omezarr-tilesource 0.2.0 → 0.3.0

package/README.md

@@ -12,7 +12,7 @@ An OpenSeadragon tile source for the OME-Zarr bioimage file format
 
 ## Prerequisites
 
-OpenSeadragon 5 or newer
+OpenSeadragon 6 or newer
 
 ## Installation
 
@@ -39,9 +39,11 @@ const tileSource2 = {
     type: "ome-zarr",
     url: url,
     // zip: undefined,  // undefined = OME-Zarr ZIP auto-detection based on .ozx suffix
-    // t: undefined,
-    // c: undefined,
-    // z: undefined
+    // c: undefined,  // undefined = composite of all active channels (requires dataType "context2d")
+    // z: undefined,  // undefined = omero metadata default
+    // t: undefined,  // undefined = omero metadata default
+    // dataType: undefined,  // "context2d" (default, rendered tiles) or "ome-zarr" (raw single-channel chunks)
+    // autoBoost: undefined  // boost brightness of dark tiles (default false)
 };
 
 // direct instantiation with URL (works with any OME-Zarr storage backend)
@@ -51,9 +53,11 @@ const tileSource3 = new OMEZarrTileSource(url);
 const tileSource4 = new OMEZarrTileSource({
     url: url,
     // zip: undefined,  // undefined = OME-Zarr ZIP auto-detection based on .ozx suffix
-    // t: undefined,
-    // c: undefined,
-    // z: undefined
+    // c: undefined,  // undefined = composite of all active channels (requires dataType "context2d")
+    // z: undefined,  // undefined = omero metadata default
+    // t: undefined,  // undefined = omero metadata default
+    // dataType: undefined,  // "context2d" (default, rendered tiles) or "ome-zarr" (raw single-channel chunks)
+    // autoBoost: undefined  // boost brightness of dark tiles (default false)
 });
 
 const viewer = OpenSeadragon(
@@ -67,6 +71,25 @@ const viewer = OpenSeadragon(
 );
 ```
 
+## Data pipeline
+
+By default (`dataType: "context2d"`), tiles are rendered by the tile source and
+passed to OpenSeadragon as 2D canvas contexts, using the rendering settings
+(color, color LUT/map, contrast limits, inversion) from the omero metadata. For
+multi-channel images without `c`, all active channels are rendered into a
+composite image.
+
+With `dataType: "ome-zarr"`, tiles are instead downloaded as raw single-channel
+zarrita chunks and passed to OpenSeadragon with the data type `ome-zarr` (see
+the `OMEZarrTileData` type). Multi-channel images therefore require the `c`
+option. A converter from `ome-zarr` to `context2d` is registered on
+`OpenSeadragon.converter` when the module is imported (and by
+`OMEZarrTileSource.enable`). It reads the rendering settings at conversion time
+from the omero channel referenced by the tile data (`OMEZarrTileData.channel`).
+The channel object is shared by all tiles of a tile source, so advanced users
+may modify it (e.g. from a `tile-invalidated` handler) and re-render the cached
+tiles using `viewer.requestInvalidate()`.
+
 ## Example
 
 [Example](https://tissuumaps.github.io/OMEZarrTileSource)

package/dist/{__vite-browser-external-YbutIfMq-Cv1_GH0S.js → __vite-browser-external-YbutIfMq-DmIpWUUk.js}

@@ -1,4 +1,4 @@
-//#region node_modules/.pnpm/ome-zarr.js@0.0.19/node_modules/ome-zarr.js/dist/__vite-browser-external-YbutIfMq.js
+//#region node_modules/.pnpm/ome-zarr.js@0.0.20/node_modules/ome-zarr.js/dist/__vite-browser-external-YbutIfMq.js
 var e = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
 	__proto__: null,
 	default: {}

package/dist/omezarr-tilesource.d.ts

@@ -1,21 +1,24 @@
+import { Channel } from 'ome-zarr.js';
 import { default as default_2 } from 'openseadragon';
+import * as zarr from 'zarrita';
+
+export declare interface OMEZarrTileData {
+    chunk: zarr.Chunk<zarr.NumberDataType | zarr.BigintDataType>;
+    channel: Channel;
+    autoBoost?: boolean;
+}
 
 export declare class OMEZarrTileSource extends default_2.TileSource {
-    static readonly DUMMY_XHR: XMLHttpRequest;
     readonly url: string;
-    width: number;
-    height: number;
-    aspectRatio: number;
-    dimensions: default_2.Point;
-    maxLevel: number;
-    ready: boolean;
     readonly zip?: boolean;
-    readonly t?: number;
     readonly c?: number;
     readonly z?: number;
-    private _omero?;
-    private _multiscale?;
-    private _axisIndices?;
+    readonly t?: number;
+    readonly dataType: "ome-zarr" | "context2d";
+    readonly autoBoost?: boolean;
+    width: number;
+    height: number;
+    private _image?;
     private _arrays?;
     constructor(url: string);
     constructor(options: OMEZarrTileSourceOptions);
@@ -31,24 +34,20 @@ export declare class OMEZarrTileSource extends default_2.TileSource {
     downloadTileStart(context: default_2.ImageJob): void;
     downloadTileAbort(context: default_2.ImageJob): void;
     static enable(os?: typeof default_2): void;
-    private static _getMultiscale;
-    private static _getAxisIndices;
+    private static _learnConverters;
+    private _getActiveChannelIndices;
+    private static _render;
 }
 
-export declare type OMEZarrTileSourceClass = typeof OMEZarrTileSource;
-
 export declare interface OMEZarrTileSourceOptions {
     type?: "ome-zarr";
     url: string;
     zip?: boolean;
-    t?: number;
     c?: number;
     z?: number;
+    t?: number;
+    dataType?: "ome-zarr" | "context2d";
+    autoBoost?: boolean;
 }
 
 export { }
-
-
-declare module "openseadragon" {
-    let OMEZarrTileSource: OMEZarrTileSourceClass;
-}