@fideus-labs/fidnii 0.2.0 → 0.3.0

package/dist/BufferManager.d.ts

@@ -5,6 +5,18 @@ import type { TypedArray, ZarrDtype } from "./types.js";
  * The buffer is resized to match the fetched data dimensions exactly.
  * Memory is reused when possible to avoid unnecessary allocations.
  *
+ * For multi-component images (RGB/RGBA), `componentsPerVoxel` controls
+ * how many scalar elements each spatial voxel occupies. The buffer is
+ * sized to hold `spatialPixels * componentsPerVoxel` elements, and the
+ * typed array view spans all of them. Spatial dimensions (`[z, y, x]`)
+ * track only the spatial extent; the component count is a fixed
+ * multiplier on the element count.
+ *
+ * When the source dtype is not uint8 and `componentsPerVoxel > 1`
+ * (non-uint8 RGB/RGBA), the buffer stores **uint8** data because NiiVue
+ * only supports `DT_RGB24` / `DT_RGBA32` (uint8-per-channel). The raw
+ * data is normalized to uint8 externally before being written here.
+ *
  * Memory reuse strategy:
  * - Reuse buffer if newSize <= currentCapacity
  * - Reallocate if newSize > currentCapacity OR newSize < 25% of currentCapacity
@@ -16,13 +28,27 @@ export declare class BufferManager {
     private readonly TypedArrayCtor;
     private readonly bytesPerPixel;
     private readonly dtype;
+    /**
+     * Number of scalar components per spatial voxel.
+     * 1 for scalar images, 3 for RGB, 4 for RGBA.
+     */
+    readonly componentsPerVoxel: number;
+    /**
+     * Whether this buffer stores normalized uint8 data for a non-uint8
+     * RGB/RGBA source. When `true`, {@link getTypedArray} returns a
+     * `Uint8Array` and `bytesPerPixel` is 1, regardless of the source
+     * dtype.
+     */
+    readonly isNormalizedRGB: boolean;
     /**
      * Create a new BufferManager.
      *
      * @param maxPixels - Maximum number of pixels allowed (budget)
      * @param dtype - Data type for the buffer
+     * @param componentsPerVoxel - Number of components per spatial voxel
+     *   (default: 1; pass 3 for RGB, 4 for RGBA)
      */
-    constructor(maxPixels: number, dtype: ZarrDtype);
+    constructor(maxPixels: number, dtype: ZarrDtype, componentsPerVoxel?: number);
     /**
      * Resize the buffer to fit the given dimensions.
      *
@@ -44,7 +70,8 @@ export declare class BufferManager {
     /**
      * Get a typed array view over the current buffer region.
      *
-     * The view is sized to match currentDimensions, not the full buffer capacity.
+     * The view is sized to match `spatialPixels × componentsPerVoxel`,
+     * not the full buffer capacity.
      */
     getTypedArray(): TypedArray;
     /**
@@ -52,11 +79,17 @@ export declare class BufferManager {
      */
     getDimensions(): [number, number, number];
     /**
-     * Get the total number of pixels in the current buffer region.
+     * Get the total number of spatial pixels in the current buffer region.
+     * This does NOT include the component multiplier.
      */
     getPixelCount(): number;
     /**
-     * Get the buffer capacity in pixels.
+     * Get the total number of scalar elements in the current buffer region.
+     * For multi-component images, this is `spatialPixels × componentsPerVoxel`.
+     */
+    getElementCount(): number;
+    /**
+     * Get the buffer capacity in scalar elements.
      */
     getCapacity(): number;
     /**

package/dist/BufferManager.d.ts.map

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package/dist/BufferManager.js

@@ -7,6 +7,18 @@ import { getBytesPerPixel, getTypedArrayConstructor } from "./types.js";
  * The buffer is resized to match the fetched data dimensions exactly.
  * Memory is reused when possible to avoid unnecessary allocations.
  *
+ * For multi-component images (RGB/RGBA), `componentsPerVoxel` controls
+ * how many scalar elements each spatial voxel occupies. The buffer is
+ * sized to hold `spatialPixels * componentsPerVoxel` elements, and the
+ * typed array view spans all of them. Spatial dimensions (`[z, y, x]`)
+ * track only the spatial extent; the component count is a fixed
+ * multiplier on the element count.
+ *
+ * When the source dtype is not uint8 and `componentsPerVoxel > 1`
+ * (non-uint8 RGB/RGBA), the buffer stores **uint8** data because NiiVue
+ * only supports `DT_RGB24` / `DT_RGBA32` (uint8-per-channel). The raw
+ * data is normalized to uint8 externally before being written here.
+ *
  * Memory reuse strategy:
  * - Reuse buffer if newSize <= currentCapacity
  * - Reallocate if newSize > currentCapacity OR newSize < 25% of currentCapacity
@@ -18,17 +30,41 @@ export class BufferManager {
     TypedArrayCtor;
     bytesPerPixel;
     dtype;
+    /**
+     * Number of scalar components per spatial voxel.
+     * 1 for scalar images, 3 for RGB, 4 for RGBA.
+     */
+    componentsPerVoxel;
+    /**
+     * Whether this buffer stores normalized uint8 data for a non-uint8
+     * RGB/RGBA source. When `true`, {@link getTypedArray} returns a
+     * `Uint8Array` and `bytesPerPixel` is 1, regardless of the source
+     * dtype.
+     */
+    isNormalizedRGB;
     /**
      * Create a new BufferManager.
      *
      * @param maxPixels - Maximum number of pixels allowed (budget)
      * @param dtype - Data type for the buffer
+     * @param componentsPerVoxel - Number of components per spatial voxel
+     *   (default: 1; pass 3 for RGB, 4 for RGBA)
      */
-    constructor(maxPixels, dtype) {
+    constructor(maxPixels, dtype, componentsPerVoxel = 1) {
         this.maxPixels = maxPixels;
         this.dtype = dtype;
-        this.TypedArrayCtor = getTypedArrayConstructor(dtype);
-        this.bytesPerPixel = getBytesPerPixel(dtype);
+        this.componentsPerVoxel = componentsPerVoxel;
+        // Non-uint8 RGB/RGBA: the output buffer stores normalized uint8 data
+        // because NiiVue only supports uint8-per-channel color rendering.
+        this.isNormalizedRGB = componentsPerVoxel > 1 && dtype !== "uint8";
+        if (this.isNormalizedRGB) {
+            this.TypedArrayCtor = Uint8Array;
+            this.bytesPerPixel = 1;
+        }
+        else {
+            this.TypedArrayCtor = getTypedArrayConstructor(dtype);
+            this.bytesPerPixel = getBytesPerPixel(dtype);
+        }
         // Initialize with empty buffer - will be allocated on first resize
         this.currentDimensions = [0, 0, 0];
         this.buffer = new ArrayBuffer(0);
@@ -47,17 +83,20 @@ export class BufferManager {
      * @returns TypedArray view over the (possibly new) buffer
      */
     resize(dimensions) {
-        const requiredPixels = dimensions[0] * dimensions[1] * dimensions[2];
-        if (requiredPixels > this.maxPixels) {
-            console.warn(`[fidnii] BufferManager: Requested dimensions [${dimensions.join(", ")}] = ${requiredPixels} pixels exceeds maxPixels (${this.maxPixels}). ` +
+        const spatialPixels = dimensions[0] * dimensions[1] * dimensions[2];
+        if (spatialPixels > this.maxPixels) {
+            console.warn(`[fidnii] BufferManager: Requested dimensions [${dimensions.join(", ")}] = ${spatialPixels} pixels exceeds maxPixels (${this.maxPixels}). ` +
                 `Proceeding anyway (likely at lowest resolution).`);
         }
-        const currentCapacityPixels = this.buffer.byteLength / this.bytesPerPixel;
-        const utilizationRatio = currentCapacityPixels > 0 ? requiredPixels / currentCapacityPixels : 0;
-        const needsReallocation = requiredPixels > currentCapacityPixels || utilizationRatio < 0.25;
+        // Total elements = spatial pixels × components per voxel
+        const requiredElements = spatialPixels * this.componentsPerVoxel;
+        const currentCapacityElements = this.buffer.byteLength / this.bytesPerPixel;
+        const utilizationRatio = currentCapacityElements > 0
+            ? requiredElements / currentCapacityElements
+            : 0;
+        const needsReallocation = requiredElements > currentCapacityElements || utilizationRatio < 0.25;
         if (needsReallocation) {
-            // Allocate new buffer
-            const newByteLength = requiredPixels * this.bytesPerPixel;
+            const newByteLength = requiredElements * this.bytesPerPixel;
             this.buffer = new ArrayBuffer(newByteLength);
         }
         this.currentDimensions = [...dimensions];
@@ -72,13 +111,14 @@ export class BufferManager {
     /**
      * Get a typed array view over the current buffer region.
      *
-     * The view is sized to match currentDimensions, not the full buffer capacity.
+     * The view is sized to match `spatialPixels × componentsPerVoxel`,
+     * not the full buffer capacity.
      */
     getTypedArray() {
-        const pixelCount = this.currentDimensions[0] *
+        const spatialPixels = this.currentDimensions[0] *
             this.currentDimensions[1] *
             this.currentDimensions[2];
-        return new this.TypedArrayCtor(this.buffer, 0, pixelCount);
+        return new this.TypedArrayCtor(this.buffer, 0, spatialPixels * this.componentsPerVoxel);
     }
     /**
      * Get the current buffer dimensions [z, y, x].
@@ -87,7 +127,8 @@ export class BufferManager {
         return [...this.currentDimensions];
     }
     /**
-     * Get the total number of pixels in the current buffer region.
+     * Get the total number of spatial pixels in the current buffer region.
+     * This does NOT include the component multiplier.
      */
     getPixelCount() {
         return (this.currentDimensions[0] *
@@ -95,7 +136,14 @@ export class BufferManager {
             this.currentDimensions[2]);
     }
     /**
-     * Get the buffer capacity in pixels.
+     * Get the total number of scalar elements in the current buffer region.
+     * For multi-component images, this is `spatialPixels × componentsPerVoxel`.
+     */
+    getElementCount() {
+        return this.getPixelCount() * this.componentsPerVoxel;
+    }
+    /**
+     * Get the buffer capacity in scalar elements.
      */
     getCapacity() {
         return this.buffer.byteLength / this.bytesPerPixel;
@@ -122,9 +170,9 @@ export class BufferManager {
      * Clear the current buffer region to zeros.
      */
     clear() {
-        const pixelCount = this.getPixelCount();
-        if (pixelCount > 0) {
-            const view = new Uint8Array(this.buffer, 0, pixelCount * this.bytesPerPixel);
+        const elementCount = this.getElementCount();
+        if (elementCount > 0) {
+            const view = new Uint8Array(this.buffer, 0, elementCount * this.bytesPerPixel);
             view.fill(0);
         }
     }
@@ -135,9 +183,9 @@ export class BufferManager {
      * @returns True if current buffer can fit the dimensions
      */
     canAccommodate(dimensions) {
-        const requiredPixels = dimensions[0] * dimensions[1] * dimensions[2];
-        const currentCapacityPixels = this.buffer.byteLength / this.bytesPerPixel;
-        return requiredPixels <= currentCapacityPixels;
+        const requiredElements = dimensions[0] * dimensions[1] * dimensions[2] * this.componentsPerVoxel;
+        const currentCapacityElements = this.buffer.byteLength / this.bytesPerPixel;
+        return requiredElements <= currentCapacityElements;
     }
 }
 //# sourceMappingURL=BufferManager.js.map

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package/dist/OMEZarrNVImage.d.ts

@@ -44,6 +44,21 @@ export declare class OMEZarrNVImage extends NVImage {
     private isLoading;
     /** Data type of the volume */
     private readonly dtype;
+    /**
+     * Channel dimension info, or `null` for scalar (single-component) images.
+     * When non-null, the image has a `"c"` dimension and is treated as
+     * multi-component (RGB/RGBA) data.
+     */
+    private readonly _channelInfo;
+    /**
+     * Whether the image is 2D (no `"z"` dimension).
+     */
+    private readonly _is2D;
+    /**
+     * Whether to negate the y-scale in the NIfTI affine for 2D images
+     * so that NiiVue renders them right-side up.
+     */
+    private readonly _flipY2D;
     /** Full volume bounds in world space */
     private readonly _volumeBounds;
     /** Current buffer bounds in world space (may differ from full volume when clipped) */
@@ -210,6 +225,17 @@ export declare class OMEZarrNVImage extends NVImage {
      * @param levelIndex - The resolution level index
      */
     private ensureOmeroMetadata;
+    /**
+     * Get per-channel normalization windows for non-uint8 RGB/RGBA.
+     *
+     * Uses OMERO `window.start`/`window.end` (or `window.min`/`window.max`)
+     * when available. Falls back to computing min/max from the raw data.
+     *
+     * @param data - Raw multi-component data from the zarr fetch
+     * @param components - Number of components per voxel (3 or 4)
+     * @returns Per-channel windows for normalization to uint8
+     */
+    private _getChannelWindows;
     /**
      * Handle clip plane change from NiiVue.
      * This is called when the user interacts with clip planes in NiiVue.

package/dist/OMEZarrNVImage.d.ts.map

@@ -1 +1 @@
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package/dist/OMEZarrNVImage.js

@@ -8,9 +8,10 @@ import { NIFTI1 } from "nifti-reader-js";
 import { BufferManager } from "./BufferManager.js";
 import { alignToChunks, clipPlanesToNiivue, clipPlanesToPixelRegion, createDefaultClipPlanes, MAX_CLIP_PLANES, normalizeVector, validateClipPlanes, } from "./ClipPlanes.js";
 import { OMEZarrNVImageEvent, } from "./events.js";
+import { computeChannelMinMax, normalizeToUint8 } from "./normalize.js";
 import { RegionCoalescer } from "./RegionCoalescer.js";
 import { getChunkShape, getVolumeShape, select2DResolution, selectResolution, } from "./ResolutionSelector.js";
-import { getBytesPerPixel, getNiftiDataType, parseZarritaDtype, } from "./types.js";
+import { getBytesPerPixel, getChannelInfo, getNiftiDataType, getRGBNiftiDataType, isRGBImage, NiftiDataType, needsRGBNormalization, parseZarritaDtype, } from "./types.js";
 import { affineToNiftiSrows, calculateWorldBounds, createAffineFromNgffImage, } from "./utils/affine.js";
 import { worldToPixel } from "./utils/coordinates.js";
 import { boundsApproxEqual, computeViewportBounds2D, computeViewportBounds3D, } from "./ViewportBounds.js";
@@ -57,6 +58,21 @@ export class OMEZarrNVImage extends NVImage {
     isLoading = false;
     /** Data type of the volume */
     dtype;
+    /**
+     * Channel dimension info, or `null` for scalar (single-component) images.
+     * When non-null, the image has a `"c"` dimension and is treated as
+     * multi-component (RGB/RGBA) data.
+     */
+    _channelInfo;
+    /**
+     * Whether the image is 2D (no `"z"` dimension).
+     */
+    _is2D;
+    /**
+     * Whether to negate the y-scale in the NIfTI affine for 2D images
+     * so that NiiVue renders them right-side up.
+     */
+    _flipY2D;
     /** Full volume bounds in world space */
     _volumeBounds;
     /** Current buffer bounds in world space (may differ from full volume when clipped) */
@@ -152,6 +168,18 @@ export class OMEZarrNVImage extends NVImage {
         // Get data type from highest resolution image
         const highResImage = this.multiscales.images[0];
         this.dtype = parseZarritaDtype(highResImage.data.dtype);
+        // Detect channel (component) dimension for multi-component images
+        this._channelInfo = getChannelInfo(highResImage);
+        // Validate multi-component images: only RGB (3) / RGBA (4) are supported
+        if (this._channelInfo && !isRGBImage(highResImage)) {
+            throw new Error(`Unsupported multi-component image: found ${this._channelInfo.components} ` +
+                `components with dtype '${this.dtype}'. Only RGB (3 components) ` +
+                `and RGBA (4 components) images are supported. For other ` +
+                `multi-component images, select a single component before loading.`);
+        }
+        // Detect 2D images (no z axis) and store y-flip preference
+        this._is2D = highResImage.dims.indexOf("z") === -1;
+        this._flipY2D = options.flipY2D ?? true;
         // Calculate volume bounds from highest resolution for most accurate bounds
         const highResAffine = createAffineFromNgffImage(highResImage);
         const highResShape = getVolumeShape(highResImage);
@@ -162,8 +190,11 @@ export class OMEZarrNVImage extends NVImage {
         const selection = selectResolution(this.multiscales, this.maxPixels, this._clipPlanes, this._volumeBounds);
         this.targetLevelIndex = selection.levelIndex;
         this.currentLevelIndex = this.multiscales.images.length - 1;
-        // Create buffer manager (dynamic sizing, no pre-allocation)
-        this.bufferManager = new BufferManager(this.maxPixels, this.dtype);
+        // Create buffer manager (dynamic sizing, no pre-allocation).
+        // For multi-component images, each spatial voxel has multiple
+        // scalar elements (e.g. 3 for RGB, 4 for RGBA).
+        const componentsPerVoxel = this._channelInfo?.components ?? 1;
+        this.bufferManager = new BufferManager(this.maxPixels, this.dtype, componentsPerVoxel);
         // Initialize NVImage properties with placeholder values
         // Actual values will be set when data is first loaded
         this.initializeNVImageProperties();
@@ -213,15 +244,23 @@ export class OMEZarrNVImage extends NVImage {
         this.hdr = hdr;
         // Placeholder dimensions (will be updated when data loads)
         hdr.dims = [3, 1, 1, 1, 1, 1, 1, 1];
-        // Set data type
-        hdr.datatypeCode = getNiftiDataType(this.dtype);
-        hdr.numBitsPerVoxel = getBytesPerPixel(this.dtype) * 8;
+        // Set data type — use RGB24/RGBA32 for multi-component images
+        // (any dtype; non-uint8 data is normalized to uint8 at load time)
+        if (this._channelInfo && isRGBImage(this.multiscales.images[0])) {
+            const rgbCode = getRGBNiftiDataType(this._channelInfo);
+            hdr.datatypeCode = rgbCode;
+            hdr.numBitsPerVoxel = rgbCode === NiftiDataType.RGB24 ? 24 : 32;
+        }
+        else {
+            hdr.datatypeCode = getNiftiDataType(this.dtype);
+            hdr.numBitsPerVoxel = getBytesPerPixel(this.dtype) * 8;
+        }
         // Placeholder pixel dimensions
         hdr.pixDims = [1, 1, 1, 1, 0, 0, 0, 0];
-        // Placeholder affine (identity)
+        // Placeholder affine (identity, with y-flip for 2D images)
         hdr.affine = [
             [1, 0, 0, 0],
-            [0, 1, 0, 0],
+            [0, this._flipY2D && this._is2D ? -1 : 1, 0, 0],
             [0, 0, 1, 0],
             [0, 0, 0, 1],
         ];
@@ -367,8 +406,22 @@ export class OMEZarrNVImage extends NVImage {
         const result = await this.coalescer.fetchRegion(ngffImage, levelIndex, fetchRegion, requesterId);
         // Resize buffer to match fetched data exactly (no upsampling!)
         const targetData = this.bufferManager.resize(fetchedShape);
-        // Direct copy of fetched data
-        targetData.set(result.data);
+        // For non-uint8 RGB/RGBA, we need OMERO metadata *before* copying
+        // so we can normalize the raw data to uint8 using channel windows.
+        const normalize = needsRGBNormalization(ngffImage, this.dtype);
+        if (normalize && !this.isLabelImage) {
+            await this.ensureOmeroMetadata(ngffImage, levelIndex);
+        }
+        if (normalize && this._channelInfo) {
+            // Non-uint8 RGB/RGBA: normalize raw data to uint8 using OMERO windows
+            const windows = this._getChannelWindows(result.data, this._channelInfo.components);
+            const normalized = normalizeToUint8(result.data, this._channelInfo.components, windows);
+            targetData.set(normalized);
+        }
+        else {
+            // uint8 RGB or scalar: direct copy
+            targetData.set(result.data);
+        }
         // Update this.img to point to the (possibly new) buffer
         this.img = this.bufferManager.getTypedArray();
         // Update NVImage header with correct dimensions and transforms
@@ -377,8 +430,9 @@ export class OMEZarrNVImage extends NVImage {
             // Label images: apply a discrete colormap instead of OMERO windowing
             this._applyLabelColormap(this, result.data);
         }
-        else {
-            // Compute or apply OMERO metadata for cal_min/cal_max
+        else if (!normalize) {
+            // Scalar / uint8 RGB: compute or apply OMERO for cal_min/cal_max.
+            // (Normalized RGB already consumed the OMERO window above.)
             await this.ensureOmeroMetadata(ngffImage, levelIndex);
         }
         // Reset global_min so NiiVue's refreshLayers() re-runs calMinMax() on real data.
@@ -447,11 +501,8 @@ export class OMEZarrNVImage extends NVImage {
         affine[12] += regionStart[2] * sx; // x offset
         affine[13] += regionStart[1] * sy; // y offset
         affine[14] += regionStart[0] * sz; // z offset
-        // Update affine in header
-        const srows = affineToNiftiSrows(affine);
-        this.hdr.affine = [srows.srow_x, srows.srow_y, srows.srow_z, [0, 0, 0, 1]];
-        // Update current buffer bounds
-        // Buffer starts at region.chunkAlignedStart and has extent fetchedShape
+        // Update current buffer bounds from the un-flipped affine
+        // (bounds stay in OME-Zarr world space for clip plane math)
         this._currentBufferBounds = {
             min: [
                 affine[12], // x offset (world coord of buffer origin)
@@ -464,6 +515,15 @@ export class OMEZarrNVImage extends NVImage {
                 affine[14] + fetchedShape[0] * sz,
             ],
         };
+        // For 2D images, negate y-scale so NiiVue's calculateRAS() flips
+        // the rows to account for top-to-bottom pixel storage order.
+        if (this._flipY2D && this._is2D) {
+            affine[5] = -sy;
+            affine[13] += (fetchedShape[1] - 1) * sy;
+        }
+        // Update affine in header
+        const srows = affineToNiftiSrows(affine);
+        this.hdr.affine = [srows.srow_x, srows.srow_y, srows.srow_z, [0, 0, 0, 1]];
         // Recalculate RAS orientation
         this.calculateRAS();
     }
@@ -581,13 +641,49 @@ export class OMEZarrNVImage extends NVImage {
             const needsCompute = isPreviewLevel ||
                 (isTargetLevel && this._omeroComputedForLevel !== this.targetLevelIndex);
             if (needsCompute) {
-                const computedOmero = await computeOmeroFromNgffImage(ngffImage);
+                // Pass the chunk cache so decoded chunks from OMERO statistics
+                // computation are reused by subsequent zarrGet() calls.
+                const omeroOpts = this._chunkCache
+                    ? { cache: this._chunkCache }
+                    : undefined;
+                const computedOmero = await computeOmeroFromNgffImage(ngffImage, omeroOpts);
                 this._omero = computedOmero;
                 this._omeroComputedForLevel = levelIndex;
                 this.applyOmeroToHeader();
             }
         }
     }
+    /**
+     * Get per-channel normalization windows for non-uint8 RGB/RGBA.
+     *
+     * Uses OMERO `window.start`/`window.end` (or `window.min`/`window.max`)
+     * when available. Falls back to computing min/max from the raw data.
+     *
+     * @param data - Raw multi-component data from the zarr fetch
+     * @param components - Number of components per voxel (3 or 4)
+     * @returns Per-channel windows for normalization to uint8
+     */
+    _getChannelWindows(data, components) {
+        if (this._omero?.channels?.length) {
+            const windows = [];
+            for (let c = 0; c < components; c++) {
+                const channel = this._omero.channels[Math.min(c, this._omero.channels.length - 1)];
+                const win = channel?.window;
+                if (win) {
+                    windows.push({
+                        start: win.start ?? win.min ?? 0,
+                        end: win.end ?? win.max ?? 1,
+                    });
+                }
+                else {
+                    windows.push({ start: 0, end: 1 });
+                }
+            }
+            return windows;
+        }
+        // No OMERO metadata: fall back to per-channel min/max from data
+        return computeChannelMinMax(data, components);
+    }
     /**
      * Handle clip plane change from NiiVue.
      * This is called when the user interacts with clip planes in NiiVue.
@@ -1438,14 +1534,22 @@ export class OMEZarrNVImage extends NVImage {
      * Create a new slab buffer state for a slice type.
      */
     _createSlabBuffer(sliceType) {
-        const bufferManager = new BufferManager(this.maxPixels, this.dtype);
+        const componentsPerVoxel = this._channelInfo?.components ?? 1;
+        const bufferManager = new BufferManager(this.maxPixels, this.dtype, componentsPerVoxel);
         const nvImage = new NVImage();
         // Initialize with placeholder NIfTI header (same as main image setup)
         const hdr = new NIFTI1();
         nvImage.hdr = hdr;
         hdr.dims = [3, 1, 1, 1, 1, 1, 1, 1];
-        hdr.datatypeCode = getNiftiDataType(this.dtype);
-        hdr.numBitsPerVoxel = getBytesPerPixel(this.dtype) * 8;
+        if (this._channelInfo && isRGBImage(this.multiscales.images[0])) {
+            const rgbCode = getRGBNiftiDataType(this._channelInfo);
+            hdr.datatypeCode = rgbCode;
+            hdr.numBitsPerVoxel = rgbCode === NiftiDataType.RGB24 ? 24 : 32;
+        }
+        else {
+            hdr.datatypeCode = getNiftiDataType(this.dtype);
+            hdr.numBitsPerVoxel = getBytesPerPixel(this.dtype) * 8;
+        }
         hdr.pixDims = [1, 1, 1, 1, 0, 0, 0, 0];
         hdr.affine = [
             [1, 0, 0, 0],
@@ -1657,7 +1761,17 @@ export class OMEZarrNVImage extends NVImage {
         const result = await this.coalescer.fetchRegion(ngffImage, levelIndex, fetchRegion, `slab-${SLICE_TYPE[sliceType]}-${levelIndex}`);
         // Resize buffer and copy data
         const targetData = slabState.bufferManager.resize(fetchedShape);
-        targetData.set(result.data);
+        const normalize = needsRGBNormalization(ngffImage, this.dtype);
+        if (normalize && this._channelInfo) {
+            // Non-uint8 RGB/RGBA: normalize raw data to uint8 using OMERO windows
+            const windows = this._getChannelWindows(result.data, this._channelInfo.components);
+            const normalized = normalizeToUint8(result.data, this._channelInfo.components, windows);
+            targetData.set(normalized);
+        }
+        else {
+            // uint8 RGB or scalar: direct copy
+            targetData.set(result.data);
+        }
         slabState.nvImage.img =
             slabState.bufferManager.getTypedArray();
         // Update slab position tracking
@@ -1669,8 +1783,9 @@ export class OMEZarrNVImage extends NVImage {
             // Label images: apply discrete colormap to the slab NVImage
             this._applyLabelColormap(slabState.nvImage, result.data);
         }
-        else if (this._omero) {
-            // Apply OMERO metadata if available
+        else if (this._omero && !normalize) {
+            // Apply OMERO metadata for scalar / uint8 RGB.
+            // Normalized RGB already consumed the OMERO window during normalization.
             this._applyOmeroToSlabHeader(slabState.nvImage);
         }
         // Reset global_min so NiiVue recalculates intensity ranges
@@ -1752,6 +1867,11 @@ export class OMEZarrNVImage extends NVImage {
         affine[12] += fetchStart[2] * sx; // x offset
         affine[13] += fetchStart[1] * sy; // y offset
         affine[14] += fetchStart[0] * sz; // z offset
+        // For 2D images, negate y-scale before normalization
+        if (this._flipY2D && this._is2D) {
+            affine[5] = -sy;
+            affine[13] += (fetchedShape[1] - 1) * sy;
+        }
         // Apply normalization to the entire affine (scale columns + translation)
         for (let i = 0; i < 15; i++) {
             affine[i] *= normalizationScale;