@fideus-labs/ngff-zarr 0.1.0 → 0.2.0

package/script/methods/itkwasm.js

@@ -30,28 +30,99 @@ const downsample_1 = require("@itk-wasm/downsample");
 const zarr = __importStar(require("zarrita"));
 const ngff_image_js_1 = require("../types/ngff_image.js");
 const SPATIAL_DIMS = ["x", "y", "z"];
+/**
+ * Calculate the incremental factor needed to reach the target size from the previous size.
+ * This ensures exact target sizes when downsampling incrementally.
+ */
+function calculateIncrementalFactor(previousSize, targetSize) {
+    if (targetSize <= 0) {
+        return 1;
+    }
+    // Start with the theoretical factor
+    let factor = Math.floor(Math.ceil(previousSize / (targetSize + 0.5)));
+    // Verify this gives us the right size
+    let actualSize = Math.floor(previousSize / factor);
+    if (actualSize !== targetSize) {
+        // Adjust factor to get exact target
+        factor = Math.max(1, Math.floor(previousSize / targetSize));
+        actualSize = Math.floor(previousSize / factor);
+        // If still not exact, try ceil
+        if (actualSize !== targetSize) {
+            factor = Math.max(1, Math.ceil(previousSize / targetSize));
+        }
+    }
+    return Math.max(1, factor);
+}
 /**
  * Convert dimension scale factors to ITK-Wasm format
+ * This computes the incremental scale factor relative to the previous scale,
+ * not the absolute scale factor from the original image.
+ *
+ * When originalImage and previousImage are provided, calculates the exact
+ * incremental factor needed to reach the target size from the previous size.
+ * This ensures we get exact 1x, 2x, 3x, 4x sizes even with incremental downsampling.
  */
-function dimScaleFactors(dims, scaleFactor, previousDimFactors) {
+function dimScaleFactors(dims, scaleFactor, previousDimFactors, originalImage, previousImage) {
     const dimFactors = {};
     if (typeof scaleFactor === "number") {
-        for (const dim of dims) {
-            if (SPATIAL_DIMS.includes(dim)) {
-                dimFactors[dim] = scaleFactor;
+        if (originalImage !== undefined && previousImage !== undefined) {
+            // Calculate target size: floor(original_size / scale_factor)
+            // Then calculate incremental factor from previous size to target size
+            for (const dim of dims) {
+                if (SPATIAL_DIMS.includes(dim)) {
+                    const dimIndex = originalImage.dims.indexOf(dim);
+                    const originalSize = originalImage.data.shape[dimIndex];
+                    const targetSize = Math.floor(originalSize / scaleFactor);
+                    const prevDimIndex = previousImage.dims.indexOf(dim);
+                    const previousSize = previousImage.data.shape[prevDimIndex];
+                    dimFactors[dim] = calculateIncrementalFactor(previousSize, targetSize);
+                }
+                else {
+                    dimFactors[dim] = 1;
+                }
             }
-            else {
-                dimFactors[dim] = previousDimFactors[dim] || 1;
+        }
+        else {
+            // Fallback to old behavior when images not provided
+            for (const dim of dims) {
+                if (SPATIAL_DIMS.includes(dim)) {
+                    // Divide by previous factor to get incremental scaling
+                    // Use Math.floor to truncate (matching Python's int() behavior)
+                    const incrementalFactor = scaleFactor /
+                        (previousDimFactors[dim] || 1);
+                    dimFactors[dim] = Math.max(1, Math.floor(incrementalFactor));
+                }
+                else {
+                    dimFactors[dim] = previousDimFactors[dim] || 1;
+                }
             }
         }
     }
     else {
-        for (const dim of dims) {
-            if (dim in scaleFactor) {
-                dimFactors[dim] = scaleFactor[dim];
+        if (originalImage !== undefined && previousImage !== undefined) {
+            for (const dim in scaleFactor) {
+                const dimIndex = originalImage.dims.indexOf(dim);
+                const originalSize = originalImage.data.shape[dimIndex];
+                const targetSize = Math.floor(originalSize / scaleFactor[dim]);
+                const prevDimIndex = previousImage.dims.indexOf(dim);
+                const previousSize = previousImage.data.shape[prevDimIndex];
+                dimFactors[dim] = calculateIncrementalFactor(previousSize, targetSize);
             }
-            else {
-                dimFactors[dim] = previousDimFactors[dim] || 1;
+        }
+        else {
+            // Fallback to old behavior when images not provided
+            for (const dim in scaleFactor) {
+                // Divide by previous factor to get incremental scaling
+                // Use Math.floor to truncate (matching Python's int() behavior)
+                const incrementalFactor = scaleFactor[dim] /
+                    (previousDimFactors[dim] || 1);
+                dimFactors[dim] = Math.max(1, Math.floor(incrementalFactor));
+            }
+        }
+        // Add dims not in scale_factor with factor of 1
+        for (const dim of dims) {
+            if (!(dim in dimFactors)) {
+                dimFactors[dim] = 1;
             }
         }
     }
@@ -68,10 +139,8 @@ function updatePreviousDimFactors(scaleFactor, spatialDims, previousDimFactors)
         }
     }
     else {
-        for (const dim of spatialDims) {
-            if (dim in scaleFactor) {
-                updated[dim] = scaleFactor[dim];
-            }
+        for (const dim in scaleFactor) {
+            updated[dim] = scaleFactor[dim];
         }
     }
     return updated;
@@ -86,38 +155,17 @@ function nextScaleMetadata(image, dimFactors, spatialDims) {
         if (spatialDims.includes(dim)) {
             const factor = dimFactors[dim];
             scale[dim] = image.scale[dim] * factor;
+            // Add offset to account for pixel center shift when downsampling
             translation[dim] = image.translation[dim] +
                 0.5 * (factor - 1) * image.scale[dim];
         }
         else {
-            // Only copy non-spatial dimensions if they exist in the source
-            if (dim in image.scale) {
-                scale[dim] = image.scale[dim];
-            }
-            if (dim in image.translation) {
-                translation[dim] = image.translation[dim];
-            }
+            scale[dim] = image.scale[dim];
+            translation[dim] = image.translation[dim];
         }
     }
     return [translation, scale];
 }
-/**
- * Compute Gaussian kernel sigma values in pixel units for downsampling.
- *
- * Formula: sigma = sqrt((k^2 - 1^2)/(2*sqrt(2*ln(2)))^2)
- *
- * Reference:
- * - https://discourse.itk.org/t/resampling-to-isotropic-signal-processing-theory/1403/16
- * - https://doi.org/10.1007/978-3-319-24571-3_81
- * - http://discovery.ucl.ac.uk/1469251/1/scale-factor-point-5.pdf
- *
- * @param shrinkFactors - Shrink ratio along each axis
- * @returns Standard deviation of Gaussian kernel along each axis
- */
-function computeSigma(shrinkFactors) {
-    const denominator = Math.pow(2 * Math.sqrt(2 * Math.log(2)), 2);
-    return shrinkFactors.map((factor) => Math.sqrt((factor * factor - 1) / denominator));
-}
 /**
  * Convert zarr array to ITK-Wasm Image format
  * If isVector is true, ensures "c" dimension is last by transposing if needed
@@ -158,6 +206,9 @@ async function zarrToItkImage(array, dims, isVector = false) {
     // For vector images, the last dimension is the component count, not a spatial dimension
     const spatialShape = isVector ? shape.slice(0, -1) : shape;
     const components = isVector ? shape[shape.length - 1] : 1;
+    // ITK expects size in physical space order [x, y, z], but spatialShape is in array order [z, y, x]
+    // So we need to reverse it
+    const itkSize = [...spatialShape].reverse();
     // Create ITK-Wasm image
     const itkImage = {
         imageType: {
@@ -170,8 +221,8 @@ async function zarrToItkImage(array, dims, isVector = false) {
         origin: spatialShape.map(() => 0),
         spacing: spatialShape.map(() => 1),
         direction: createIdentityMatrix(spatialShape.length),
-        size: spatialShape,
-        data,
+        size: itkSize,
+        data: data,
         metadata: new Map(),
     };
     return itkImage;
@@ -204,12 +255,6 @@ function copyTypedArray(data) {
     else if (data instanceof Int32Array) {
         return new Int32Array(data);
     }
-    else if (data instanceof BigInt64Array) {
-        return new BigInt64Array(data);
-    }
-    else if (data instanceof BigUint64Array) {
-        return new BigUint64Array(data);
-    }
     else {
         // Convert to Float32Array as fallback
         return new Float32Array(data);
@@ -230,23 +275,17 @@ function transposeArray(data, shape, permutation, componentType) {
         case "int8":
             output = new Int8Array(totalSize);
             break;
-        case "int16":
-            output = new Int16Array(totalSize);
-            break;
         case "uint16":
             output = new Uint16Array(totalSize);
             break;
-        case "int32":
-            output = new Int32Array(totalSize);
+        case "int16":
+            output = new Int16Array(totalSize);
             break;
         case "uint32":
             output = new Uint32Array(totalSize);
             break;
-        case "int64":
-            output = new BigInt64Array(totalSize);
-            break;
-        case "uint64":
-            output = new BigUint64Array(totalSize);
+        case "int32":
+            output = new Int32Array(totalSize);
             break;
         case "float64":
             output = new Float64Array(totalSize);
@@ -301,10 +340,6 @@ function getItkComponentType(data) {
         return "uint32";
     if (data instanceof Int32Array)
         return "int32";
-    if (data instanceof BigUint64Array)
-        return "uint64";
-    if (data instanceof BigInt64Array)
-        return "int64";
     if (data instanceof Float64Array)
         return "float64";
     return "float32";
@@ -321,12 +356,25 @@ function createIdentityMatrix(dimension) {
 }
 /**
  * Convert ITK-Wasm Image back to zarr array
+ * Uses the provided store instead of creating a new one
+ *
+ * Important: ITK-Wasm stores size in physical space order [x, y, z], but data in
+ * column-major order (x contiguous). This column-major layout with size [x, y, z]
+ * is equivalent to C-order (row-major) with shape [z, y, x]. We reverse the size
+ * to get the zarr shape and use C-order strides for that reversed shape.
+ *
+ * @param itkImage - The ITK-Wasm image to convert
+ * @param store - The zarr store to write to
+ * @param path - The path within the store
+ * @param chunkShape - The chunk shape (in spatial dimension order, will be adjusted for components)
+ * @param targetDims - The target dimension order (e.g., ["c", "z", "y", "x"])
  */
-async function itkImageToZarr(itkImage, path, chunkShape) {
-    // Use in-memory store
-    const store = new Map();
+async function itkImageToZarr(itkImage, store, path, chunkShape, targetDims) {
     const root = zarr.root(store);
-    // Determine data type
+    if (!itkImage.data) {
+        throw new Error("ITK image data is null or undefined");
+    }
+    // Determine data type - support all ITK TypedArray types
     let dataType;
     if (itkImage.data instanceof Uint8Array) {
         dataType = "uint8";
@@ -334,44 +382,125 @@ async function itkImageToZarr(itkImage, path, chunkShape) {
     else if (itkImage.data instanceof Int8Array) {
         dataType = "int8";
     }
-    else if (itkImage.data instanceof Int16Array) {
-        dataType = "int16";
-    }
     else if (itkImage.data instanceof Uint16Array) {
         dataType = "uint16";
     }
-    else if (itkImage.data instanceof Int32Array) {
-        dataType = "int32";
+    else if (itkImage.data instanceof Int16Array) {
+        dataType = "int16";
     }
     else if (itkImage.data instanceof Uint32Array) {
         dataType = "uint32";
     }
-    else if (itkImage.data instanceof BigInt64Array) {
-        dataType = "int64";
+    else if (itkImage.data instanceof Int32Array) {
+        dataType = "int32";
     }
-    else if (itkImage.data instanceof BigUint64Array) {
-        dataType = "uint64";
+    else if (itkImage.data instanceof Float32Array) {
+        dataType = "float32";
     }
     else if (itkImage.data instanceof Float64Array) {
         dataType = "float64";
     }
-    else if (itkImage.data instanceof Float32Array) {
-        dataType = "float32";
+    else {
+        throw new Error(`Unsupported data type: ${itkImage.data.constructor.name}`);
+    }
+    // ITK stores size/spacing/origin in physical space order [x, y, z],
+    // but the data buffer is in C-order (row-major) which means [z, y, x] indexing.
+    // We need to reverse the size to match the data layout, just like we do for spacing/origin.
+    const shape = [...itkImage.size].reverse();
+    // For vector images, the components are stored in the data but not in the size
+    // The actual data length includes components
+    const components = itkImage.imageType.components || 1;
+    const isVector = components > 1;
+    // Validate data length matches expected shape (including components for vector images)
+    const spatialElements = shape.reduce((a, b) => a * b, 1);
+    const expectedLength = spatialElements * components;
+    if (itkImage.data.length !== expectedLength) {
+        console.error(`[ERROR] Data length mismatch in itkImageToZarr:`);
+        console.error(`  ITK image size (physical order):`, itkImage.size);
+        console.error(`  Shape (reversed):`, shape);
+        console.error(`  Components:`, components);
+        console.error(`  Expected data length:`, expectedLength);
+        console.error(`  Actual data length:`, itkImage.data.length);
+        throw new Error(`Data length (${itkImage.data.length}) doesn't match expected shape ${shape} with ${components} components (${expectedLength} elements)`);
+    }
+    // Determine the final shape and whether we need to transpose
+    // ITK image data has shape [...spatialDimsReversed, components] (with c at end)
+    // If targetDims is provided, we need to match that order
+    let zarrShape;
+    let zarrChunkShape;
+    let finalData = itkImage.data;
+    if (isVector && targetDims) {
+        // Find where "c" should be in targetDims
+        const cIndex = targetDims.indexOf("c");
+        if (cIndex === -1) {
+            throw new Error("Vector image but 'c' not found in targetDims");
+        }
+        // Current shape is [z, y, x, c] (spatial reversed + c at end)
+        // Target shape should match targetDims order
+        const currentShape = [...shape, components];
+        // Build target shape based on targetDims
+        zarrShape = new Array(targetDims.length);
+        const spatialDims = shape.slice(); // [z, y, x]
+        let spatialIdx = 0;
+        for (let i = 0; i < targetDims.length; i++) {
+            if (targetDims[i] === "c") {
+                zarrShape[i] = components;
+            }
+            else {
+                zarrShape[i] = spatialDims[spatialIdx++];
+            }
+        }
+        // If c is not at the end, we need to transpose
+        if (cIndex !== targetDims.length - 1) {
+            // Build permutation: where does each target dim come from in current shape?
+            const permutation = [];
+            spatialIdx = 0;
+            for (let i = 0; i < targetDims.length; i++) {
+                if (targetDims[i] === "c") {
+                    permutation.push(currentShape.length - 1); // c is at end of current
+                }
+                else {
+                    permutation.push(spatialIdx++);
+                }
+            }
+            // Transpose the data
+            finalData = transposeArray(itkImage.data, currentShape, permutation, getItkComponentType(itkImage.data));
+        }
+        // Chunk shape should match zarrShape
+        zarrChunkShape = new Array(zarrShape.length);
+        spatialIdx = 0;
+        for (let i = 0; i < targetDims.length; i++) {
+            if (targetDims[i] === "c") {
+                zarrChunkShape[i] = components;
+            }
+            else {
+                zarrChunkShape[i] = chunkShape[spatialIdx++];
+            }
+        }
     }
     else {
-        dataType = "float32";
+        // No targetDims or not a vector - use default behavior
+        zarrShape = isVector ? [...shape, components] : shape;
+        zarrChunkShape = isVector ? [...chunkShape, components] : chunkShape;
+    }
+    // Chunk shape should match the dimensionality of zarrShape
+    if (zarrChunkShape.length !== zarrShape.length) {
+        throw new Error(`chunkShape length (${zarrChunkShape.length}) must match shape length (${zarrShape.length})`);
     }
     const array = await zarr.create(root.resolve(path), {
-        shape: itkImage.size,
-        chunk_shape: chunkShape,
+        shape: zarrShape,
+        chunk_shape: zarrChunkShape,
         data_type: dataType,
         fill_value: 0,
     });
-    // Write data
-    await zarr.set(array, [], {
-        data: itkImage.data,
-        shape: itkImage.size,
-        stride: calculateStride(itkImage.size),
+    // Write data - preserve the actual data type, don't cast to Float32Array
+    // Shape and stride should match the ITK image size order
+    // Use null for each dimension to select the entire array
+    const selection = zarrShape.map(() => null);
+    await zarr.set(array, selection, {
+        data: finalData,
+        shape: zarrShape,
+        stride: calculateStride(zarrShape),
     });
     return array;
 }
@@ -387,316 +516,115 @@ function calculateStride(shape) {
     return stride;
 }
 /**
- * Process channel-first data by downsampling each channel separately
+ * Perform Gaussian downsampling using ITK-Wasm
  */
-async function downsampleChannelFirst(image, dimFactors, spatialDims, smoothing) {
-    // Get the channel index and count
-    const cIndex = image.dims.indexOf("c");
-    const result = await zarr.get(image.data);
-    const channelCount = result.shape[cIndex];
-    // Process each channel separately
-    const downsampledChannels = [];
-    for (let channelIdx = 0; channelIdx < channelCount; channelIdx++) {
-        // Extract single channel data
-        const channelSlice = extractChannel(result, cIndex, channelIdx);
-        // Create temporary zarr array for this channel
-        const store = new Map();
-        const root = zarr.root(store);
-        const channelDims = image.dims.filter((d) => d !== "c");
-        const channelShape = result.shape.filter((_, i) => i !== cIndex);
-        const chunkShape = channelShape.map((s) => Math.min(s, 256));
-        const channelArray = await zarr.create(root.resolve("channel"), {
-            shape: channelShape,
-            chunk_shape: chunkShape,
-            data_type: getItkComponentType(result.data),
-            fill_value: 0,
-        });
-        await zarr.set(channelArray, [], {
-            data: channelSlice,
-            shape: channelShape,
-            stride: calculateStride(channelShape),
-        });
-        // Create NgffImage for this channel (unused but kept for potential future use)
-        // const _channelImage = new NgffImage({
-        //   data: channelArray,
-        //   dims: channelDims,
-        //   scale: Object.fromEntries(
-        //     Object.entries(image.scale).filter(([k]) => k !== "c")
-        //   ),
-        //   translation: Object.fromEntries(
-        //     Object.entries(image.translation).filter(([k]) => k !== "c")
-        //   ),
-        //   name: image.name,
-        //   axesUnits: image.axesUnits,
-        //   computedCallbacks: image.computedCallbacks,
-        // });
-        // Downsample this channel
-        const itkImage = await zarrToItkImage(channelArray, channelDims, false);
-        const shrinkFactors = [];
-        for (let i = 0; i < channelDims.length; i++) {
-            const dim = channelDims[i];
-            if (SPATIAL_DIMS.includes(dim)) {
-                shrinkFactors.push(dimFactors[dim] || 1);
-            }
-            else {
-                shrinkFactors.push(1); // Non-spatial dimensions don't shrink
-            }
-        }
-        let downsampled;
-        if (smoothing === "gaussian") {
-            const blockSize = itkImage.size.slice().reverse();
-            const sigma = computeSigma(shrinkFactors);
-            const { radius: _radius } = await (0, downsample_1.gaussianKernelRadiusNode)({
-                size: blockSize,
-                sigma,
-            });
-            const result = await (0, downsample_1.downsampleNode)(itkImage, {
-                shrinkFactors,
-                cropRadius: shrinkFactors.map(() => 0),
-            });
-            downsampled = result.downsampled;
-        }
-        else if (smoothing === "bin_shrink") {
-            const result = await (0, downsample_1.downsampleBinShrinkNode)(itkImage, {
-                shrinkFactors,
-            });
-            downsampled = result.downsampled;
-        }
-        else if (smoothing === "label_image") {
-            const blockSize = itkImage.size.slice().reverse();
-            const sigma = computeSigma(shrinkFactors);
-            const { radius: _radius } = await (0, downsample_1.gaussianKernelRadiusNode)({
-                size: blockSize,
-                sigma,
+async function downsampleGaussian(image, dimFactors, spatialDims) {
+    // Handle time dimension by processing each time slice independently
+    if (image.dims.includes("t")) {
+        const tDimIndex = image.dims.indexOf("t");
+        const tSize = image.data.shape[tDimIndex];
+        const newDims = image.dims.filter((dim) => dim !== "t");
+        // Downsample each time slice
+        const downsampledSlices = [];
+        for (let t = 0; t < tSize; t++) {
+            // Extract time slice
+            const selection = new Array(image.data.shape.length).fill(null);
+            selection[tDimIndex] = t;
+            const sliceData = await zarr.get(image.data, selection);
+            // Create temporary zarr array for this slice
+            const sliceStore = new Map();
+            const sliceRoot = zarr.root(sliceStore);
+            const sliceShape = image.data.shape.filter((_, i) => i !== tDimIndex);
+            const sliceChunkShape = sliceShape.map((s) => Math.min(s, 256));
+            const sliceArray = await zarr.create(sliceRoot.resolve("slice"), {
+                shape: sliceShape,
+                chunk_shape: sliceChunkShape,
+                data_type: image.data.dtype,
+                fill_value: 0,
             });
-            const result = await (0, downsample_1.downsampleLabelImageNode)(itkImage, {
-                shrinkFactors,
-                cropRadius: shrinkFactors.map(() => 0),
+            const fullSelection = new Array(sliceShape.length).fill(null);
+            await zarr.set(sliceArray, fullSelection, sliceData);
+            // Create NgffImage for this slice (without 't' dimension)
+            const sliceImage = new ngff_image_js_1.NgffImage({
+                data: sliceArray,
+                dims: newDims,
+                scale: Object.fromEntries(Object.entries(image.scale).filter(([dim]) => dim !== "t")),
+                translation: Object.fromEntries(Object.entries(image.translation).filter(([dim]) => dim !== "t")),
+                name: image.name,
+                axesUnits: image.axesUnits
+                    ? Object.fromEntries(Object.entries(image.axesUnits).filter(([dim]) => dim !== "t"))
+                    : undefined,
+                computedCallbacks: image.computedCallbacks,
             });
-            downsampled = result.downsampled;
-        }
-        else {
-            throw new Error(`Unknown smoothing method: ${smoothing}`);
+            // Recursively downsample this slice (without 't', so no infinite loop)
+            const downsampledSlice = await downsampleGaussian(sliceImage, dimFactors, spatialDims);
+            downsampledSlices.push(downsampledSlice.data);
         }
-        // Convert back to zarr array
-        const downsampledChunkShape = downsampled.size.map((s) => Math.min(s, 256));
-        const downsampledArray = await itkImageToZarr(downsampled, "downsampled_channel", downsampledChunkShape);
-        downsampledChannels.push(downsampledArray);
-    }
-    // Combine all channels back together
-    const combinedArray = await combineChannels(downsampledChannels, cIndex, image.dims);
-    // Compute new metadata
-    const [translation, scale] = nextScaleMetadata(image, dimFactors, spatialDims);
-    return new ngff_image_js_1.NgffImage({
-        data: combinedArray,
-        dims: image.dims,
-        scale,
-        translation,
-        name: image.name,
-        axesUnits: image.axesUnits,
-        computedCallbacks: image.computedCallbacks,
-    });
-}
-/**
- * Extract a single channel from the data
- */
-function extractChannel(result, cIndex, channelIdx) {
-    const typedData = result.data;
-    const shape = result.shape;
-    // Calculate output size (all dims except channel)
-    const outputSize = shape.reduce((acc, s, i) => (i === cIndex ? acc : acc * s), 1);
-    let output;
-    if (typedData instanceof Uint8Array) {
-        output = new Uint8Array(outputSize);
-    }
-    else if (typedData instanceof Int8Array) {
-        output = new Int8Array(outputSize);
-    }
-    else if (typedData instanceof Int16Array) {
-        output = new Int16Array(outputSize);
-    }
-    else if (typedData instanceof Uint16Array) {
-        output = new Uint16Array(outputSize);
-    }
-    else if (typedData instanceof Int32Array) {
-        output = new Int32Array(outputSize);
-    }
-    else if (typedData instanceof Uint32Array) {
-        output = new Uint32Array(outputSize);
-    }
-    else if (typedData instanceof BigInt64Array) {
-        output = new BigInt64Array(outputSize);
-    }
-    else if (typedData instanceof BigUint64Array) {
-        output = new BigUint64Array(outputSize);
-    }
-    else if (typedData instanceof Float64Array) {
-        output = new Float64Array(outputSize);
-    }
-    else {
-        output = new Float32Array(outputSize);
-    }
-    // Calculate strides
-    const stride = calculateStride(shape);
-    const outputShape = shape.filter((_, i) => i !== cIndex);
-    const _outputStride = calculateStride(outputShape);
-    // Extract channel
-    const indices = new Array(shape.length).fill(0);
-    let outputIdx = 0;
-    for (let i = 0; i < outputSize; i++) {
-        // Set channel index
-        indices[cIndex] = channelIdx;
-        // Calculate source index
-        let sourceIdx = 0;
-        for (let j = 0; j < shape.length; j++) {
-            sourceIdx += indices[j] * stride[j];
-        }
-        output[outputIdx++] = typedData[sourceIdx];
-        // Increment indices (skip channel dimension)
-        for (let j = shape.length - 1; j >= 0; j--) {
-            if (j === cIndex)
-                continue;
-            indices[j]++;
-            if (indices[j] < shape[j])
-                break;
-            indices[j] = 0;
-        }
-    }
-    return output;
-}
-/**
- * Combine multiple channel arrays back into a single multi-channel array
- */
-async function combineChannels(channels, cIndex, _originalDims) {
-    // Read all channel data
-    const channelData = await Promise.all(channels.map((c) => zarr.get(c)));
-    // Determine combined shape
-    const firstChannel = channelData[0];
-    const channelShape = firstChannel.shape;
-    const combinedShape = [...channelShape];
-    combinedShape.splice(cIndex, 0, channels.length);
-    // Create combined array
-    const store = new Map();
-    const root = zarr.root(store);
-    const chunkShape = combinedShape.map((s) => Math.min(s, 256));
-    const dataType = getItkComponentType(firstChannel.data);
-    const combinedArray = await zarr.create(root.resolve("combined"), {
-        shape: combinedShape,
-        chunk_shape: chunkShape,
-        data_type: dataType,
-        fill_value: 0,
-    });
-    // Combine all channels
-    const totalSize = combinedShape.reduce((acc, s) => acc * s, 1);
-    let combined;
-    if (dataType === "uint8") {
-        combined = new Uint8Array(totalSize);
-    }
-    else if (dataType === "int8") {
-        combined = new Int8Array(totalSize);
-    }
-    else if (dataType === "int16") {
-        combined = new Int16Array(totalSize);
-    }
-    else if (dataType === "uint16") {
-        combined = new Uint16Array(totalSize);
-    }
-    else if (dataType === "int32") {
-        combined = new Int32Array(totalSize);
-    }
-    else if (dataType === "uint32") {
-        combined = new Uint32Array(totalSize);
-    }
-    else if (dataType === "int64") {
-        combined = new BigInt64Array(totalSize);
-    }
-    else if (dataType === "uint64") {
-        combined = new BigUint64Array(totalSize);
-    }
-    else if (dataType === "float64") {
-        combined = new Float64Array(totalSize);
-    }
-    else {
-        combined = new Float32Array(totalSize);
-    }
-    const stride = calculateStride(combinedShape);
-    const _channelStride = calculateStride(channelShape);
-    // Copy each channel's data
-    for (let c = 0; c < channels.length; c++) {
-        const channelTypedData = channelData[c].data;
-        const indices = new Array(combinedShape.length).fill(0);
-        for (let i = 0; i < channelTypedData.length; i++) {
-            // Set channel index
-            indices[cIndex] = c;
-            // Calculate target index in combined array
-            let targetIdx = 0;
-            for (let j = 0; j < combinedShape.length; j++) {
-                targetIdx += indices[j] * stride[j];
-            }
-            combined[targetIdx] = channelTypedData[i];
-            // Increment indices (skip channel dimension)
-            for (let j = combinedShape.length - 1; j >= 0; j--) {
-                if (j === cIndex)
-                    continue;
-                indices[j]++;
-                if (indices[j] < combinedShape[j])
-                    break;
-                indices[j] = 0;
+        // Combine downsampled slices back into a single array with 't' dimension
+        const firstSlice = downsampledSlices[0];
+        const combinedShape = [...image.data.shape];
+        combinedShape[tDimIndex] = tSize;
+        // Update spatial dimensions based on downsampled size
+        for (let i = 0; i < image.dims.length; i++) {
+            if (i !== tDimIndex) {
+                const sliceIndex = i < tDimIndex ? i : i - 1;
+                combinedShape[i] = firstSlice.shape[sliceIndex];
             }
         }
+        // Create combined array
+        const combinedStore = new Map();
+        const combinedRoot = zarr.root(combinedStore);
+        const combinedArray = await zarr.create(combinedRoot.resolve("combined"), {
+            shape: combinedShape,
+            chunk_shape: combinedShape.map((s) => Math.min(s, 256)),
+            data_type: image.data.dtype,
+            fill_value: 0,
+        });
+        // Copy each downsampled slice into the combined array
+        for (let t = 0; t < tSize; t++) {
+            const sliceData = await zarr.get(downsampledSlices[t]);
+            const targetSelection = new Array(combinedShape.length).fill(null);
+            targetSelection[tDimIndex] = t;
+            await zarr.set(combinedArray, targetSelection, sliceData);
+        }
+        // Compute new metadata (time dimension unchanged, spatial dimensions downsampled)
+        const [translation, scale] = nextScaleMetadata(image, dimFactors, spatialDims);
+        return new ngff_image_js_1.NgffImage({
+            data: combinedArray,
+            dims: image.dims,
+            scale: { ...image.scale, ...scale },
+            translation: { ...image.translation, ...translation },
+            name: image.name,
+            axesUnits: image.axesUnits,
+            computedCallbacks: image.computedCallbacks,
+        });
     }
-    // Write combined data
-    await zarr.set(combinedArray, [], {
-        data: combined,
-        shape: combinedShape,
-        stride,
-    });
-    return combinedArray;
-}
-/**
- * Perform Gaussian downsampling using ITK-Wasm
- */
-async function downsampleGaussian(image, dimFactors, spatialDims) {
-    const cIndex = image.dims.indexOf("c");
-    const isVector = cIndex === image.dims.length - 1;
-    const isChannelFirst = cIndex !== -1 && cIndex < image.dims.length - 1 &&
-        !isVector;
-    // If channel is first (before spatial dims), process each channel separately
-    if (isChannelFirst) {
-        return await downsampleChannelFirst(image, dimFactors, spatialDims, "gaussian");
-    }
+    const isVector = image.dims.includes("c");
     // Convert to ITK-Wasm format
     const itkImage = await zarrToItkImage(image.data, image.dims, isVector);
-    // Prepare shrink factors - need to be for spatial dimensions only
-    // For vector images, the last dimension (c) is NOT a spatial dimension in the ITK image
+    // Prepare shrink factors - need to be for ALL dimensions in ITK order (reversed)
     const shrinkFactors = [];
-    const effectiveDims = isVector ? image.dims.slice(0, -1) : image.dims;
-    for (let i = 0; i < effectiveDims.length; i++) {
-        const dim = effectiveDims[i];
+    for (let i = image.dims.length - 1; i >= 0; i--) {
+        const dim = image.dims[i];
         if (SPATIAL_DIMS.includes(dim)) {
             shrinkFactors.push(dimFactors[dim] || 1);
         }
-        else {
-            shrinkFactors.push(1); // Non-spatial dimensions don't shrink
-        }
     }
-    // Compute kernel radius - sigma should also be for ALL dimensions
-    const blockSize = itkImage.size.slice().reverse();
-    const sigma = computeSigma(shrinkFactors);
-    const { radius: _radius } = await (0, downsample_1.gaussianKernelRadiusNode)({
-        size: blockSize,
-        sigma,
-    });
+    // Use all zeros for cropRadius
+    const cropRadius = new Array(shrinkFactors.length).fill(0);
     // Perform downsampling
     const { downsampled } = await (0, downsample_1.downsampleNode)(itkImage, {
         shrinkFactors,
-        cropRadius: shrinkFactors.map(() => 0),
+        cropRadius: cropRadius,
     });
     // Compute new metadata
     const [translation, scale] = nextScaleMetadata(image, dimFactors, spatialDims);
-    // Convert back to zarr array
-    const chunkShape = downsampled.size.map((s) => Math.min(s, 256));
-    const array = await itkImageToZarr(downsampled, "downsampled", chunkShape);
+    // Convert back to zarr array in a new in-memory store
+    // Each downsampled image gets its own store - toNgffZarr will handle copying to target
+    const store = new Map();
+    // Chunk shape needs to be in zarr order (reversed from ITK order)
+    const chunkShape = downsampled.size.map((s) => Math.min(s, 256)).reverse();
+    const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims);
     return new ngff_image_js_1.NgffImage({
         data: array,
         dims: image.dims,
@@ -711,28 +639,97 @@ async function downsampleGaussian(image, dimFactors, spatialDims) {
  * Perform bin shrink downsampling using ITK-Wasm
  */
 async function downsampleBinShrinkImpl(image, dimFactors, spatialDims) {
-    const cIndex = image.dims.indexOf("c");
-    const isVector = cIndex === image.dims.length - 1;
-    const isChannelFirst = cIndex !== -1 && cIndex < image.dims.length - 1 &&
-        !isVector;
-    // If channel is first (before spatial dims), process each channel separately
-    if (isChannelFirst) {
-        return await downsampleChannelFirst(image, dimFactors, spatialDims, "bin_shrink");
+    // Handle time dimension by processing each time slice independently
+    if (image.dims.includes("t")) {
+        const tDimIndex = image.dims.indexOf("t");
+        const tSize = image.data.shape[tDimIndex];
+        const newDims = image.dims.filter((dim) => dim !== "t");
+        // Downsample each time slice
+        const downsampledSlices = [];
+        for (let t = 0; t < tSize; t++) {
+            // Extract time slice
+            const selection = new Array(image.data.shape.length).fill(null);
+            selection[tDimIndex] = t;
+            const sliceData = await zarr.get(image.data, selection);
+            // Create temporary zarr array for this slice
+            const sliceStore = new Map();
+            const sliceRoot = zarr.root(sliceStore);
+            const sliceShape = image.data.shape.filter((_, i) => i !== tDimIndex);
+            const sliceChunkShape = sliceShape.map((s) => Math.min(s, 256));
+            const sliceArray = await zarr.create(sliceRoot.resolve("slice"), {
+                shape: sliceShape,
+                chunk_shape: sliceChunkShape,
+                data_type: image.data.dtype,
+                fill_value: 0,
+            });
+            const fullSelection = new Array(sliceShape.length).fill(null);
+            await zarr.set(sliceArray, fullSelection, sliceData);
+            // Create NgffImage for this slice (without 't' dimension)
+            const sliceImage = new ngff_image_js_1.NgffImage({
+                data: sliceArray,
+                dims: newDims,
+                scale: Object.fromEntries(Object.entries(image.scale).filter(([dim]) => dim !== "t")),
+                translation: Object.fromEntries(Object.entries(image.translation).filter(([dim]) => dim !== "t")),
+                name: image.name,
+                axesUnits: image.axesUnits
+                    ? Object.fromEntries(Object.entries(image.axesUnits).filter(([dim]) => dim !== "t"))
+                    : undefined,
+                computedCallbacks: image.computedCallbacks,
+            });
+            // Recursively downsample this slice
+            const downsampledSlice = await downsampleBinShrinkImpl(sliceImage, dimFactors, spatialDims);
+            downsampledSlices.push(downsampledSlice.data);
+        }
+        // Combine downsampled slices back into a single array with 't' dimension
+        const firstSlice = downsampledSlices[0];
+        const combinedShape = [...image.data.shape];
+        combinedShape[tDimIndex] = tSize;
+        // Update spatial dimensions based on downsampled size
+        for (let i = 0; i < image.dims.length; i++) {
+            if (i !== tDimIndex) {
+                const sliceIndex = i < tDimIndex ? i : i - 1;
+                combinedShape[i] = firstSlice.shape[sliceIndex];
+            }
+        }
+        // Create combined array
+        const combinedStore = new Map();
+        const combinedRoot = zarr.root(combinedStore);
+        const combinedArray = await zarr.create(combinedRoot.resolve("combined"), {
+            shape: combinedShape,
+            chunk_shape: combinedShape.map((s) => Math.min(s, 256)),
+            data_type: image.data.dtype,
+            fill_value: 0,
+        });
+        // Copy each downsampled slice into the combined array
+        for (let t = 0; t < tSize; t++) {
+            const sliceData = await zarr.get(downsampledSlices[t]);
+            const targetSelection = new Array(combinedShape.length).fill(null);
+            targetSelection[tDimIndex] = t;
+            await zarr.set(combinedArray, targetSelection, sliceData);
+        }
+        // Compute new metadata
+        const [translation, scale] = nextScaleMetadata(image, dimFactors, spatialDims);
+        return new ngff_image_js_1.NgffImage({
+            data: combinedArray,
+            dims: image.dims,
+            scale: { ...image.scale, ...scale },
+            translation: { ...image.translation, ...translation },
+            name: image.name,
+            axesUnits: image.axesUnits,
+            computedCallbacks: image.computedCallbacks,
+        });
     }
+    const isVector = image.dims.includes("c");
     // Convert to ITK-Wasm format
     const itkImage = await zarrToItkImage(image.data, image.dims, isVector);
-    // Prepare shrink factors - need to be for spatial dimensions only
-    // For vector images, the last dimension (c) is NOT a spatial dimension in the ITK image
+    // Prepare shrink factors - only for spatial dimensions in ITK order (reversed)
+    // ITK bin shrink does not expect shrink factors for non-spatial dimensions like 'c'
     const shrinkFactors = [];
-    const effectiveDims = isVector ? image.dims.slice(0, -1) : image.dims;
-    for (let i = 0; i < effectiveDims.length; i++) {
-        const dim = effectiveDims[i];
+    for (let i = image.dims.length - 1; i >= 0; i--) {
+        const dim = image.dims[i];
         if (SPATIAL_DIMS.includes(dim)) {
             shrinkFactors.push(dimFactors[dim] || 1);
         }
-        else {
-            shrinkFactors.push(1); // Non-spatial dimensions don't shrink
-        }
     }
     // Perform downsampling
     const { downsampled } = await (0, downsample_1.downsampleBinShrinkNode)(itkImage, {
@@ -740,9 +737,12 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims) {
     });
     // Compute new metadata
     const [translation, scale] = nextScaleMetadata(image, dimFactors, spatialDims);
-    // Convert back to zarr array
-    const chunkShape = downsampled.size.map((s) => Math.min(s, 256));
-    const array = await itkImageToZarr(downsampled, "downsampled", chunkShape);
+    // Convert back to zarr array in a new in-memory store
+    // Each downsampled image gets its own store - toNgffZarr will handle copying to target
+    const store = new Map();
+    // Chunk shape needs to be in zarr order (reversed from ITK order)
+    const chunkShape = downsampled.size.map((s) => Math.min(s, 256)).reverse();
+    const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims);
     return new ngff_image_js_1.NgffImage({
         data: array,
         dims: image.dims,
@@ -757,22 +757,93 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims) {
  * Perform label image downsampling using ITK-Wasm
  */
 async function downsampleLabelImageImpl(image, dimFactors, spatialDims) {
-    const cIndex = image.dims.indexOf("c");
-    const isVector = cIndex === image.dims.length - 1;
-    const isChannelFirst = cIndex !== -1 && cIndex < image.dims.length - 1 &&
-        !isVector;
-    // If channel is first (before spatial dims), process each channel separately
-    if (isChannelFirst) {
-        return await downsampleChannelFirst(image, dimFactors, spatialDims, "label_image");
+    // Handle time dimension by processing each time slice independently
+    if (image.dims.includes("t")) {
+        const tDimIndex = image.dims.indexOf("t");
+        const tSize = image.data.shape[tDimIndex];
+        const newDims = image.dims.filter((dim) => dim !== "t");
+        // Downsample each time slice
+        const downsampledSlices = [];
+        for (let t = 0; t < tSize; t++) {
+            // Extract time slice
+            const selection = new Array(image.data.shape.length).fill(null);
+            selection[tDimIndex] = t;
+            const sliceData = await zarr.get(image.data, selection);
+            // Create temporary zarr array for this slice
+            const sliceStore = new Map();
+            const sliceRoot = zarr.root(sliceStore);
+            const sliceShape = image.data.shape.filter((_, i) => i !== tDimIndex);
+            const sliceChunkShape = sliceShape.map((s) => Math.min(s, 256));
+            const sliceArray = await zarr.create(sliceRoot.resolve("slice"), {
+                shape: sliceShape,
+                chunk_shape: sliceChunkShape,
+                data_type: image.data.dtype,
+                fill_value: 0,
+            });
+            const fullSelection = new Array(sliceShape.length).fill(null);
+            await zarr.set(sliceArray, fullSelection, sliceData);
+            // Create NgffImage for this slice (without 't' dimension)
+            const sliceImage = new ngff_image_js_1.NgffImage({
+                data: sliceArray,
+                dims: newDims,
+                scale: Object.fromEntries(Object.entries(image.scale).filter(([dim]) => dim !== "t")),
+                translation: Object.fromEntries(Object.entries(image.translation).filter(([dim]) => dim !== "t")),
+                name: image.name,
+                axesUnits: image.axesUnits
+                    ? Object.fromEntries(Object.entries(image.axesUnits).filter(([dim]) => dim !== "t"))
+                    : undefined,
+                computedCallbacks: image.computedCallbacks,
+            });
+            // Recursively downsample this slice
+            const downsampledSlice = await downsampleLabelImageImpl(sliceImage, dimFactors, spatialDims);
+            downsampledSlices.push(downsampledSlice.data);
+        }
+        // Combine downsampled slices back into a single array with 't' dimension
+        const firstSlice = downsampledSlices[0];
+        const combinedShape = [...image.data.shape];
+        combinedShape[tDimIndex] = tSize;
+        // Update spatial dimensions based on downsampled size
+        for (let i = 0; i < image.dims.length; i++) {
+            if (i !== tDimIndex) {
+                const sliceIndex = i < tDimIndex ? i : i - 1;
+                combinedShape[i] = firstSlice.shape[sliceIndex];
+            }
+        }
+        // Create combined array
+        const combinedStore = new Map();
+        const combinedRoot = zarr.root(combinedStore);
+        const combinedArray = await zarr.create(combinedRoot.resolve("combined"), {
+            shape: combinedShape,
+            chunk_shape: combinedShape.map((s) => Math.min(s, 256)),
+            data_type: image.data.dtype,
+            fill_value: 0,
+        });
+        // Copy each downsampled slice into the combined array
+        for (let t = 0; t < tSize; t++) {
+            const sliceData = await zarr.get(downsampledSlices[t]);
+            const targetSelection = new Array(combinedShape.length).fill(null);
+            targetSelection[tDimIndex] = t;
+            await zarr.set(combinedArray, targetSelection, sliceData);
+        }
+        // Compute new metadata
+        const [translation, scale] = nextScaleMetadata(image, dimFactors, spatialDims);
+        return new ngff_image_js_1.NgffImage({
+            data: combinedArray,
+            dims: image.dims,
+            scale: { ...image.scale, ...scale },
+            translation: { ...image.translation, ...translation },
+            name: image.name,
+            axesUnits: image.axesUnits,
+            computedCallbacks: image.computedCallbacks,
+        });
     }
+    const isVector = image.dims.includes("c");
     // Convert to ITK-Wasm format
     const itkImage = await zarrToItkImage(image.data, image.dims, isVector);
-    // Prepare shrink factors - need to be for spatial dimensions only
-    // For vector images, the last dimension (c) is NOT a spatial dimension in the ITK image
+    // Prepare shrink factors - need to be for ALL dimensions in ITK order (reversed)
     const shrinkFactors = [];
-    const effectiveDims = isVector ? image.dims.slice(0, -1) : image.dims;
-    for (let i = 0; i < effectiveDims.length; i++) {
-        const dim = effectiveDims[i];
+    for (let i = image.dims.length - 1; i >= 0; i--) {
+        const dim = image.dims[i];
         if (SPATIAL_DIMS.includes(dim)) {
             shrinkFactors.push(dimFactors[dim] || 1);
         }
@@ -780,23 +851,21 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims) {
             shrinkFactors.push(1); // Non-spatial dimensions don't shrink
         }
     }
-    // Compute kernel radius
-    const blockSize = itkImage.size.slice().reverse();
-    const sigma = computeSigma(shrinkFactors);
-    const { radius: _radius } = await (0, downsample_1.gaussianKernelRadiusNode)({
-        size: blockSize,
-        sigma,
-    });
+    // Use all zeros for cropRadius
+    const cropRadius = new Array(shrinkFactors.length).fill(0);
     // Perform downsampling
     const { downsampled } = await (0, downsample_1.downsampleLabelImageNode)(itkImage, {
         shrinkFactors,
-        cropRadius: shrinkFactors.map(() => 0),
+        cropRadius: cropRadius,
     });
     // Compute new metadata
     const [translation, scale] = nextScaleMetadata(image, dimFactors, spatialDims);
-    // Convert back to zarr array
-    const chunkShape = downsampled.size.map((s) => Math.min(s, 256));
-    const array = await itkImageToZarr(downsampled, "downsampled", chunkShape);
+    // Convert back to zarr array in a new in-memory store
+    // Each downsampled image gets its own store - toNgffZarr will handle copying to target
+    const store = new Map();
+    // Chunk shape needs to be in zarr order (reversed from ITK order)
+    const chunkShape = downsampled.size.map((s) => Math.min(s, 256)).reverse();
+    const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims);
     return new ngff_image_js_1.NgffImage({
         data: array,
         dims: image.dims,
@@ -812,31 +881,104 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims) {
  */
 async function downsampleItkWasm(ngffImage, scaleFactors, smoothing) {
     const multiscales = [ngffImage];
-    let previousImage = ngffImage;
     const dims = ngffImage.dims;
+    const spatialDims = dims.filter((dim) => SPATIAL_DIMS.includes(dim));
+    // Two strategies:
+    // 1. gaussian / label_image: hybrid absolute scale factors (each element is absolute from original)
+    //    using dimScaleFactors to choose incremental vs from-original for exact sizes.
+    // 2. bin_shrink: treat provided scaleFactors sequence as incremental factors applied successively.
+    let previousImage = ngffImage;
     let previousDimFactors = {};
-    for (const dim of dims) {
+    for (const dim of dims)
         previousDimFactors[dim] = 1;
-    }
-    const spatialDims = dims.filter((dim) => SPATIAL_DIMS.includes(dim));
-    for (const scaleFactor of scaleFactors) {
-        const dimFactors = dimScaleFactors(dims, scaleFactor, previousDimFactors);
-        previousDimFactors = updatePreviousDimFactors(scaleFactor, spatialDims, previousDimFactors);
+    for (let i = 0; i < scaleFactors.length; i++) {
+        const scaleFactor = scaleFactors[i];
+        let sourceImage;
+        let sourceDimFactors;
+        if (smoothing === "bin_shrink") {
+            // Purely incremental: scaleFactor is the shrink for this step
+            sourceImage = previousImage; // always from previous
+            sourceDimFactors = {};
+            if (typeof scaleFactor === "number") {
+                for (const dim of spatialDims)
+                    sourceDimFactors[dim] = scaleFactor;
+            }
+            else {
+                for (const dim of spatialDims) {
+                    sourceDimFactors[dim] = scaleFactor[dim] || 1;
+                }
+            }
+            // Non-spatial dims factor 1
+            for (const dim of dims) {
+                if (!(dim in sourceDimFactors))
+                    sourceDimFactors[dim] = 1;
+            }
+        }
+        else {
+            // Hybrid absolute strategy
+            const dimFactors = dimScaleFactors(dims, scaleFactor, previousDimFactors, ngffImage, previousImage);
+            // Decide if we can be incremental
+            let canDownsampleIncrementally = true;
+            for (const dim of Object.keys(dimFactors)) {
+                const dimIndex = ngffImage.dims.indexOf(dim);
+                if (dimIndex >= 0) {
+                    const originalSize = ngffImage.data.shape[dimIndex];
+                    const targetSize = Math.floor(originalSize /
+                        (typeof scaleFactor === "number"
+                            ? scaleFactor
+                            : scaleFactor[dim]));
+                    const prevDimIndex = previousImage.dims.indexOf(dim);
+                    const previousSize = previousImage.data.shape[prevDimIndex];
+                    if (Math.floor(previousSize / dimFactors[dim]) !== targetSize) {
+                        canDownsampleIncrementally = false;
+                        break;
+                    }
+                }
+            }
+            if (canDownsampleIncrementally) {
+                sourceImage = previousImage;
+                sourceDimFactors = dimFactors;
+            }
+            else {
+                sourceImage = ngffImage;
+                const originalDimFactors = {};
+                for (const dim of dims)
+                    originalDimFactors[dim] = 1;
+                sourceDimFactors = dimScaleFactors(dims, scaleFactor, originalDimFactors);
+            }
+        }
         let downsampled;
         if (smoothing === "gaussian") {
-            downsampled = await downsampleGaussian(previousImage, dimFactors, spatialDims);
+            downsampled = await downsampleGaussian(sourceImage, sourceDimFactors, spatialDims);
         }
         else if (smoothing === "bin_shrink") {
-            downsampled = await downsampleBinShrinkImpl(previousImage, dimFactors, spatialDims);
+            downsampled = await downsampleBinShrinkImpl(sourceImage, sourceDimFactors, spatialDims);
         }
         else if (smoothing === "label_image") {
-            downsampled = await downsampleLabelImageImpl(previousImage, dimFactors, spatialDims);
+            downsampled = await downsampleLabelImageImpl(sourceImage, sourceDimFactors, spatialDims);
         }
         else {
             throw new Error(`Unknown smoothing method: ${smoothing}`);
         }
         multiscales.push(downsampled);
+        // Update for next iteration
         previousImage = downsampled;
+        if (smoothing === "bin_shrink") {
+            // Accumulate cumulative factors (multiply) for bin_shrink to reflect total shrink so far
+            if (typeof scaleFactor === "number") {
+                for (const dim of spatialDims) {
+                    previousDimFactors[dim] *= scaleFactor;
+                }
+            }
+            else {
+                for (const dim of spatialDims) {
+                    previousDimFactors[dim] *= scaleFactor[dim] || 1;
+                }
+            }
+        }
+        else {
+            previousDimFactors = updatePreviousDimFactors(scaleFactor, spatialDims, previousDimFactors);
+        }
     }
     return multiscales;
 }