AICS Volume Viewer

This is a WebGL canvas-based volume viewer. It can display multichannel volume data of 8-bit intensity values. Volume data is provided to the core 3d viewer in two parts. The first part is via a json object containing dimensions and other metadata. The second part is the volume data itself.

The volume-viewer package exposes two key modules:

• View3d is the viewing component that contains a canvas and supports zoom/pan/rotate interaction with the volume.
• Volume is the class that holds the volume data. After initialization, this is generally a read-only holder for raw data.

It also provides the following two utility modules:

• VolumeLoader is a convenience class for downloading and unpacking texture atlases from .png files (up to 3 channels per png) into a Volume.
• VolumeMaker is a convenience module for creating simple test volume data

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

• raw Uint8Arrays of 3d volume data (one Uint8Array per channel). ( Volume.setChannelDataFromVolume )
• texture atlases (png files or Uint8Arrays containing volume slices tiled across a 2d image) ( 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 volume viewer up and running is as follows:

import { View3d, Volume, VolumeLoader, VolumeMaker } from "volume-viewer";

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

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

// create a volume image with dimensions passed in via jsondata
// this json format is documented in Volume.ts as ImageInfo
const aimg = new Volume(jsondata);

// tell the viewer about the image
view3D.addVolume(aimg);

// load volume data into the image.  volumeData here is an array of Uint8Arrays.
// each element in volumeData is a flattened 3d volume stored in xyz order in a Uint8Array.
// Intensities must have been be scaled to fit in uint8.
for (let i = 0; i < volumeData.length; ++i) {
  aimg.setChannelDataFromVolume(i, volumeData[i], [0, 255]);
  // optional: initialize with a lookup table suitable for visualizing noisy biological data
  const hmin = aimg.getHistogram(i).findBinOfPercentile(0.5);
  const hmax = aimg.getHistogram(i).findBinOfPercentile(0.983);
  const lut = new Lut().createFromMinMax(hmin, hmax);
  aimg.setLut(i, lut);
}

// enable only the first 3 channels
for (var ch = 0; ch < aimg.num_channels; ++ch) {
  view3D.setVolumeChannelEnabled(aimg, ch, ch < 3);
}

// set some viewing parameters
view3D.updateDensity(aimg, 0.05);
view3D.updateExposure(0.75);
// tell the viewer to update because new data has been added.
view3D.updateActiveChannels(aimg);
view3D.updateLuts(aimg);

React example

• in VolumeViewer.jsx

import * as React from "react";

import { View3d, Volume, VolumeLoader, VolumeMaker } from 'volume-viewer';


const url = 'https://s3-us-west-2.amazonaws.com/bisque.allencell.org/v1.4.0/Cell-Viewer_Thumbnails/AICS-11/';
const volumeToLoad = 'AICS-11_3136_atlas.json';
export class VolumeViewer extends React.Component {
    constructor(props) {
        super(props);
        this.volumeViewer = React.createRef();
    }

    componentDidMount() {
        const ref = this.volumeViewer;
        if (!ref.current) {
            return;
        }
        const el = ref.current;
        this.view3D = new View3d(el);
        // to download a volume encoded as a json plus tiled png images:
        // this format is documented in Volume.ts as ImageInfo
        return fetch(`${url}/${volumeToLoad}`)
            .then((response) => {
                return response.json();
            })
            .then(jsondata => {
                // when json file is received, create Volume object
                const aimg = new Volume(jsondata);
                // tell the 3d view about it.
                this.view3D.addVolume(aimg);

                jsondata.images = jsondata.images.map(img => ({ ...img, name: `${url$}${img.name}` }));
                // download the volume data itself in the form of tiled png files
                VolumeLoader.loadVolumeAtlasData(aimg, jsondata.images, (url, channelIndex) => {
                    // initialize each channel as it arrives and tell the view to update.
                    const hmin = aimg.getHistogram(channelIndex).findBinOfPercentile(0.5);
                    const hmax = aimg.getHistogram(channelIndex).findBinOfPercentile(0.983);
                    const lut = new Lut().createFromMinMax(hmin, hmax);
                    aimg.setLut(i, lut);

                    this.view3D.setVolumeChannelEnabled(aimg, channelIndex, channelIndex < 3);
                    this.view3D.updateActiveChannels(aimg);

                    this.view3D.updateLuts(aimg);
                });
                // set some initial viewing parameters
                this.view3D.setCameraMode('3D');
                this.view3D.updateDensity(aimg, 0.05);
                this.view3D.updateExposure(0.75);
            });
    }

    render() {
        return (
            <div
                style={{height: 1000, width: '100%'}}
                ref={this.volumeViewer}
            />
        )
    }

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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