Vol-E core

This is a WebGL canvas-based volume viewer. It can display multichannel volume data with high channel counts, and is optimized for OME-Zarr files. With OME-Zarr, the viewer can prefetch and cache Zarr chunks in browser memory for optimized performance.

The Vol-E core package exposes several key modules:

• View3d is the viewing component that contains a canvas and supports zoom/pan/rotate interaction with the volume via VolumeDrawable.
• Volume is the class that holds the volume dimensions and a collection of Channels that contain the volume pixel data. After initialization, this is generally a read-only holder for raw data.
• VolumeLoaderContext is an interface that lets you initialize asynchronous data loading of different formats via its createLoader method.
• IVolumeLoader is an interface for requesting volume dimensions and data.
• LoadSpec is a small bundle of information to guide the IVolumeLoader on exactly what to load.

There are several ways to deliver volume data to the viewer:

• Load OME-Zarr from publicly accessible web links. Authentication is not explicitly supported in Vol-E.
• Load raw TypedArrays of 3d volume data ( see RawArrayLoader and Volume.setChannelDataFromVolume ).
• (legacy) Load texture atlases as .png files or Uint8Arrays containing volume slices tiled across a 2d image ( see JsonImageInfoLoader and Volume.setChannelDataFromAtlas ).

Example

See public/index.ts for a working example. (npm install; npm run dev will run that code)

The basic code to get the viewer up and running is as follows:

// find a div that will hold the viewer
const el = document.getElementById("vol-e");

// create the loaderContext
const loaderContext = new VolumeLoaderContext(CACHE_MAX_SIZE, CONCURRENCY_LIMIT, PREFETCH_CONCURRENCY_LIMIT);

// create the viewer.  it will try to fill the parent element.
const view3D = new View3d(el);
view3D.loaderContext = loaderContext;

// ensure the loader worker is ready
await loaderContext.onOpen();
// get the actual loader.  In most cases this will create a WorkerLoader that uses a OmeZarrLoader internally.
const loader = await loaderContext.createLoader(path);

const loadSpec = new LoadSpec();
// give the loader a callback to call when it receives channel data asynchronously
const volume = await loader.createVolume(loadSpec, (v: Volume, channelIndex: number) => {
  const currentVol = v;

  // currently, this must be called when channel data arrives (here in this callback)
  view3D.onVolumeData(currentVol, [channelIndex]);

  view3D.setVolumeChannelEnabled(currentVol, channelIndex, true);

  // these calls tell the viewer that things are out of date
  view3D.updateActiveChannels(currentVol);
  view3D.updateLuts(currentVol);
  view3D.redraw();
});
// tell the viewer about the image
view3D.addVolume(volume);
// start requesting volume data
loader.loadVolumeData(volume);

React example

See vole-app for a complete application that wraps View3D in a React component.

Acknowledgements

The ray marched volume shader is a heavily modified version of one that has its origins in Bisque. The core path tracing implementation was adapted from ExposureRender.

BisQue license

Center for Bio-Image Informatics, University of California at Santa Barbara

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