@fideus-labs/ngff-zarr 0.10.0 → 0.12.0

package/esm/browser-mod.d.ts

@@ -1,26 +1,29 @@
-export * from "./types/units.js";
-export * from "./types/methods.js";
-export * from "./types/array_interface.js";
-export * from "./types/zarr_metadata.js";
-export * from "./types/ngff_image.js";
-export * from "./types/multiscales.js";
-export * from "./schemas/units.js";
+export { type ChunkCache, fromNgffZarr, type FromNgffZarrOptions, type MemoryStore, } from "./io/from_ngff_zarr-browser.js";
+export { itkImageToNgffImage, type ItkImageToNgffImageOptions, } from "./io/itk_image_to_ngff_image.js";
+export { dataTypeToComponentType, ngffImageToItkImage, type NgffImageToItkImageOptions, } from "./io/ngff_image_to_itk_image.js";
+export type { MemoryStoreToZipOptions } from "./io/rfc9_zip.js";
+export { getZipFileCompressionMethod, getZipFileList, memoryStoreToZip, orderFilesForRfc9, readOzxVersion, } from "./io/rfc9_zip.js";
+export { isOzxPath, toNgffZarr, type ToNgffZarrOptions, toNgffZarrOzx, type ToNgffZarrOzxOptions, } from "./io/to_ngff_zarr-browser.js";
+export * from "./process/to_multiscales-browser.js";
 export * from "./schemas/methods.js";
-export * from "./schemas/zarr_metadata.js";
-export * from "./schemas/ngff_image.js";
 export * from "./schemas/multiscales.js";
-export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
-export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
-export { getMethodMetadata } from "./utils/method_metadata.js";
-export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, terminateOmeroWorkerPool, } from "./utils/compute_omero.js";
+export * from "./schemas/ngff_image.js";
+export * from "./schemas/units.js";
+export * from "./schemas/zarr_metadata.js";
+export * from "./types/array_interface.js";
+export * from "./types/methods.js";
+export * from "./types/multiscales.js";
+export * from "./types/ngff_image.js";
+export * from "./types/units.js";
+export * from "./types/zarr_metadata.js";
+export type { ZarrCodec } from "./utils/codecs.js";
+export { bytesOnlyCodecs, defaultCodecs } from "./utils/codecs.js";
 export type { ComputeOmeroFromMultiscalesOptions, ComputeOmeroOptions, } from "./utils/compute_omero.js";
-export { buildOmeroFromAccumulators, computeChannelStatistics, createAccumulator, extractChannel, finalizeStatistics, QUANTILE_SAMPLE_SIZE, updateAccumulator, validateQuantiles, } from "./utils/compute_omero-shared.js";
+export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, terminateOmeroWorkerPool, } from "./utils/compute_omero.js";
 export type { ChannelStatisticsAccumulator } from "./utils/compute_omero-shared.js";
+export { buildOmeroFromAccumulators, computeChannelStatistics, createAccumulator, extractChannel, finalizeStatistics, QUANTILE_SAMPLE_SIZE, updateAccumulator, validateQuantiles, } from "./utils/compute_omero-shared.js";
+export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
+export { getMethodMetadata } from "./utils/method_metadata.js";
+export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
 export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
-export { type ChunkCache, fromNgffZarr, type FromNgffZarrOptions, type MemoryStore, } from "./io/from_ngff_zarr-browser.js";
-export { isOzxPath, toNgffZarr, type ToNgffZarrOptions, toNgffZarrOzx, type ToNgffZarrOzxOptions, } from "./io/to_ngff_zarr-browser.js";
-export { getZipFileCompressionMethod, getZipFileList, memoryStoreToZip, orderFilesForRfc9, readOzxVersion, } from "./io/rfc9_zip.js";
-export type { MemoryStoreToZipOptions } from "./io/rfc9_zip.js";
-export * from "./process/to_multiscales-browser.js";
-export { itkImageToNgffImage, type ItkImageToNgffImageOptions, } from "./io/itk_image_to_ngff_image.js";
 //# sourceMappingURL=browser-mod.d.ts.map

package/esm/browser-mod.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"browser-mod.d.ts","sourceRoot":"","sources":["../src/browser-mod.ts"],"names":[],"mappings":"AAWA,OAAO,EACL,KAAK,UAAU,EACf,YAAY,EACZ,KAAK,mBAAmB,EACxB,KAAK,WAAW,GACjB,MAAM,gCAAgC,CAAC;AAExC,OAAO,EACL,mBAAmB,EACnB,KAAK,0BAA0B,GAChC,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,uBAAuB,EACvB,mBAAmB,EACnB,KAAK,0BAA0B,GAChC,MAAM,iCAAiC,CAAC;AACzC,YAAY,EAAE,uBAAuB,EAAE,MAAM,kBAAkB,CAAC;AAEhE,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,gBAAgB,EAChB,iBAAiB,EACjB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,SAAS,EACT,UAAU,EACV,KAAK,iBAAiB,EACtB,aAAa,EACb,KAAK,oBAAoB,GAC1B,MAAM,8BAA8B,CAAC;AAEtC,cAAc,qCAAqC,CAAC;AACpD,cAAc,sBAAsB,CAAC;AACrC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,kBAAkB,CAAC;AACjC,cAAc,0BAA0B,CAAC;AACzC,YAAY,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AACnD,OAAO,EAAE,eAAe,EAAE,aAAa,EAAE,MAAM,mBAAmB,CAAC;AACnE,YAAY,EACV,kCAAkC,EAClC,mBAAmB,GACpB,MAAM,0BAA0B,CAAC;AAElC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAClC,YAAY,EAAE,4BAA4B,EAAE,MAAM,iCAAiC,CAAC;AAEpF,OAAO,EACL,0BAA0B,EAC1B,wBAAwB,EACxB,iBAAiB,EACjB,cAAc,EACd,kBAAkB,EAClB,oBAAoB,EACpB,iBAAiB,EACjB,iBAAiB,GAClB,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC"}

package/esm/browser-mod.js

@@ -5,34 +5,36 @@
 //
 // The browser versions support MemoryStore (Map) and HTTP/HTTPS URLs (read-only),
 // but not local file paths (which require Node.js/Deno filesystem APIs).
-export * from "./types/units.js";
-export * from "./types/methods.js";
-export * from "./types/array_interface.js";
-export * from "./types/zarr_metadata.js";
-export * from "./types/ngff_image.js";
-export * from "./types/multiscales.js";
-export * from "./schemas/units.js";
-export * from "./schemas/methods.js";
-export * from "./schemas/zarr_metadata.js";
-export * from "./schemas/ngff_image.js";
-export * from "./schemas/multiscales.js";
-export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
-export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
-export { getMethodMetadata } from "./utils/method_metadata.js";
-// OMERO computation with WorkerPool
-export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, terminateOmeroWorkerPool, } from "./utils/compute_omero.js";
-// Shared OMERO computation functions for benchmarking and direct use
-export { buildOmeroFromAccumulators, computeChannelStatistics, createAccumulator, extractChannel, finalizeStatistics, QUANTILE_SAMPLE_SIZE, updateAccumulator, validateQuantiles, } from "./utils/compute_omero-shared.js";
-export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
 // Browser-compatible I/O modules
 // Note: Uses browser-specific versions that don't import @zarrita/storage
 // (which contains Node.js-specific modules like node:fs, node:buffer, node:path)
 export { fromNgffZarr, } from "./io/from_ngff_zarr-browser.js";
-export { isOzxPath, toNgffZarr, toNgffZarrOzx, } from "./io/to_ngff_zarr-browser.js";
+// ITK-Wasm conversion utilities
+export { itkImageToNgffImage, } from "./io/itk_image_to_ngff_image.js";
+export { dataTypeToComponentType, ngffImageToItkImage, } from "./io/ngff_image_to_itk_image.js";
 // RFC-9 exports
 export { getZipFileCompressionMethod, getZipFileList, memoryStoreToZip, orderFilesForRfc9, readOzxVersion, } from "./io/rfc9_zip.js";
+export { isOzxPath, toNgffZarr, toNgffZarrOzx, } from "./io/to_ngff_zarr-browser.js";
 // Browser-compatible processing modules
 export * from "./process/to_multiscales-browser.js";
-// ITK-Wasm conversion utilities
-export { itkImageToNgffImage, } from "./io/itk_image_to_ngff_image.js";
+export * from "./schemas/methods.js";
+export * from "./schemas/multiscales.js";
+export * from "./schemas/ngff_image.js";
+export * from "./schemas/units.js";
+export * from "./schemas/zarr_metadata.js";
+export * from "./types/array_interface.js";
+export * from "./types/methods.js";
+export * from "./types/multiscales.js";
+export * from "./types/ngff_image.js";
+export * from "./types/units.js";
+export * from "./types/zarr_metadata.js";
+export { bytesOnlyCodecs, defaultCodecs } from "./utils/codecs.js";
+// OMERO computation with WorkerPool
+export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, terminateOmeroWorkerPool, } from "./utils/compute_omero.js";
+// Shared OMERO computation functions for benchmarking and direct use
+export { buildOmeroFromAccumulators, computeChannelStatistics, createAccumulator, extractChannel, finalizeStatistics, QUANTILE_SAMPLE_SIZE, updateAccumulator, validateQuantiles, } from "./utils/compute_omero-shared.js";
+export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
+export { getMethodMetadata } from "./utils/method_metadata.js";
+export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
+export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
 //# sourceMappingURL=browser-mod.js.map

package/esm/browser-mod.js.map

@@ -1 +1 @@
-{"version":3,"file":"browser-mod.js","sourceRoot":"","sources":["../src/browser-mod.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,oCAAoC;AACpC,wEAAwE;AACxE,EAAE;AACF,kFAAkF;AAClF,yEAAyE;AACzE,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AAEvC,cAAc,oBAAoB,CAAC;AACnC,cAAc,sBAAsB,CAAC;AACrC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,oCAAoC;AACpC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAMlC,qEAAqE;AACrE,OAAO,EACL,0BAA0B,EAC1B,wBAAwB,EACxB,iBAAiB,EACjB,cAAc,EACd,kBAAkB,EAClB,oBAAoB,EACpB,iBAAiB,EACjB,iBAAiB,GAClB,MAAM,iCAAiC,CAAC;AAEzC,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AAE/E,iCAAiC;AACjC,0EAA0E;AAC1E,iFAAiF;AACjF,OAAO,EAEL,YAAY,GAGb,MAAM,gCAAgC,CAAC;AACxC,OAAO,EACL,SAAS,EACT,UAAU,EAEV,aAAa,GAEd,MAAM,8BAA8B,CAAC;AAEtC,gBAAgB;AAChB,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,gBAAgB,EAChB,iBAAiB,EACjB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAG1B,wCAAwC;AACxC,cAAc,qCAAqC,CAAC;AAEpD,gCAAgC;AAChC,OAAO,EACL,mBAAmB,GAEpB,MAAM,iCAAiC,CAAC"}
+{"version":3,"file":"browser-mod.js","sourceRoot":"","sources":["../src/browser-mod.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,oCAAoC;AACpC,wEAAwE;AACxE,EAAE;AACF,kFAAkF;AAClF,yEAAyE;AAEzE,iCAAiC;AACjC,0EAA0E;AAC1E,iFAAiF;AACjF,OAAO,EAEL,YAAY,GAGb,MAAM,gCAAgC,CAAC;AACxC,gCAAgC;AAChC,OAAO,EACL,mBAAmB,GAEpB,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,uBAAuB,EACvB,mBAAmB,GAEpB,MAAM,iCAAiC,CAAC;AAEzC,gBAAgB;AAChB,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,gBAAgB,EAChB,iBAAiB,EACjB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,SAAS,EACT,UAAU,EAEV,aAAa,GAEd,MAAM,8BAA8B,CAAC;AACtC,wCAAwC;AACxC,cAAc,qCAAqC,CAAC;AACpD,cAAc,sBAAsB,CAAC;AACrC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,kBAAkB,CAAC;AACjC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EAAE,eAAe,EAAE,aAAa,EAAE,MAAM,mBAAmB,CAAC;AAKnE,oCAAoC;AACpC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAElC,qEAAqE;AACrE,OAAO,EACL,0BAA0B,EAC1B,wBAAwB,EACxB,iBAAiB,EACjB,cAAc,EACd,kBAAkB,EAClB,oBAAoB,EACpB,iBAAiB,EACjB,iBAAiB,GAClB,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC"}

package/esm/io/itk_image_to_ngff_image.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"itk_image_to_ngff_image.d.ts","sourceRoot":"","sources":["../../src/io/itk_image_to_ngff_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,UAAU,CAAC;AAKtC,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAMnD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,wBAAwB,CAAC,EAAE,OAAO,CAAC;IAEnC;;;OAGG;IACH,IAAI,CAAC,EAAE,MAAM,CAAC;IAEd;;;;;OAKG;IACH,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CAC5B;AAED;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,KAAK,EACf,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,SAAS,CAAC,CAoIpB"}
+{"version":3,"file":"itk_image_to_ngff_image.d.ts","sourceRoot":"","sources":["../../src/io/itk_image_to_ngff_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,UAAU,CAAC;AAKtC,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AASnD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,wBAAwB,CAAC,EAAE,OAAO,CAAC;IAEnC;;;OAGG;IACH,IAAI,CAAC,EAAE,MAAM,CAAC;IAEd;;;;;OAKG;IACH,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CAC5B;AA2BD;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,KAAK,EACf,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,SAAS,CAAC,CA0KpB"}

package/esm/io/itk_image_to_ngff_image.js

@@ -7,9 +7,30 @@ import * as zarr from "zarrita";
 // Import the get_strides function from zarrita utilities
 import { _zarrita_internal_get_strides as getStrides } from "zarrita";
 import { NgffImage } from "../types/ngff_image.js";
-import { itkLpsToAnatomicalOrientation } from "../types/rfc4.js";
+import { itkDirectionToAnatomicalOrientation, itkLpsToAnatomicalOrientation, } from "../types/rfc4.js";
 import { defaultCodecs } from "../utils/codecs.js";
 import { zarrSet } from "../utils/worker_pool.js";
+/**
+ * Check whether an ITK direction matrix is the identity matrix.
+ *
+ * When the direction is identity, the image axes align directly with
+ * the physical LPS axes and the simple LPS lookup is sufficient.
+ *
+ * @param direction - Flat (row-major) direction matrix from ITK-Wasm
+ * @param n - Number of spatial dimensions (2 or 3)
+ * @returns `true` if every element matches the identity matrix
+ */
+function isIdentityDirection(direction, n) {
+    for (let row = 0; row < n; row++) {
+        for (let col = 0; col < n; col++) {
+            const expected = row === col ? 1 : 0;
+            if (Number(direction[row * n + col]) !== expected) {
+                return false;
+            }
+        }
+    }
+    return true;
+}
 /**
  * Convert an ITK-Wasm Image to an NgffImage, preserving spatial metadata.
  *
@@ -116,14 +137,50 @@ export async function itkImageToNgffImage(itkImage, options = {}) {
     };
     // Write all data to the zarr array using worker-accelerated set function
     // This handles chunking and encoding automatically
-    await zarrSet(zarrArray, selection, dataChunk); // Add anatomical orientation if requested
+    await zarrSet(zarrArray, selection, dataChunk);
+    // Add anatomical orientation if requested
     let axesOrientations;
     if (addAnatomicalOrientation) {
         axesOrientations = {};
-        for (const dim of spatialDims) {
-            const orientation = itkLpsToAnatomicalOrientation(dim);
-            if (orientation !== undefined) {
-                axesOrientations[dim] = orientation;
+        const direction = itkImage.direction;
+        const nSpatial = spatialDims.length;
+        // Check whether the direction matrix is available and has a
+        // non-identity rotation (permutation or oblique).
+        const hasDirection = direction !== undefined && direction.length > 0;
+        const hasNonIdentityDirection = hasDirection &&
+            !isIdentityDirection(direction, nSpatial);
+        if (hasNonIdentityDirection) {
+            // Use the direction cosine matrix to determine each axis'
+            // anatomical orientation. The direction matrix is stored
+            // row-major as a flat array: direction[row * nSpatial + col].
+            //
+            // spatialDims is in array order (e.g. ["z", "y", "x"]) and
+            // maps to reversed ITK axis indices:
+            //   spatialDims[0] = "z" → ITK axis 2 → direction column 2
+            //   spatialDims[1] = "y" → ITK axis 1 → direction column 1
+            //   spatialDims[2] = "x" → ITK axis 0 → direction column 0
+            //
+            // Column j of the direction matrix contains the LPS-space
+            // direction cosine for ITK axis j.
+            for (let i = 0; i < nSpatial; i++) {
+                const dim = spatialDims[i];
+                // Reverse index: spatialDims[0] → last ITK axis, etc.
+                const itkAxisIndex = nSpatial - 1 - i;
+                // Extract direction column, handling both 2D and 3D cases
+                const col = [];
+                for (let row = 0; row < nSpatial; row++) {
+                    col.push(Number(direction[row * nSpatial + itkAxisIndex]));
+                }
+                axesOrientations[dim] = itkDirectionToAnatomicalOrientation(col);
+            }
+        }
+        else {
+            // Identity direction or no direction: fall back to LPS labels
+            for (const dim of spatialDims) {
+                const orientation = itkLpsToAnatomicalOrientation(dim);
+                if (orientation !== undefined) {
+                    axesOrientations[dim] = orientation;
+                }
             }
         }
     }

package/esm/io/itk_image_to_ngff_image.js.map

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package/esm/io/to_ngff_zarr-browser.d.ts

@@ -14,6 +14,14 @@ export interface ToNgffZarrOptions {
 export interface ToNgffZarrOzxOptions {
     /** List of RFC numbers to enable (e.g., [4] for RFC 4 anatomical orientation) */
     enabledRfcs?: number[] | undefined;
+    /**
+     * Optional progress callback invoked after each chunk is written.
+     * Reports cumulative progress across all scale levels.
+     *
+     * @param completedChunks - Number of chunks written so far
+     * @param totalChunks - Total number of chunks to write across all levels
+     */
+    onProgress?: ((completedChunks: number, totalChunks: number) => void) | undefined;
 }
 /**
  * Browser-compatible version of toNgffZarr.

package/esm/io/to_ngff_zarr-browser.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"to_ngff_zarr-browser.d.ts","sourceRoot":"","sources":["../../src/io/to_ngff_zarr-browser.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAEhC,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAI3D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,6BAA6B,CAAC;AAI/D,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAC;AAE1C,MAAM,WAAW,iBAAiB;IAChC,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC7D;AAED;;;GAGG;AACH,MAAM,WAAW,oBAAoB;IACnC,iFAAiF;IACjF,WAAW,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;IACnC;;;;;;OAMG;IACH,UAAU,CAAC,EACP,CAAC,CAAC,eAAe,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,KAAK,IAAI,CAAC,GACxD,SAAS,CAAC;CACf;AAED;;;;GAIG;AACH,wBAAsB,UAAU,CAC9B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,WAAW,EAAE,WAAW,EACxB,OAAO,GAAE,iBAAsB,GAC9B,OAAO,CAAC,IAAI,CAAC,CAyFf;AA0VD;;;;;;;;;;;;;;;GAeG;AACH,wBAAsB,aAAa,CACjC,WAAW,EAAE,WAAW,EACxB,QAAQ,GAAE,oBAAyB,GAClC,OAAO,CAAC,UAAU,CAAC,CAmBrB"}

package/esm/io/to_ngff_zarr-browser.js

@@ -3,8 +3,8 @@
 // Browser-compatible version of to_ngff_zarr that doesn't import @zarrita/storage
 // (which contains Node.js-specific modules like node:fs, node:buffer, node:path)
 import * as zarr from "zarrita";
-import { createWriteQueue, zarrGet, zarrSet } from "../utils/worker_pool.js";
 import { defaultCodecs } from "../utils/codecs.js";
+import { createWriteQueue, zarrGet, zarrSet } from "../utils/worker_pool.js";
 import { memoryStoreToZip } from "./rfc9_zip.js";
 import { writeMultiscalesToMemoryStore } from "./to_ngff_zarr_ozx_common.js";
 export { isOzxPath } from "./rfc9_zip.js";
@@ -141,7 +141,7 @@ function getTypedArrayConstructor(dtype) {
         throw new Error(`Unsupported data type for typed array: ${dtype}`);
     }
 }
-async function _writeImage(group, image, arrayPath) {
+async function _writeImage(group, image, arrayPath, onProgress) {
     try {
         const chunks = getChunksFromImage(image);
         // Convert LazyArray dtype to zarrita DataType
@@ -156,7 +156,7 @@ async function _writeImage(group, image, arrayPath) {
             fill_value: 0,
             codecs: defaultCodecs(zarrDataType),
         });
-        await _writeArrayData(zarrArray, image);
+        await _writeArrayData(zarrArray, image, onProgress);
     }
     catch (error) {
         throw new Error(`Failed to write image array: ${error instanceof Error ? error.message : String(error)}`);
@@ -169,7 +169,7 @@ function getChunksFromImage(image) {
     }
     return image.data.shape.map((dim) => Math.min(dim, 1024));
 }
-async function _writeArrayData(zarrArray, image) {
+async function _writeArrayData(zarrArray, image, onProgress) {
     try {
         // Get array shape for chunk calculation - we don't need the full data here
         const shape = image.data.shape;
@@ -184,7 +184,7 @@ async function _writeArrayData(zarrArray, image) {
             });
         }
         // Wait for all chunks to be written
-        await writeQueue.onIdle();
+        await writeQueue.onIdle(onProgress);
     }
     catch (error) {
         throw new Error(`Failed to write array data: ${error instanceof Error ? error.message : String(error)}`);
@@ -349,7 +349,7 @@ export async function toNgffZarrOzx(multiscales, _options = {}) {
     // Create a memory store to hold the zarr data
     const memoryStore = new Map();
     // Use the shared write function
-    await writeMultiscalesToMemoryStore(memoryStore, multiscales, enabledRfcs, _writeImage);
+    await writeMultiscalesToMemoryStore(memoryStore, multiscales, enabledRfcs, _writeImage, _options.onProgress ?? null);
     // Convert the memory store to ZIP data
     const zipData = memoryStoreToZip(memoryStore, { version: "0.5" });
     return zipData;

package/esm/io/to_ngff_zarr-browser.js.map

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package/esm/io/to_ngff_zarr.d.ts

@@ -21,6 +21,14 @@ export interface ToNgffZarrOptions {
 export interface ToNgffZarrOzxOptions {
     /** List of RFC numbers to enable (e.g., [4] for RFC 4 anatomical orientation) */
     enabledRfcs?: number[] | undefined;
+    /**
+     * Optional progress callback invoked after each chunk is written.
+     * Reports cumulative progress across all scale levels.
+     *
+     * @param completedChunks - Number of chunks written so far
+     * @param totalChunks - Total number of chunks to write across all levels
+     */
+    onProgress?: ((completedChunks: number, totalChunks: number) => void) | undefined;
 }
 /**
  * Write multiscales data to an OME-Zarr store.

package/esm/io/to_ngff_zarr.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"to_ngff_zarr.d.ts","sourceRoot":"","sources":["../../src/io/to_ngff_zarr.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAE3D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AASvD,MAAM,WAAW,iBAAiB;IAChC,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB;;;;;OAKG;IACH,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC5D,iFAAiF;IACjF,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;CACxB;AAED;;;GAGG;AACH,MAAM,WAAW,oBAAoB;IACnC,iFAAiF;IACjF,WAAW,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;CACpC;AAED;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AACH,wBAAsB,UAAU,CAC9B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,WAAW,EAAE,WAAW,EACxB,OAAO,GAAE,iBAAsB,GAC9B,OAAO,CAAC,IAAI,CAAC,CAwIf;AAuVD;;;;;;;;;;;;;;;;;;;GAmBG;AACH,wBAAsB,aAAa,CACjC,IAAI,EAAE,MAAM,EACZ,WAAW,EAAE,WAAW,EACxB,OAAO,GAAE,oBAAyB,GACjC,OAAO,CAAC,IAAI,CAAC,CAyBf;AAED;;;;;;;;;;;;GAYG;AACH,wBAAsB,iBAAiB,CACrC,WAAW,EAAE,WAAW,EACxB,OAAO,GAAE,oBAAyB,GACjC,OAAO,CAAC,UAAU,CAAC,CAerB"}
+{"version":3,"file":"to_ngff_zarr.d.ts","sourceRoot":"","sources":["../../src/io/to_ngff_zarr.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAEhC,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAI3D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAOvD,MAAM,WAAW,iBAAiB;IAChC,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB;;;;;OAKG;IACH,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC5D,iFAAiF;IACjF,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;CACxB;AAED;;;GAGG;AACH,MAAM,WAAW,oBAAoB;IACnC,iFAAiF;IACjF,WAAW,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;IACnC;;;;;;OAMG;IACH,UAAU,CAAC,EACP,CAAC,CAAC,eAAe,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,KAAK,IAAI,CAAC,GACxD,SAAS,CAAC;CACf;AAED;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AACH,wBAAsB,UAAU,CAC9B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,WAAW,EAAE,WAAW,EACxB,OAAO,GAAE,iBAAsB,GAC9B,OAAO,CAAC,IAAI,CAAC,CAwIf;AA0VD;;;;;;;;;;;;;;;;;;;GAmBG;AACH,wBAAsB,aAAa,CACjC,IAAI,EAAE,MAAM,EACZ,WAAW,EAAE,WAAW,EACxB,OAAO,GAAE,oBAAyB,GACjC,OAAO,CAAC,IAAI,CAAC,CAyBf;AAED;;;;;;;;;;;;GAYG;AACH,wBAAsB,iBAAiB,CACrC,WAAW,EAAE,WAAW,EACxB,OAAO,GAAE,oBAAyB,GACjC,OAAO,CAAC,UAAU,CAAC,CAoBrB"}

package/esm/io/to_ngff_zarr.js

@@ -1,8 +1,8 @@
 // SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
 // SPDX-License-Identifier: MIT
 import * as zarr from "zarrita";
-import { createWriteQueue, zarrGet, zarrSet } from "../utils/worker_pool.js";
 import { defaultCodecs } from "../utils/codecs.js";
+import { createWriteQueue, zarrGet, zarrSet } from "../utils/worker_pool.js";
 import { isOzxPath, memoryStoreToZip } from "./rfc9_zip.js";
 import { processAxesForRfcs, writeMultiscalesToMemoryStore, } from "./to_ngff_zarr_ozx_common.js";
 /**
@@ -192,7 +192,7 @@ function getTypedArrayConstructor(dtype) {
         throw new Error(`Unsupported data type for typed array: ${dtype}`);
     }
 }
-async function _writeImage(group, image, arrayPath) {
+async function _writeImage(group, image, arrayPath, onProgress) {
     try {
         const chunks = getChunksFromImage(image);
         // Convert LazyArray dtype to zarrita DataType
@@ -207,7 +207,7 @@ async function _writeImage(group, image, arrayPath) {
             fill_value: 0,
             codecs: defaultCodecs(zarrDataType),
         });
-        await _writeArrayData(zarrArray, image);
+        await _writeArrayData(zarrArray, image, onProgress);
     }
     catch (error) {
         throw new Error(`Failed to write image array: ${error instanceof Error ? error.message : String(error)}`);
@@ -220,7 +220,7 @@ function getChunksFromImage(image) {
     }
     return image.data.shape.map((dim) => Math.min(dim, 1024));
 }
-async function _writeArrayData(zarrArray, image) {
+async function _writeArrayData(zarrArray, image, onProgress) {
     try {
         // Get array shape for chunk calculation - we don't need the full data here
         const shape = image.data.shape;
@@ -235,7 +235,7 @@ async function _writeArrayData(zarrArray, image) {
             });
         }
         // Wait for all chunks to be written
-        await writeQueue.onIdle();
+        await writeQueue.onIdle(onProgress);
     }
     catch (error) {
         throw new Error(`Failed to write array data: ${error instanceof Error ? error.message : String(error)}`);
@@ -438,7 +438,7 @@ export async function toNgffZarrOzxData(multiscales, options = {}) {
     // Write to the memory store using existing toNgffZarr logic
     // but we need to inline the core logic since toNgffZarr would
     // try to detect .ozx again
-    await _writeToMemoryStore(memoryStore, multiscales, enabledRfcs);
+    await _writeToMemoryStore(memoryStore, multiscales, enabledRfcs, options.onProgress ?? null);
     // Convert the memory store to ZIP data
     const zipData = memoryStoreToZip(memoryStore, { version: "0.5" });
     return zipData;
@@ -447,7 +447,7 @@ export async function toNgffZarrOzxData(multiscales, options = {}) {
  * Internal function to write multiscales to a memory store.
  * Used by toNgffZarrOzxData to avoid recursion with toNgffZarr.
  */
-async function _writeToMemoryStore(store, multiscales, enabledRfcs) {
-    await writeMultiscalesToMemoryStore(store, multiscales, enabledRfcs, _writeImage);
+async function _writeToMemoryStore(store, multiscales, enabledRfcs, onProgress) {
+    await writeMultiscalesToMemoryStore(store, multiscales, enabledRfcs, _writeImage, onProgress);
 }
 //# sourceMappingURL=to_ngff_zarr.js.map

package/esm/io/to_ngff_zarr.js.map

@@ -1 +1 @@
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package/esm/io/to_ngff_zarr_ozx_common.d.ts

@@ -46,6 +46,8 @@ export declare function createRfc9RootAttributes(multiscalesMetadata: Record<str
  * @param multiscales - Multiscales data to write
  * @param enabledRfcs - Optional list of RFC numbers to enable
  * @param writeImage - Function to write individual images
+ * @param onProgress - Optional progress callback for cumulative chunk
+ *   progress across all scale levels
  */
-export declare function writeMultiscalesToMemoryStore(store: MemoryStore, multiscales: Multiscales, enabledRfcs: number[] | undefined, writeImage: (group: zarr.Group<MemoryStore>, image: NgffImage, path: string) => Promise<void>): Promise<void>;
+export declare function writeMultiscalesToMemoryStore(store: MemoryStore, multiscales: Multiscales, enabledRfcs: number[] | undefined, writeImage: (group: zarr.Group<MemoryStore>, image: NgffImage, path: string, onProgress?: ((completedChunks: number, totalChunks: number) => void) | null) => Promise<void>, onProgress?: ((completedChunks: number, totalChunks: number) => void) | null): Promise<void>;
 //# sourceMappingURL=to_ngff_zarr_ozx_common.d.ts.map

package/esm/io/to_ngff_zarr_ozx_common.d.ts.map

@@ -1 +1 @@
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