@fideus-labs/ngff-zarr 0.19.0 → 0.22.0

package/esm/types/rfc4.js

@@ -50,6 +50,18 @@ export var AnatomicalOrientationValues;
     AnatomicalOrientationValues["ProximalToDistal"] = "proximal-to-distal";
     // Describes the directional orientation from the periphery of an anatomical structure or limb to the center of the body
     AnatomicalOrientationValues["DistalToProximal"] = "distal-to-proximal";
+    // Describes the directional orientation from the outer surface (superficial) to the inner depth (deep) of a layered tissue such as skin, gut, or cortex
+    AnatomicalOrientationValues["SuperficialToDeep"] = "superficial-to-deep";
+    // Describes the directional orientation from the inner depth (deep) to the outer surface (superficial) of a layered tissue such as skin, gut, or cortex
+    AnatomicalOrientationValues["DeepToSuperficial"] = "deep-to-superficial";
+    // Describes the directional orientation from the apical surface (apical) to the basal surface (basal) of an epithelial layer or polarized cell structure
+    AnatomicalOrientationValues["ApicalToBasal"] = "apical-to-basal";
+    // Describes the directional orientation from the basal surface (basal) to the apical surface (apical) of an epithelial layer or polarized cell structure
+    AnatomicalOrientationValues["BasalToApical"] = "basal-to-apical";
+    // Describes the directional orientation from the tip (apex) to the broad base (base) of an organ such as the heart or lung
+    AnatomicalOrientationValues["ApexToBase"] = "apex-to-base";
+    // Describes the directional orientation from the broad base (base) to the tip (apex) of an organ such as the heart or lung
+    AnatomicalOrientationValues["BaseToApex"] = "base-to-apex";
 })(AnatomicalOrientationValues || (AnatomicalOrientationValues = {}));
 /**
  * Create an anatomical orientation object.
@@ -86,6 +98,31 @@ export const RAS = {
     y: createAnatomicalOrientation(AnatomicalOrientationValues.PosteriorToAnterior),
     z: createAnatomicalOrientation(AnatomicalOrientationValues.InferiorToSuperior),
 };
+/**
+ * Preset anatomical orientation coordinate systems, keyed by lowercased name.
+ */
+const ORIENTATION_PRESETS = {
+    lps: LPS,
+    ras: RAS,
+};
+/**
+ * Resolve an anatomical orientation preset name to per-axis orientations.
+ *
+ * @param name - A preset coordinate-system name: "LPS" or "RAS" (case-insensitive)
+ * @returns A mapping of spatial axis name to AnatomicalOrientation
+ * @throws Error if the name is not a recognized preset
+ */
+export function orientationFromName(name) {
+    const preset = ORIENTATION_PRESETS[name.toLowerCase()];
+    if (preset === undefined) {
+        const supported = Object.keys(ORIENTATION_PRESETS)
+            .map((p) => p.toUpperCase())
+            .join(", ");
+        throw new Error(`Unknown anatomical orientation preset: "${name}". ` +
+            `Supported presets: ${supported}.`);
+    }
+    return { ...preset };
+}
 /**
  * Convert ITK LPS coordinate system to anatomical orientation.
  *
@@ -218,12 +255,6 @@ export function anatomicalOrientationToItkDirection(orientation) {
     }
     return undefined;
 }
-/**
- * Check if RFC 4 is enabled in the list of enabled RFCs.
- */
-export function isRfc4Enabled(enabledRfcs) {
-    return enabledRfcs !== undefined && enabledRfcs.includes(4);
-}
 /**
  * Add anatomical orientation to an axis object.
  *

package/esm/types/rfc4.js.map

@@ -1 +1 @@
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+{"version":3,"file":"rfc4.js","sourceRoot":"","sources":["../../src/types/rfc4.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B;;;;;GAKG;AAEH;;;;;GAKG;AACH,MAAM,CAAN,IAAY,2BAiDX;AAjDD,WAAY,2BAA2B;IACrC,wHAAwH;IACxH,4DAA6B,CAAA;IAC7B,wHAAwH;IACxH,4DAA6B,CAAA;IAC7B,6HAA6H;IAC7H,4EAA6C,CAAA;IAC7C,6HAA6H;IAC7H,4EAA6C,CAAA;IAC7C,qHAAqH;IACrH,0EAA2C,CAAA;IAC3C,qHAAqH;IACrH,0EAA2C,CAAA;IAC3C,oIAAoI;IACpI,oEAAqC,CAAA;IACrC,oIAAoI;IACpI,oEAAqC,CAAA;IACrC,+GAA+G;IAC/G,kEAAmC,CAAA;IACnC,+GAA+G;IAC/G,kEAAmC,CAAA;IACnC,gHAAgH;IAChH,oEAAqC,CAAA;IACrC,gHAAgH;IAChH,oEAAqC,CAAA;IACrC,gLAAgL;IAChL,oEAAqC,CAAA;IACrC,gLAAgL;IAChL,oEAAqC,CAAA;IACrC,4HAA4H;IAC5H,oEAAqC,CAAA;IACrC,4HAA4H;IAC5H,oEAAqC,CAAA;IACrC,wHAAwH;IACxH,sEAAuC,CAAA;IACvC,wHAAwH;IACxH,sEAAuC,CAAA;IACvC,wJAAwJ;IACxJ,wEAAyC,CAAA;IACzC,wJAAwJ;IACxJ,wEAAyC,CAAA;IACzC,yJAAyJ;IACzJ,gEAAiC,CAAA;IACjC,yJAAyJ;IACzJ,gEAAiC,CAAA;IACjC,2HAA2H;IAC3H,0DAA2B,CAAA;IAC3B,2HAA2H;IAC3H,0DAA2B,CAAA;AAC7B,CAAC,EAjDW,2BAA2B,KAA3B,2BAA2B,QAiDtC;AAUD;;GAEG;AACH,MAAM,UAAU,2BAA2B,CACzC,KAAkC;IAElC,OAAO;QACL,IAAI,EAAE,YAAY;QAClB,KAAK;KACN,CAAC;AACJ,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,CAAC,MAAM,GAAG,GAA0C;IACxD,CAAC,EAAE,2BAA2B,CAAC,2BAA2B,CAAC,WAAW,CAAC;IACvE,CAAC,EAAE,2BAA2B,CAC5B,2BAA2B,CAAC,mBAAmB,CAChD;IACD,CAAC,EAAE,2BAA2B,CAC5B,2BAA2B,CAAC,kBAAkB,CAC/C;CACF,CAAC;AAEF;;;;;;;GAOG;AACH,MAAM,CAAC,MAAM,GAAG,GAA0C;IACxD,CAAC,EAAE,2BAA2B,CAAC,2BAA2B,CAAC,WAAW,CAAC;IACvE,CAAC,EAAE,2BAA2B,CAC5B,2BAA2B,CAAC,mBAAmB,CAChD;IACD,CAAC,EAAE,2BAA2B,CAC5B,2BAA2B,CAAC,kBAAkB,CAC/C;CACF,CAAC;AAEF;;GAEG;AACH,MAAM,mBAAmB,GAGrB;IACF,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;CACT,CAAC;AAEF;;;;;;GAMG;AACH,MAAM,UAAU,mBAAmB,CACjC,IAAY;IAEZ,MAAM,MAAM,GAAG,mBAAmB,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC,CAAC;IACvD,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;QACzB,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,mBAAmB,CAAC;aAC/C,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC;aAC3B,IAAI,CAAC,IAAI,CAAC,CAAC;QACd,MAAM,IAAI,KAAK,CACb,2CAA2C,IAAI,KAAK;YAClD,sBAAsB,SAAS,GAAG,CACrC,CAAC;IACJ,CAAC;IACD,OAAO,EAAE,GAAG,MAAM,EAAE,CAAC;AACvB,CAAC;AAED;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,6BAA6B,CAC3C,QAAgB;IAEhB,OAAO,GAAG,CAAC,QAAQ,CAAC,CAAC;AACvB,CAAC;AAED;;;;GAIG;AACH,MAAM,sBAAsB,GAAG,CAAC,CAAC;AAEjC;;;;;;;;;;;;;;;;;;GAkBG;AACH,MAAM,qBAAqB,GAGrB;IACJ;QACE,2BAA2B,CAAC,WAAW;QACvC,2BAA2B,CAAC,WAAW;KACxC;IACD;QACE,2BAA2B,CAAC,mBAAmB;QAC/C,2BAA2B,CAAC,mBAAmB;KAChD;IACD;QACE,2BAA2B,CAAC,kBAAkB;QAC9C,2BAA2B,CAAC,kBAAkB;KAC/C;CACF,CAAC;AAEF;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AACH,MAAM,UAAU,mCAAmC,CACjD,eAAkC;IAElC,IAAI,eAAe,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC/B,MAAM,IAAI,KAAK,CACb,wEAAwE,eAAe,CAAC,MAAM,EAAE,CACjG,CAAC;IACJ,CAAC;IACD,+DAA+D;IAC/D,IAAI,YAAY,GAAG,CAAC,CAAC;IACrB,IAAI,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,eAAe,CAAC,CAAC,CAAC,CAAC,CAAC;IAC1C,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,eAAe,CAAC,MAAM,EAAE,sBAAsB,CAAC,CAAC;IACnE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3B,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,eAAe,CAAC,CAAC,CAAC,CAAC,CAAC;QAC5C,IAAI,MAAM,GAAG,MAAM,EAAE,CAAC;YACpB,MAAM,GAAG,MAAM,CAAC;YAChB,YAAY,GAAG,CAAC,CAAC;QACnB,CAAC;IACH,CAAC;IAED,mEAAmE;IACnE,MAAM,IAAI,GAAG,qBAAqB,CAAC,YAAY,CAAC,CAAC;IACjD,MAAM,KAAK,GAAG,eAAe,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IACrE,OAAO,2BAA2B,CAAC,KAAK,CAAC,CAAC;AAC5C,CAAC;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,MAAM,UAAU,mCAAmC,CACjD,WAAwC;IAExC,KACE,IAAI,SAAS,GAAG,CAAC,EACjB,SAAS,GAAG,qBAAqB,CAAC,MAAM,EACxC,SAAS,EAAE,EACX,CAAC;QACD,MAAM,CAAC,GAAG,EAAE,GAAG,CAAC,GAAG,qBAAqB,CAAC,SAAS,CAAC,CAAC;QACpD,IAAI,WAAW,KAAK,GAAG,EAAE,CAAC;YACxB,MAAM,GAAG,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;YACtB,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC;YACnB,OAAO,GAAG,CAAC;QACb,CAAC;QACD,IAAI,WAAW,KAAK,GAAG,EAAE,CAAC;YACxB,MAAM,GAAG,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;YACtB,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC;YACpB,OAAO,GAAG,CAAC;QACb,CAAC;IACH,CAAC;IACD,OAAO,SAAS,CAAC;AACnB,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,8BAA8B,CAC5C,QAAiC,EACjC,WAAkC;IAElC,OAAO;QACL,GAAG,QAAQ;QACX,WAAW,EAAE;YACX,IAAI,EAAE,WAAW,CAAC,IAAI;YACtB,KAAK,EAAE,WAAW,CAAC,KAAK;SACzB;KACF,CAAC;AACJ,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,mCAAmC,CACjD,QAAiC;IAEjC,MAAM,EAAE,WAAW,EAAE,YAAY,EAAE,GAAG,IAAI,EAAE,GAAG,QAAQ,CAAC;IACxD,OAAO,IAAI,CAAC;AACd,CAAC"}

package/esm/types/supported_versions.d.ts

@@ -7,8 +7,23 @@ export declare enum NgffVersion {
     V03 = "0.3",
     V04 = "0.4",
     V05 = "0.5",
-    LATEST = "0.5"
+    V06 = "0.6",
+    /**
+     * Draft development version of the OME-Zarr v0.6 (RFC-5) spec. Stores are
+     * tagged on disk with this string while the spec is still in development;
+     * see {@link V06_ONDISK_VERSION}. Temporary — tracks the upstream dev release.
+     */
+    V06dev4 = "0.6.dev4",
+    LATEST = "0.6.dev4"
 }
+/**
+ * The on-disk `ome.version` string written for OME-Zarr v0.6. The v0.6 / RFC-5
+ * spec is still a draft, so stores are tagged with the development version
+ * `0.6.dev4` even though the library's public `version` option is `"0.6"`.
+ * This is a temporary shim that tracks the upstream spec's dev releases;
+ * mirrors the Python port writing `"0.6.dev4"` for a requested version `"0.6"`.
+ */
+export declare const V06_ONDISK_VERSION: NgffVersion;
 /**
  * Supported NGFF specification versions
  */
@@ -17,4 +32,11 @@ export declare const SUPPORTED_VERSIONS: readonly NgffVersion[];
  * Check if a version string is supported
  */
 export declare function isSupportedVersion(version: string): version is NgffVersion;
+/**
+ * Whether an `ome.version` string identifies an OME-Zarr v0.6 store, including
+ * draft development versions such as `0.6.dev4`. Mirrors the Python port's
+ * `version.startswith("0.6")` check so a store written by either implementation
+ * reads back as v0.6.
+ */
+export declare function isV06Version(version: string): boolean;
 //# sourceMappingURL=supported_versions.d.ts.map

package/esm/types/supported_versions.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"supported_versions.d.ts","sourceRoot":"","sources":["../../src/types/supported_versions.ts"],"names":[],"mappings":"AAGA;;GAEG;AAEH,oBAAY,WAAW;IACrB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,MAAM,QAAQ;CACf;AAED;;GAEG;AACH,eAAO,MAAM,kBAAkB,EAAE,SAAS,WAAW,EAM3C,CAAC;AAEX;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,IAAI,WAAW,CAE1E"}
+{"version":3,"file":"supported_versions.d.ts","sourceRoot":"","sources":["../../src/types/supported_versions.ts"],"names":[],"mappings":"AAGA;;GAEG;AAEH,oBAAY,WAAW;IACrB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX;;;;OAIG;IACH,OAAO,aAAa;IACpB,MAAM,aAAa;CACpB;AAED;;;;;;GAMG;AACH,eAAO,MAAM,kBAAkB,EAAE,WAAiC,CAAC;AAEnE;;GAEG;AACH,eAAO,MAAM,kBAAkB,EAAE,SAAS,WAAW,EAQ3C,CAAC;AAEX;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,IAAI,WAAW,CAE1E;AAED;;;;;GAKG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAErD"}

package/esm/types/supported_versions.js

@@ -10,8 +10,23 @@ export var NgffVersion;
     NgffVersion["V03"] = "0.3";
     NgffVersion["V04"] = "0.4";
     NgffVersion["V05"] = "0.5";
-    NgffVersion["LATEST"] = "0.5";
+    NgffVersion["V06"] = "0.6";
+    /**
+     * Draft development version of the OME-Zarr v0.6 (RFC-5) spec. Stores are
+     * tagged on disk with this string while the spec is still in development;
+     * see {@link V06_ONDISK_VERSION}. Temporary — tracks the upstream dev release.
+     */
+    NgffVersion["V06dev4"] = "0.6.dev4";
+    NgffVersion["LATEST"] = "0.6.dev4";
 })(NgffVersion || (NgffVersion = {}));
+/**
+ * The on-disk `ome.version` string written for OME-Zarr v0.6. The v0.6 / RFC-5
+ * spec is still a draft, so stores are tagged with the development version
+ * `0.6.dev4` even though the library's public `version` option is `"0.6"`.
+ * This is a temporary shim that tracks the upstream spec's dev releases;
+ * mirrors the Python port writing `"0.6.dev4"` for a requested version `"0.6"`.
+ */
+export const V06_ONDISK_VERSION = NgffVersion.V06dev4;
 /**
  * Supported NGFF specification versions
  */
@@ -21,6 +36,8 @@ export const SUPPORTED_VERSIONS = [
     NgffVersion.V03,
     NgffVersion.V04,
     NgffVersion.V05,
+    NgffVersion.V06,
+    NgffVersion.V06dev4,
 ];
 /**
  * Check if a version string is supported
@@ -28,4 +45,13 @@ export const SUPPORTED_VERSIONS = [
 export function isSupportedVersion(version) {
     return Object.values(NgffVersion).includes(version);
 }
+/**
+ * Whether an `ome.version` string identifies an OME-Zarr v0.6 store, including
+ * draft development versions such as `0.6.dev4`. Mirrors the Python port's
+ * `version.startswith("0.6")` check so a store written by either implementation
+ * reads back as v0.6.
+ */
+export function isV06Version(version) {
+    return version.startsWith("0.6");
+}
 //# sourceMappingURL=supported_versions.js.map

package/esm/types/supported_versions.js.map

@@ -1 +1 @@
-{"version":3,"file":"supported_versions.js","sourceRoot":"","sources":["../../src/types/supported_versions.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAE/B;;GAEG;AAEH,MAAM,CAAN,IAAY,WAOX;AAPD,WAAY,WAAW;IACrB,0BAAW,CAAA;IACX,0BAAW,CAAA;IACX,0BAAW,CAAA;IACX,0BAAW,CAAA;IACX,0BAAW,CAAA;IACX,6BAAc,CAAA;AAChB,CAAC,EAPW,WAAW,KAAX,WAAW,QAOtB;AAED;;GAEG;AACH,MAAM,CAAC,MAAM,kBAAkB,GAA2B;IACxD,WAAW,CAAC,GAAG;IACf,WAAW,CAAC,GAAG;IACf,WAAW,CAAC,GAAG;IACf,WAAW,CAAC,GAAG;IACf,WAAW,CAAC,GAAG;CACP,CAAC;AAEX;;GAEG;AACH,MAAM,UAAU,kBAAkB,CAAC,OAAe;IAChD,OAAO,MAAM,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,OAAsB,CAAC,CAAC;AACrE,CAAC"}
+{"version":3,"file":"supported_versions.js","sourceRoot":"","sources":["../../src/types/supported_versions.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAE/B;;GAEG;AAEH,MAAM,CAAN,IAAY,WAcX;AAdD,WAAY,WAAW;IACrB,0BAAW,CAAA;IACX,0BAAW,CAAA;IACX,0BAAW,CAAA;IACX,0BAAW,CAAA;IACX,0BAAW,CAAA;IACX,0BAAW,CAAA;IACX;;;;OAIG;IACH,mCAAoB,CAAA;IACpB,kCAAmB,CAAA;AACrB,CAAC,EAdW,WAAW,KAAX,WAAW,QActB;AAED;;;;;;GAMG;AACH,MAAM,CAAC,MAAM,kBAAkB,GAAgB,WAAW,CAAC,OAAO,CAAC;AAEnE;;GAEG;AACH,MAAM,CAAC,MAAM,kBAAkB,GAA2B;IACxD,WAAW,CAAC,GAAG;IACf,WAAW,CAAC,GAAG;IACf,WAAW,CAAC,GAAG;IACf,WAAW,CAAC,GAAG;IACf,WAAW,CAAC,GAAG;IACf,WAAW,CAAC,GAAG;IACf,WAAW,CAAC,OAAO;CACX,CAAC;AAEX;;GAEG;AACH,MAAM,UAAU,kBAAkB,CAAC,OAAe;IAChD,OAAO,MAAM,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,OAAsB,CAAC,CAAC;AACrE,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,YAAY,CAAC,OAAe;IAC1C,OAAO,OAAO,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;AACnC,CAAC"}

package/esm/types/zarr_metadata.d.ts

@@ -2,6 +2,12 @@ import type { AxesType, SupportedDims, Units } from "./units.js";
 import { NgffVersion } from "./supported_versions.js";
 import type { NgffImage } from "./ngff_image.js";
 import type { AnatomicalOrientation } from "./rfc4.js";
+/**
+ * Name of the implicit coordinate system generated for a multiscale image,
+ * matching the Python port. Datasets map their array index space into this
+ * system via a scale + translation sequence.
+ */
+export declare const INTRINSIC_COORDINATE_SYSTEM_NAME = "intrinsic";
 /**
  * Orientation metadata for spatial axes (RFC 4).
  * This interface represents the serialized form in the zarr metadata.
@@ -16,18 +22,81 @@ export interface Axis {
     unit: Units | undefined;
     orientation?: AxisOrientation | AnatomicalOrientation | undefined;
 }
+/**
+ * RFC 5 / OME-Zarr v0.6 coordinate-system reference used by the `input` and
+ * `output` fields of a transformation. Mirrors the Python
+ * `CoordinateSystemIdentifier` dataclass and the spec `inputOutput` object: a
+ * transformation references either a coordinate system by `name` or a dataset
+ * array by `path`.
+ */
+export interface CoordinateSystemIdentifier {
+    path?: string;
+    name?: string;
+}
+/**
+ * RFC 5 / OME-Zarr v0.6 coordinate system: a named set of axes. The implicit
+ * "intrinsic" coordinate system is generated for the multiscale image.
+ */
+export interface CoordinateSystem {
+    name: string;
+    axes: Axis[];
+}
 export interface Identity {
     type: "identity";
+    input?: CoordinateSystemIdentifier;
+    output?: CoordinateSystemIdentifier;
+    name?: string;
 }
 export interface Scale {
     scale: number[];
     type: "scale";
+    input?: CoordinateSystemIdentifier;
+    output?: CoordinateSystemIdentifier;
+    name?: string;
 }
 export interface Translation {
     translation: number[];
     type: "translation";
+    input?: CoordinateSystemIdentifier;
+    output?: CoordinateSystemIdentifier;
+    name?: string;
+}
+/** RFC 5 rotation transformation (v0.6). */
+export interface Rotation {
+    rotation: number[][];
+    type: "rotation";
+    path?: string;
+    input?: CoordinateSystemIdentifier;
+    output?: CoordinateSystemIdentifier;
+    name?: string;
+}
+/** RFC 5 affine transformation (v0.6). */
+export interface Affine {
+    affine: number[][];
+    type: "affine";
+    path?: string;
+    input?: CoordinateSystemIdentifier;
+    output?: CoordinateSystemIdentifier;
+    name?: string;
+}
+/** RFC 5 sequence transformation, chaining sub-transformations (v0.6). */
+export interface TransformSequence {
+    transformations: V06Transform[];
+    type: "sequence";
+    input?: CoordinateSystemIdentifier;
+    output?: CoordinateSystemIdentifier;
+    name?: string;
 }
+/**
+ * Simple per-dataset transform used by the v0.4/v0.5 in-memory model and as the
+ * extracted scale/translation of a v0.6 dataset.
+ */
 export type Transform = Scale | Translation;
+/**
+ * Full RFC 5 / v0.6 transformation union. Used for top-level multiscale
+ * `coordinateTransformations` and the per-dataset `sequence` on the wire.
+ */
+export type V06Transform = Identity | Scale | Translation | Rotation | Affine | TransformSequence;
 export interface Dataset {
     path: string;
     coordinateTransformations: Transform[];
@@ -59,12 +128,31 @@ export interface MethodMetadata {
 export interface MetadataInterface {
     axes: Axis[];
     datasets: Dataset[];
-    coordinateTransformations: Transform[] | undefined;
+    /**
+     * Top-level multiscale transformations. For v0.4/v0.5 these are simple
+     * {@link Transform}s; for RFC 5 / v0.6 they may be any {@link V06Transform}
+     * (rotation, affine, sequence, ...) referencing coordinate systems.
+     */
+    coordinateTransformations: V06Transform[] | undefined;
+    /**
+     * RFC 5 / OME-Zarr v0.6 coordinate systems. Populated when reading a v0.6
+     * store and by `toMultiscales` (the implicit "intrinsic" system). Unused when
+     * serializing v0.4/v0.5, where axes live on the multiscale entry directly.
+     */
+    coordinateSystems?: CoordinateSystem[];
     omero: Omero | undefined;
     name: string;
     version: string;
     type?: string;
     metadata?: MethodMetadata;
+    /**
+     * Unrecognized keys that leaked into the `multiscales[]` entry (a malformed
+     * or double-namespaced v0.5 document). Captured verbatim so the v0.5
+     * namespacing rules (`zarr-format`, `ome-namespace`) can flag them; mirrors
+     * the Rust port's `#[serde(flatten)]` `extra` passthrough. It is a read-side
+     * validation aid only and is never serialized back to the store.
+     */
+    extra?: Record<string, unknown>;
 }
 /**
  * Result from parsing zarr attributes
@@ -97,4 +185,8 @@ export declare function validateColor(color: string): void;
 export declare function createScale(scale: number[]): Scale;
 export declare function createTranslation(translation: number[]): Translation;
 export declare function createIdentity(): Identity;
+export declare function createRotation(rotation: number[][]): Rotation;
+export declare function createAffine(affine: number[][]): Affine;
+export declare function createTransformSequence(transformations: V06Transform[]): TransformSequence;
+export declare function createCoordinateSystem(name: string, axes: Axis[]): CoordinateSystem;
 //# sourceMappingURL=zarr_metadata.d.ts.map

package/esm/types/zarr_metadata.d.ts.map

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package/esm/types/zarr_metadata.js

@@ -1,4 +1,10 @@
 import { NgffVersion } from "./supported_versions.js";
+/**
+ * Name of the implicit coordinate system generated for a multiscale image,
+ * matching the Python port. Datasets map their array index space into this
+ * system via a scale + translation sequence.
+ */
+export const INTRINSIC_COORDINATE_SYSTEM_NAME = "intrinsic";
 /**
  * Supported dimension names for backward compatibility
  */
@@ -28,6 +34,18 @@ export function createMetadataWithVersion(metadata, targetVersion) {
             version: "0.5",
         };
     }
+    else if (version === NgffVersion.V06) {
+        // The in-memory model is version-agnostic (axes + per-dataset scale and
+        // translation); v0.6 additionally exposes coordinate systems. Synthesize
+        // the implicit "intrinsic" system from the axes when one is not present, so
+        // a value converted to v0.6 carries the field the writer expects.
+        return {
+            ...metadata,
+            version: "0.6",
+            coordinateSystems: metadata.coordinateSystems ??
+                [{ name: INTRINSIC_COORDINATE_SYSTEM_NAME, axes: metadata.axes }],
+        };
+    }
     else {
         throw new Error(`Unsupported version conversion: ${metadata.version} -> ${version}`);
     }
@@ -52,4 +70,16 @@ export function createTranslation(translation) {
 export function createIdentity() {
     return { type: "identity" };
 }
+export function createRotation(rotation) {
+    return { rotation: rotation.map((row) => [...row]), type: "rotation" };
+}
+export function createAffine(affine) {
+    return { affine: affine.map((row) => [...row]), type: "affine" };
+}
+export function createTransformSequence(transformations) {
+    return { transformations: [...transformations], type: "sequence" };
+}
+export function createCoordinateSystem(name, axes) {
+    return { name, axes: [...axes] };
+}
 //# sourceMappingURL=zarr_metadata.js.map

package/esm/types/zarr_metadata.js.map

@@ -1 +1 @@
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+{"version":3,"file":"zarr_metadata.js","sourceRoot":"","sources":["../../src/types/zarr_metadata.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAItD;;;;GAIG;AACH,MAAM,CAAC,MAAM,gCAAgC,GAAG,WAAW,CAAC;AA+L5D;;GAEG;AACH,MAAM,CAAC,MAAM,cAAc,GAA6B;IACtD,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;CACK,CAAC;AAEX;;GAEG;AACH,MAAM,UAAU,yBAAyB,CACvC,QAA2B,EAC3B,aAAmC;IAEnC,MAAM,OAAO,GAAG,OAAO,aAAa,KAAK,QAAQ;QAC/C,CAAC,CAAE,aAA6B;QAChC,CAAC,CAAC,aAAa,CAAC;IAElB,IAAI,OAAO,KAAK,WAAW,CAAC,GAAG,EAAE,CAAC;QAChC,OAAO;YACL,GAAG,QAAQ;YACX,OAAO,EAAE,KAAK;SACf,CAAC;IACJ,CAAC;SAAM,IAAI,OAAO,KAAK,WAAW,CAAC,GAAG,EAAE,CAAC;QACvC,OAAO;YACL,GAAG,QAAQ;YACX,OAAO,EAAE,KAAK;SACf,CAAC;IACJ,CAAC;SAAM,IAAI,OAAO,KAAK,WAAW,CAAC,GAAG,EAAE,CAAC;QACvC,wEAAwE;QACxE,yEAAyE;QACzE,4EAA4E;QAC5E,kEAAkE;QAClE,OAAO;YACL,GAAG,QAAQ;YACX,OAAO,EAAE,KAAK;YACd,iBAAiB,EAAE,QAAQ,CAAC,iBAAiB;gBAC3C,CAAC,EAAE,IAAI,EAAE,gCAAgC,EAAE,IAAI,EAAE,QAAQ,CAAC,IAAI,EAAE,CAAC;SACpE,CAAC;IACJ,CAAC;SAAM,CAAC;QACN,MAAM,IAAI,KAAK,CACb,mCAAmC,QAAQ,CAAC,OAAO,OAAO,OAAO,EAAE,CACpE,CAAC;IACJ,CAAC;AACH,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,iBAAiB,CAAC,QAA2B;IAC3D,OAAO,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC;AAC5C,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,KAAa;IACzC,IAAI,CAAC,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACpC,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,0BAA0B,CAAC,CAAC;IACrE,CAAC;AACH,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,KAAe;IACzC,OAAO,EAAE,KAAK,EAAE,CAAC,GAAG,KAAK,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,CAAC;AAC9C,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,WAAqB;IACrD,OAAO,EAAE,WAAW,EAAE,CAAC,GAAG,WAAW,CAAC,EAAE,IAAI,EAAE,aAAa,EAAE,CAAC;AAChE,CAAC;AAED,MAAM,UAAU,cAAc;IAC5B,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,CAAC;AAC9B,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,QAAoB;IACjD,OAAO,EAAE,QAAQ,EAAE,QAAQ,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,EAAE,IAAI,EAAE,UAAU,EAAE,CAAC;AACzE,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,MAAkB;IAC7C,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,EAAE,IAAI,EAAE,QAAQ,EAAE,CAAC;AACnE,CAAC;AAED,MAAM,UAAU,uBAAuB,CACrC,eAA+B;IAE/B,OAAO,EAAE,eAAe,EAAE,CAAC,GAAG,eAAe,CAAC,EAAE,IAAI,EAAE,UAAU,EAAE,CAAC;AACrE,CAAC;AAED,MAAM,UAAU,sBAAsB,CACpC,IAAY,EACZ,IAAY;IAEZ,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,EAAE,CAAC;AACnC,CAAC"}

package/esm/utils/from_zarr_attrs.d.ts

@@ -18,4 +18,16 @@ export declare function fromZarrAttrsV04(rootAttrs: Record<string, unknown>, sto
  * is at the root level (as written by toNgffZarr).
  */
 export declare function fromZarrAttrsV05(rootAttrs: Record<string, unknown>, store: MemoryStore | zarr.FetchStore | zarr.Readable, validate?: boolean): Promise<FromZarrAttrsResult>;
+/**
+ * Parse Metadata and NgffImages from OME-Zarr v0.6 (RFC 5) root attributes.
+ *
+ * Unlike v0.4/v0.5, a v0.6 multiscale entry carries `coordinateSystems` instead
+ * of a top-level `axes` list, and maps each dataset's array index space into the
+ * implicit "intrinsic" system through a `sequence` of scale + translation. This
+ * reader recovers the version-agnostic in-memory model (axes + per-dataset scale
+ * and translation) while preserving the coordinate systems and any top-level
+ * transformations for round-tripping. Mirrors the Python
+ * `v06.zarr_metadata.Metadata._from_zarr_attrs`.
+ */
+export declare function fromZarrAttrsV06(rootAttrs: Record<string, unknown>, store: MemoryStore | zarr.FetchStore | zarr.Readable, validate?: boolean): Promise<FromZarrAttrsResult>;
 //# sourceMappingURL=from_zarr_attrs.d.ts.map

package/esm/utils/from_zarr_attrs.d.ts.map

@@ -1 +1 @@
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