@fideus-labs/ngff-zarr 0.0.1 → 0.2.0

package/script/types/hcs.js

@@ -0,0 +1,233 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.HCSPlate = exports.HCSWell = exports.LRUCache = void 0;
+class LRUCache {
+    cache;
+    maxSize;
+    constructor(options) {
+        this.cache = new Map();
+        this.maxSize = options.maxSize;
+    }
+    get(key) {
+        const value = this.cache.get(key);
+        if (value !== undefined) {
+            // Move to end (most recently used)
+            this.cache.delete(key);
+            this.cache.set(key, value);
+        }
+        return value;
+    }
+    set(key, value) {
+        if (this.cache.has(key)) {
+            // Update existing item
+            this.cache.delete(key);
+        }
+        else if (this.cache.size >= this.maxSize) {
+            // Remove least recently used item
+            const firstKey = this.cache.keys().next().value;
+            if (firstKey !== undefined) {
+                this.cache.delete(firstKey);
+            }
+        }
+        this.cache.set(key, value);
+    }
+    has(key) {
+        return this.cache.has(key);
+    }
+    clear() {
+        this.cache.clear();
+    }
+}
+exports.LRUCache = LRUCache;
+class HCSWell {
+    store;
+    path;
+    plateMetadata;
+    metadata;
+    _images;
+    constructor(options) {
+        this.store = options.store;
+        this.path = options.wellPath;
+        this.plateMetadata = { ...options.plateMetadata };
+        this.metadata = {
+            images: [...options.wellGroupMetadata.images],
+            version: options.wellGroupMetadata.version,
+        };
+        const imageCacheSize = options.imageCacheSize ?? 100;
+        this._images = new LRUCache({
+            maxSize: imageCacheSize,
+        });
+    }
+    get rowIndex() {
+        return this.plateMetadata.rowIndex;
+    }
+    get columnIndex() {
+        return this.plateMetadata.columnIndex;
+    }
+    get images() {
+        return [...this.metadata.images];
+    }
+    async getImage(fieldIndex = 0) {
+        if (fieldIndex < 0 || fieldIndex >= this.metadata.images.length) {
+            return null;
+        }
+        const imageMeta = this.metadata.images[fieldIndex];
+        const imagePath = `${this.path}/${imageMeta.path}`;
+        // Check cache first
+        const cached = this._images.get(imagePath);
+        if (cached) {
+            return cached;
+        }
+        // Load the image using fromNgffZarr
+        const { fromNgffZarr } = await Promise.resolve().then(() => __importStar(require("../io/from_ngff_zarr.js")));
+        let fullImagePath;
+        if (typeof this.store === "string") {
+            // If store is a path string, append the image path
+            fullImagePath = `${this.store}/${this.path}/${imageMeta.path}`;
+        }
+        else {
+            // For other store types, we need to handle differently
+            // This would need to be adapted based on the specific store type
+            throw new Error("Non-string store types not yet implemented for HCS");
+        }
+        try {
+            const multiscales = await fromNgffZarr(fullImagePath);
+            this._images.set(imagePath, multiscales);
+            return multiscales;
+        }
+        catch (error) {
+            console.error(`Failed to load image at ${fullImagePath}:`, error);
+            return null;
+        }
+    }
+    getImageByAcquisition(acquisitionId, fieldIndex = 0) {
+        // Find images for the specified acquisition
+        const acquisitionImages = this.metadata.images.filter((img) => img.acquisition === acquisitionId);
+        if (fieldIndex < 0 || fieldIndex >= acquisitionImages.length) {
+            return Promise.resolve(null);
+        }
+        // Find the actual image index in the full list
+        const targetImage = acquisitionImages[fieldIndex];
+        const actualIndex = this.metadata.images.indexOf(targetImage);
+        return this.getImage(actualIndex);
+    }
+    static fromStore(store, wellPath, wellMetadata, imageCacheSize) {
+        // Simplified implementation - we'll improve this when implementing the IO functions
+        const wellGroupMetadata = {
+            images: [
+                { path: "0", acquisition: 0 },
+                { path: "1", acquisition: 0 },
+            ],
+            version: "0.4",
+        };
+        return new HCSWell({
+            store,
+            wellPath,
+            plateMetadata: wellMetadata,
+            wellGroupMetadata,
+            imageCacheSize,
+        });
+    }
+}
+exports.HCSWell = HCSWell;
+class HCSPlate {
+    store;
+    metadata;
+    _wells;
+    imageCacheSize;
+    constructor(options) {
+        this.store = options.store;
+        this.metadata = {
+            columns: [...options.metadata.columns],
+            rows: [...options.metadata.rows],
+            wells: [...options.metadata.wells],
+            version: options.metadata.version,
+            acquisitions: options.metadata.acquisitions
+                ? [...options.metadata.acquisitions]
+                : undefined,
+            field_count: options.metadata.field_count,
+            name: options.metadata.name,
+        };
+        this.imageCacheSize = options.imageCacheSize;
+        const wellCacheSize = options.wellCacheSize ?? 500;
+        this._wells = new LRUCache({ maxSize: wellCacheSize });
+    }
+    get name() {
+        return this.metadata.name;
+    }
+    get rows() {
+        return [...this.metadata.rows];
+    }
+    get columns() {
+        return [...this.metadata.columns];
+    }
+    get wells() {
+        return [...this.metadata.wells];
+    }
+    get acquisitions() {
+        return this.metadata.acquisitions
+            ? [...this.metadata.acquisitions]
+            : undefined;
+    }
+    get fieldCount() {
+        return this.metadata.field_count;
+    }
+    getWell(rowName, columnName) {
+        const wellPath = `${rowName}/${columnName}`;
+        // Check if well exists in metadata
+        const wellMeta = this.metadata.wells.find((well) => well.path === wellPath);
+        if (!wellMeta) {
+            return null;
+        }
+        // Check cache first
+        const cached = this._wells.get(wellPath);
+        if (cached) {
+            return cached;
+        }
+        // Load the well
+        try {
+            const well = HCSWell.fromStore(this.store, wellPath, wellMeta, this.imageCacheSize);
+            this._wells.set(wellPath, well);
+            return well;
+        }
+        catch (error) {
+            console.error(`Failed to load well at ${wellPath}:`, error);
+            return null;
+        }
+    }
+    getWellByIndices(rowIndex, columnIndex) {
+        if (rowIndex < 0 ||
+            rowIndex >= this.metadata.rows.length ||
+            columnIndex < 0 ||
+            columnIndex >= this.metadata.columns.length) {
+            return null;
+        }
+        const rowName = this.metadata.rows[rowIndex].name;
+        const columnName = this.metadata.columns[columnIndex].name;
+        return this.getWell(rowName, columnName);
+    }
+}
+exports.HCSPlate = HCSPlate;

package/script/types/methods.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"methods.d.ts","sourceRoot":"","sources":["../../src/types/methods.ts"],"names":[],"mappings":"AAEA,oBAAY,OAAO;IACjB,gBAAgB,qBAAqB;IACrC,kBAAkB,uBAAuB;IACzC,mBAAmB,wBAAwB;CAC5C;AAED,eAAO,MAAM,aAAa,EAAE,OAAO,EAA2B,CAAC"}

package/script/types/methods.js

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.methodsValues = exports.Methods = void 0;
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
 var Methods;
 (function (Methods) {
     Methods["ITKWASM_GAUSSIAN"] = "itkwasm_gaussian";

package/script/types/multiscales.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"multiscales.d.ts","sourceRoot":"","sources":["../../src/types/multiscales.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAC;AACjD,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAC;AACnD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,cAAc,CAAC;AAE5C,MAAM,MAAM,SAAS,GACjB,MAAM,GACN,MAAM,EAAE,GACR,MAAM,EAAE,EAAE,GACV,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,SAAS,CAAC,CAAC;AAElD,MAAM,WAAW,kBAAkB;IACjC,MAAM,EAAE,SAAS,EAAE,CAAC;IACpB,QAAQ,EAAE,QAAQ,CAAC;IACnB,YAAY,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,GAAG,SAAS,CAAC;IAC9D,MAAM,EAAE,OAAO,GAAG,SAAS,CAAC;IAC5B,MAAM,EAAE,SAAS,GAAG,SAAS,CAAC;CAC/B;AAED,qBAAa,WAAW;IACtB,SAAgB,MAAM,EAAE,SAAS,EAAE,CAAC;IACpC,SAAgB,QAAQ,EAAE,QAAQ,CAAC;IACnC,SAAgB,YAAY,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,GAAG,SAAS,CAAC;IAC9E,SAAgB,MAAM,EAAE,OAAO,GAAG,SAAS,CAAC;IAC5C,SAAgB,MAAM,EAAE,SAAS,GAAG,SAAS,CAAC;gBAElC,OAAO,EAAE,kBAAkB;IAUvC,QAAQ,IAAI,MAAM;CAwBnB"}

package/script/types/ngff_image.d.ts

@@ -1,22 +1,25 @@
-import type { LazyArray } from "./lazy_array.js";
+import * as zarr from "zarrita";
 import type { Units } from "./units.js";
+import type { AnatomicalOrientation } from "./rfc4.js";
 export type ComputedCallback = () => void;
 export interface NgffImageOptions {
-    data: LazyArray;
+    data: zarr.Array<zarr.DataType, zarr.Readable>;
     dims: string[];
     scale: Record<string, number>;
     translation: Record<string, number>;
     name: string | undefined;
     axesUnits: Record<string, Units> | undefined;
+    axesOrientations?: Record<string, AnatomicalOrientation> | undefined;
     computedCallbacks: ComputedCallback[] | undefined;
 }
 export declare class NgffImage {
-    readonly data: LazyArray;
+    readonly data: zarr.Array<zarr.DataType, zarr.Readable>;
     readonly dims: string[];
     readonly scale: Record<string, number>;
     readonly translation: Record<string, number>;
     readonly name: string;
     readonly axesUnits: Record<string, Units> | undefined;
+    readonly axesOrientations: Record<string, AnatomicalOrientation> | undefined;
     readonly computedCallbacks: ComputedCallback[];
     constructor(options: NgffImageOptions);
     toString(): string;

package/script/types/ngff_image.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"ngff_image.d.ts","sourceRoot":"","sources":["../../src/types/ngff_image.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,YAAY,CAAC;AACxC,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,WAAW,CAAC;AAEvD,MAAM,MAAM,gBAAgB,GAAG,MAAM,IAAI,CAAC;AAE1C,MAAM,WAAW,gBAAgB;IAC/B,IAAI,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,QAAQ,EAAE,IAAI,CAAC,QAAQ,CAAC,CAAC;IAC/C,IAAI,EAAE,MAAM,EAAE,CAAC;IACf,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC9B,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACpC,IAAI,EAAE,MAAM,GAAG,SAAS,CAAC;IACzB,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,GAAG,SAAS,CAAC;IAC7C,gBAAgB,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,qBAAqB,CAAC,GAAG,SAAS,CAAC;IACrE,iBAAiB,EAAE,gBAAgB,EAAE,GAAG,SAAS,CAAC;CACnD;AAED,qBAAa,SAAS;IACpB,SAAgB,IAAI,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,QAAQ,EAAE,IAAI,CAAC,QAAQ,CAAC,CAAC;IAC/D,SAAgB,IAAI,EAAE,MAAM,EAAE,CAAC;IAC/B,SAAgB,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC9C,SAAgB,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACpD,SAAgB,IAAI,EAAE,MAAM,CAAC;IAC7B,SAAgB,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,GAAG,SAAS,CAAC;IAC7D,SAAgB,gBAAgB,EAC5B,MAAM,CAAC,MAAM,EAAE,qBAAqB,CAAC,GACrC,SAAS,CAAC;IACd,SAAgB,iBAAiB,EAAE,gBAAgB,EAAE,CAAC;gBAE1C,OAAO,EAAE,gBAAgB;IAarC,QAAQ,IAAI,MAAM;CA8BnB"}

package/script/types/ngff_image.js

@@ -8,6 +8,7 @@ class NgffImage {
     translation;
     name;
     axesUnits;
+    axesOrientations;
     computedCallbacks;
     constructor(options) {
         this.data = options.data;
@@ -16,19 +17,30 @@ class NgffImage {
         this.translation = { ...options.translation };
         this.name = options.name ?? "image";
         this.axesUnits = options.axesUnits ? { ...options.axesUnits } : undefined;
+        this.axesOrientations = options.axesOrientations
+            ? { ...options.axesOrientations }
+            : undefined;
         this.computedCallbacks = [...(options.computedCallbacks ?? [])];
     }
     toString() {
         const axesUnitsStr = this.axesUnits
             ? JSON.stringify(this.axesUnits)
             : "None";
+        const axesOrientationsStr = this.axesOrientations
+            ? JSON.stringify(this.axesOrientations)
+            : "None";
+        // Create array string representation using zarr.Array properties
+        const path = this.data.path || this.name;
+        const chunks = this.data.chunks.join(", ");
+        const arrayStr = `Array(name=${path}, shape=(${this.data.shape.join(", ")}), dtype=${this.data.dtype}, chunksize=(${chunks}), chunktype=TypedArray)`;
         return `NgffImage(
-    data=${this.data.toString()},
+    data=${arrayStr},
     dims=[${this.dims.map((d) => `'${d}'`).join(", ")}],
     scale=${JSON.stringify(this.scale)},
     translation=${JSON.stringify(this.translation)},
     name='${this.name}',
     axes_units=${axesUnitsStr},
+    axes_orientations=${axesOrientationsStr},
     computed_callbacks=[${this.computedCallbacks.length} callbacks]
 )`;
     }

package/script/types/rfc4.d.ts

@@ -0,0 +1,94 @@
+/**
+ * RFC 4 implementation for anatomical orientation in OME-NGFF.
+ *
+ * This module implements RFC 4 which adds anatomical orientation support
+ * to OME-NGFF axes, based on the LinkML schema.
+ */
+/**
+ * Anatomical orientation refers to the specific arrangement and directional
+ * alignment of anatomical structures within an imaging dataset. It is crucial
+ * for ensuring accurate alignment and comparison of images to anatomical atlases,
+ * facilitating consistent analysis and interpretation of biological data.
+ */
+export declare enum AnatomicalOrientationValues {
+    LeftToRight = "left-to-right",
+    RightToLeft = "right-to-left",
+    AnteriorToPosterior = "anterior-to-posterior",
+    PosteriorToAnterior = "posterior-to-anterior",
+    InferiorToSuperior = "inferior-to-superior",
+    SuperiorToInferior = "superior-to-inferior",
+    DorsalToVentral = "dorsal-to-ventral",
+    VentralToDorsal = "ventral-to-dorsal",
+    DorsalToPalmar = "dorsal-to-palmar",
+    PalmarToDorsal = "palmar-to-dorsal",
+    DorsalToPlantar = "dorsal-to-plantar",
+    PlantarToDorsal = "plantar-to-dorsal",
+    RostralToCaudal = "rostral-to-caudal",
+    CaudalToRostral = "caudal-to-rostral",
+    CranialToCaudal = "cranial-to-caudal",
+    CaudalToCranial = "caudal-to-cranial",
+    ProximalToDistal = "proximal-to-distal",
+    DistalToProximal = "distal-to-proximal"
+}
+/**
+ * Anatomical orientation specification for spatial axes.
+ */
+export interface AnatomicalOrientation {
+    readonly type: "anatomical";
+    readonly value: AnatomicalOrientationValues;
+}
+/**
+ * Create an anatomical orientation object.
+ */
+export declare function createAnatomicalOrientation(value: AnatomicalOrientationValues): AnatomicalOrientation;
+/**
+ * LPS (Left-Posterior-Superior) coordinate system orientations.
+ * In LPS, the axes increase from:
+ * - X: right-to-left (L = Left)
+ * - Y: anterior-to-posterior (P = Posterior)
+ * - Z: inferior-to-superior (S = Superior)
+ * This is the standard coordinate system used by ITK and many medical imaging applications.
+ */
+export declare const LPS: Record<string, AnatomicalOrientation>;
+/**
+ * RAS (Right-Anterior-Superior) coordinate system orientations.
+ * In RAS, the axes increase from:
+ * - X: left-to-right (R = Right)
+ * - Y: posterior-to-anterior (A = Anterior)
+ * - Z: inferior-to-superior (S = Superior)
+ * This coordinate system is commonly used in neuroimaging applications like FreeSurfer and FSL.
+ */
+export declare const RAS: Record<string, AnatomicalOrientation>;
+/**
+ * Convert ITK LPS coordinate system to anatomical orientation.
+ *
+ * ITK uses the LPS (Left-Posterior-Superior) coordinate system by default.
+ * In LPS, the axes increase from:
+ * - X: right-to-left (L = Left)
+ * - Y: anterior-to-posterior (P = Posterior)
+ * - Z: inferior-to-superior (S = Superior)
+ *
+ * @param axisName - The axis name ('x', 'y', or 'z')
+ * @returns The corresponding anatomical orientation, or undefined for non-spatial axes
+ */
+export declare function itkLpsToAnatomicalOrientation(axisName: string): AnatomicalOrientation | undefined;
+/**
+ * Check if RFC 4 is enabled in the list of enabled RFCs.
+ */
+export declare function isRfc4Enabled(enabledRfcs?: number[]): boolean;
+/**
+ * Add anatomical orientation to an axis object.
+ *
+ * @param axisDict - The axis object to modify
+ * @param orientation - The anatomical orientation to add
+ * @returns The modified axis object
+ */
+export declare function addAnatomicalOrientationToAxis(axisDict: Record<string, unknown>, orientation: AnatomicalOrientation): Record<string, unknown>;
+/**
+ * Remove anatomical orientation from an axis object.
+ *
+ * @param axisDict - The axis object to modify
+ * @returns The modified axis object
+ */
+export declare function removeAnatomicalOrientationFromAxis(axisDict: Record<string, unknown>): Record<string, unknown>;
+//# sourceMappingURL=rfc4.d.ts.map

package/script/types/rfc4.d.ts.map

@@ -0,0 +1 @@
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package/script/types/rfc4.js

@@ -0,0 +1,143 @@
+"use strict";
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+/**
+ * RFC 4 implementation for anatomical orientation in OME-NGFF.
+ *
+ * This module implements RFC 4 which adds anatomical orientation support
+ * to OME-NGFF axes, based on the LinkML schema.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RAS = exports.LPS = exports.AnatomicalOrientationValues = void 0;
+exports.createAnatomicalOrientation = createAnatomicalOrientation;
+exports.itkLpsToAnatomicalOrientation = itkLpsToAnatomicalOrientation;
+exports.isRfc4Enabled = isRfc4Enabled;
+exports.addAnatomicalOrientationToAxis = addAnatomicalOrientationToAxis;
+exports.removeAnatomicalOrientationFromAxis = removeAnatomicalOrientationFromAxis;
+/**
+ * Anatomical orientation refers to the specific arrangement and directional
+ * alignment of anatomical structures within an imaging dataset. It is crucial
+ * for ensuring accurate alignment and comparison of images to anatomical atlases,
+ * facilitating consistent analysis and interpretation of biological data.
+ */
+var AnatomicalOrientationValues;
+(function (AnatomicalOrientationValues) {
+    // Describes the directional orientation from the left side to the right lateral side of an anatomical structure or body
+    AnatomicalOrientationValues["LeftToRight"] = "left-to-right";
+    // Describes the directional orientation from the right side to the left lateral side of an anatomical structure or body
+    AnatomicalOrientationValues["RightToLeft"] = "right-to-left";
+    // Describes the directional orientation from the front (anterior) to the back (posterior) of an anatomical structure or body
+    AnatomicalOrientationValues["AnteriorToPosterior"] = "anterior-to-posterior";
+    // Describes the directional orientation from the back (posterior) to the front (anterior) of an anatomical structure or body
+    AnatomicalOrientationValues["PosteriorToAnterior"] = "posterior-to-anterior";
+    // Describes the directional orientation from below (inferior) to above (superior) in an anatomical structure or body
+    AnatomicalOrientationValues["InferiorToSuperior"] = "inferior-to-superior";
+    // Describes the directional orientation from above (superior) to below (inferior) in an anatomical structure or body
+    AnatomicalOrientationValues["SuperiorToInferior"] = "superior-to-inferior";
+    // Describes the directional orientation from the top/upper (dorsal) to the belly/lower (ventral) in an anatomical structure or body
+    AnatomicalOrientationValues["DorsalToVentral"] = "dorsal-to-ventral";
+    // Describes the directional orientation from the belly/lower (ventral) to the top/upper (dorsal) in an anatomical structure or body
+    AnatomicalOrientationValues["VentralToDorsal"] = "ventral-to-dorsal";
+    // Describes the directional orientation from the top/upper (dorsal) to the palm of the hand (palmar) in a body
+    AnatomicalOrientationValues["DorsalToPalmar"] = "dorsal-to-palmar";
+    // Describes the directional orientation from the palm of the hand (palmar) to the top/upper (dorsal) in a body
+    AnatomicalOrientationValues["PalmarToDorsal"] = "palmar-to-dorsal";
+    // Describes the directional orientation from the top/upper (dorsal) to the sole of the foot (plantar) in a body
+    AnatomicalOrientationValues["DorsalToPlantar"] = "dorsal-to-plantar";
+    // Describes the directional orientation from the sole of the foot (plantar) to the top/upper (dorsal) in a body
+    AnatomicalOrientationValues["PlantarToDorsal"] = "plantar-to-dorsal";
+    // Describes the directional orientation from the nasal (rostral) to the tail (caudal) end of an anatomical structure, typically used in reference to the central nervous system
+    AnatomicalOrientationValues["RostralToCaudal"] = "rostral-to-caudal";
+    // Describes the directional orientation from the tail (caudal) to the nasal (rostral) end of an anatomical structure, typically used in reference to the central nervous system
+    AnatomicalOrientationValues["CaudalToRostral"] = "caudal-to-rostral";
+    // Describes the directional orientation from the head (cranial) to the tail (caudal) end of an anatomical structure or body
+    AnatomicalOrientationValues["CranialToCaudal"] = "cranial-to-caudal";
+    // Describes the directional orientation from the tail (caudal) to the head (cranial) end of an anatomical structure or body
+    AnatomicalOrientationValues["CaudalToCranial"] = "caudal-to-cranial";
+    // Describes the directional orientation from the center of the body to the periphery of an anatomical structure or limb
+    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";
+})(AnatomicalOrientationValues || (exports.AnatomicalOrientationValues = AnatomicalOrientationValues = {}));
+/**
+ * Create an anatomical orientation object.
+ */
+function createAnatomicalOrientation(value) {
+    return {
+        type: "anatomical",
+        value,
+    };
+}
+/**
+ * LPS (Left-Posterior-Superior) coordinate system orientations.
+ * In LPS, the axes increase from:
+ * - X: right-to-left (L = Left)
+ * - Y: anterior-to-posterior (P = Posterior)
+ * - Z: inferior-to-superior (S = Superior)
+ * This is the standard coordinate system used by ITK and many medical imaging applications.
+ */
+exports.LPS = {
+    x: createAnatomicalOrientation(AnatomicalOrientationValues.RightToLeft),
+    y: createAnatomicalOrientation(AnatomicalOrientationValues.AnteriorToPosterior),
+    z: createAnatomicalOrientation(AnatomicalOrientationValues.InferiorToSuperior),
+};
+/**
+ * RAS (Right-Anterior-Superior) coordinate system orientations.
+ * In RAS, the axes increase from:
+ * - X: left-to-right (R = Right)
+ * - Y: posterior-to-anterior (A = Anterior)
+ * - Z: inferior-to-superior (S = Superior)
+ * This coordinate system is commonly used in neuroimaging applications like FreeSurfer and FSL.
+ */
+exports.RAS = {
+    x: createAnatomicalOrientation(AnatomicalOrientationValues.LeftToRight),
+    y: createAnatomicalOrientation(AnatomicalOrientationValues.PosteriorToAnterior),
+    z: createAnatomicalOrientation(AnatomicalOrientationValues.InferiorToSuperior),
+};
+/**
+ * Convert ITK LPS coordinate system to anatomical orientation.
+ *
+ * ITK uses the LPS (Left-Posterior-Superior) coordinate system by default.
+ * In LPS, the axes increase from:
+ * - X: right-to-left (L = Left)
+ * - Y: anterior-to-posterior (P = Posterior)
+ * - Z: inferior-to-superior (S = Superior)
+ *
+ * @param axisName - The axis name ('x', 'y', or 'z')
+ * @returns The corresponding anatomical orientation, or undefined for non-spatial axes
+ */
+function itkLpsToAnatomicalOrientation(axisName) {
+    return exports.LPS[axisName];
+}
+/**
+ * Check if RFC 4 is enabled in the list of enabled RFCs.
+ */
+function isRfc4Enabled(enabledRfcs) {
+    return enabledRfcs !== undefined && enabledRfcs.includes(4);
+}
+/**
+ * Add anatomical orientation to an axis object.
+ *
+ * @param axisDict - The axis object to modify
+ * @param orientation - The anatomical orientation to add
+ * @returns The modified axis object
+ */
+function addAnatomicalOrientationToAxis(axisDict, orientation) {
+    return {
+        ...axisDict,
+        orientation: {
+            type: orientation.type,
+            value: orientation.value,
+        },
+    };
+}
+/**
+ * Remove anatomical orientation from an axis object.
+ *
+ * @param axisDict - The axis object to modify
+ * @returns The modified axis object
+ */
+function removeAnatomicalOrientationFromAxis(axisDict) {
+    const { orientation: _orientation, ...rest } = axisDict;
+    return rest;
+}

package/script/types/units.d.ts

@@ -1,6 +1,6 @@
 export type SupportedDims = "c" | "x" | "y" | "z" | "t";
 export type SpatialDims = "x" | "y" | "z";
-export type AxesType = "time" | "space" | "channel";
+export type AxesType = "time" | "space" | "channel" | "array" | "coordinate" | "displacement";
 export type SpaceUnits = "angstrom" | "attometer" | "centimeter" | "decimeter" | "exameter" | "femtometer" | "foot" | "gigameter" | "hectometer" | "inch" | "kilometer" | "megameter" | "meter" | "micrometer" | "mile" | "millimeter" | "nanometer" | "parsec" | "petameter" | "picometer" | "terameter" | "yard" | "yoctometer" | "yottameter" | "zeptometer" | "zettameter";
 export type TimeUnits = "attosecond" | "centisecond" | "day" | "decisecond" | "exasecond" | "femtosecond" | "gigasecond" | "hectosecond" | "hour" | "kilosecond" | "megasecond" | "microsecond" | "millisecond" | "minute" | "nanosecond" | "petasecond" | "picosecond" | "second" | "terasecond" | "yoctosecond" | "yottasecond" | "zeptosecond" | "zettasecond";
 export type Units = SpaceUnits | TimeUnits;

package/script/types/units.d.ts.map

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package/script/types/zarr_metadata.d.ts

@@ -21,18 +21,25 @@ export interface Dataset {
     coordinateTransformations: Transform[];
 }
 export interface OmeroWindow {
-    min: number;
-    max: number;
-    start: number;
-    end: number;
+    min?: number;
+    max?: number;
+    start?: number;
+    end?: number;
 }
 export interface OmeroChannel {
     color: string;
     window: OmeroWindow;
-    label: string | undefined;
+    label?: string;
+    active?: boolean;
 }
 export interface Omero {
     channels: OmeroChannel[];
+    version?: string;
+}
+export interface MethodMetadata {
+    description: string;
+    method: string;
+    version: string;
 }
 export interface Metadata {
     axes: Axis[];
@@ -41,6 +48,8 @@ export interface Metadata {
     omero: Omero | undefined;
     name: string;
     version: string;
+    type?: string;
+    metadata?: MethodMetadata;
 }
 export declare function validateColor(color: string): void;
 export declare function createScale(scale: number[]): Scale;

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package/script/utils/create_queue.d.ts

@@ -0,0 +1,6 @@
+export type ChunkQueue = {
+    add(fn: () => Promise<void>): void;
+    onIdle(): Promise<void>;
+};
+export declare function createQueue(): ChunkQueue;
+//# sourceMappingURL=create_queue.d.ts.map

package/script/utils/create_queue.d.ts.map

@@ -0,0 +1 @@
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