)
+- `dorsal-to-ventral` (back/top-to-belly/bottom)
+- `ventral-to-dorsal` (belly/bottom-to-back/top)
+
+**For layered and polarized tissues (subject-local):**
+- `superficial-to-deep` (outer surface to inner depth, e.g. skin, gut, cortex)
+- `deep-to-superficial` (inner depth to outer surface)
+- `apical-to-basal` (apical to basal surface, e.g. epithelial layers, polarized cells)
+- `basal-to-apical` (basal to apical surface)
+- `apex-to-base` (tip to broad base, e.g. heart, lungs)
+- `base-to-apex` (broad base to tip)
+```
+
 Arrays are inherently discrete (see Array coordinate systems, below)
 but are often used to store discrete samples of a continuous variable.
 The continuous values "in between" discrete samples can be retrieved using an *interpolation* method.
@@ -429,7 +473,7 @@ The following transformations are supported:
 | [`bijection`](#bijection-md) | `"forward":Transformation`<br>`"inverse":Transformation` | An invertible transformation providing an explicit forward transformation and its inverse. |
 | [`byDimension`](#bydimension-md) | `"transformations":List[Transformation]`.<br>Transformations in the array MUST have<br>`"inputAxes": List[number]`, <br> and `"outputAxes": List[number]` | A high dimensional transformation using lower dimensional transformations on subsets of dimensions. |
 
-The parameter values (e.g., `scale` for a [scale transformation](#scale-md)) MUST be compatible with input and output space dimensionality (see details). 
+The parameter values (e.g., `scale` for a [scale transformation](#scale-md)) MUST be compatible with input and output space dimensionality (see details).
 
 The `input` and `output` fields are objects structured as follows:
 
@@ -471,7 +515,7 @@ Depending on which, different constraints apply to the transformations, as descr
   - Both `input` and `output` MUST specify a coordinate system `name`.
   - `path` is required when referencing a coordinate system in a multiscale image subgroup;
     it MAY be omitted or null when referencing a coordinate system defined in the scene's own `coordinateSystems`.
-  
+
 
 In any context, the values given for `name` and `path` provide an unambiguous reference to a named coordinate system.
 If the `path` field is null or omitted, this is to be interpreted as referring to a named coordinate system in the same `zarr.json` file.
@@ -1107,7 +1151,7 @@ An exact reproducibility of pixel values for images transformed and resampled by
 
 The multiscale group at `path` MUST satisfy:
   - **Dimensionality**: If the input coordinate system has `N` axes, the multiscale image at location `path` MUST have `N+1` dimensions.
-  - **Vector dimension length**: 
+  - **Vector dimension length**:
     - For `coordinates` transformations, the length of the array along the `coordinate` dimension (last axis) MUST equal `M`,
       the number of axes in the output coordinate system.
     - For `displacements` transformations, the length of the array along the `displacement` dimension (last axis) MUST equal `N`,
@@ -1275,9 +1319,9 @@ the input and output of the `forward` and `inverse` transformations are understo
 (multiscales-md)=
 
 Metadata about an image can be found under the `multiscales` key in the group-level OME-Zarr Metadata.
-Here, "image" refers to 2 to 5 dimensional data representing image
-or volumetric data with optional time or channel axes.
-It is stored in a multiple resolution representation.
+Here, "image" refers to data stored in a Zarr Array representing image,
+volumetric, time lapse, or similar data. It MAY be stored in multiple
+resolutions.
 
 `multiscales` contains an array of objects where each entry describes a multiscale image.
 Each object provides the following fields:
@@ -1295,15 +1339,26 @@ Each object provides the following fields:
 : The `coordinateSystems` field is a JSON array containing [coordinate system metadata](#coordinate-systems-md)
   The following conditions apply to all coordinate systems inside multiscales metadata:
 
-  - The length of `axes` must be between 2 and 5 and MUST be equal to the dimensionality of the Zarr arrays storing the image data (see `datasets:path`).
-  - `axes` MUST contain 2 or 3 entries of `type:space`
-  - `axes` MAY contain one additional entry of `type:time`
-  - `axes` MAY contain one additional entry of `type:channel` or a null / custom type.
-  - `axes` entries MUST be ordered by `type` where the `time` axis must come first (if present),
-    followed by the  `channel` or custom axis (if present) and the axes of type `space`.
-  - If there are three spatial axes where two correspond to the image plane (`yx`)
-    and images are stacked along the other (anisotropic) axis (`z`),
-    the spatial axes SHOULD be ordered as `zyx`.
+1. The length of the axis names MUST match the number of axes of the array.
+2. *If* a dataset contains exactly 2 spatial dimensions, those dimensions
+   SHOULD be named 'y' and 'x', except where rule 4 applies.
+3. *If* a dataset contains exactly 3 spatial dimensions, those dimensions
+   SHOULD be named 'z', 'y', and 'x', except where rule 4 applies.
+4. *If* a dataset contains exactly 1 time dimension, it should be named 't'.
+5. When image data axes map straightforwardly to axes with common names in
+   the relevant field of practice, those axes SHOULD be named according to
+   such conventions. For example, spatial frequency axes resulting from a
+   Fourier transformation of 'z', 'y', and 'x' SHOULD be named 'w', 'v', and
+   'u', respectively. Similarly, a temporal frequency axis resulting from
+   a Fourier transformation of the 't' axis SHOULD be named 'w' or 'ω'.
+6. Axis names MUST NOT be repeated within a dataset, and SHOULD NOT be
+   different only by upper/lower-case. For example, the same dataset SHOULD
+   NOT have both an 'X' and an 'x' axis.
+7. The order of the axes MUST match their ordering within the data if
+   applicable. For example, if the axes are ordered as "DZYX", where 'D' is a
+   field of displacement vectors, then the vectors must be ordered as "ZYX"
+   within the array.
+
 
 ```{hint}
 (spec:hint:multiscales-intrinsic-coordinate-system)=
@@ -1320,8 +1375,7 @@ is the coordinate system that is referenced by all multiscale coordinate transfo
   - Each object in `datasets` MUST contain the field `path`,
     whose value is a string containing the path to the Zarr array for this resolution relative to the current Zarr group.
   - The `path`s MUST be ordered from largest (i.e. highest resolution) to smallest.
-  - Every Zarr array referred to by a `path` MUST have the same number of dimensions and datatype,
-    and MUST NOT have more than 5 dimensions.
+  - Every Zarr array referred to by a `path` MUST have the same number of dimensions and datatype.
   - The number of dimensions and order MUST correspond to number and order of `axes`.
 
   Each object in `datasets` MUST contain the field `coordinateTransformations`,
@@ -1576,7 +1630,7 @@ The `zarr.json` under the `labels` group contains a JSON object with the key `la
 {
   "attributes": {
     "ome": {
-      "version": "0.6rc0",
+      "version": "0.9.dev1",
       "labels": [
         "cell_segmentation"
       ]
@@ -1870,7 +1924,7 @@ If they do so, it is RECOMMENDED that the scene's first entry under the `coordin
 If no coordinate system is defined therein, but only in the respective linked multiscale groups,
 viewers may want to expose a choice for the user to select a coordinate system for display when opening the dataset for the first time.
 
- 
+
 
 ```
 

schemas/_version.schema

@@ -1,10 +1,10 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/_version.schema",
+  "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/_version.schema",
   "title": "OME-Zarr version",
   "description": "OME-Zarr version.",
   "type": "string",
   "enum": [
-    "0.6rc0"
+    "0.9.dev1"
   ]
 }