vitessce / Vitessce

Visual Integration Tool for Exploration of Spatial Single-Cell Experiments

• Latest release demo
• Previous demos
• Previous releases on NPM

Integrations

Vitessce is being used in the following projects:

• HuBMAP Data Portal

Architecture

For more information, see the glossary.

Data

The demo features data from several collaborators, with preprocessing done by vitessce-data.

Usage

Vitessce components can be used in React projects by installing the package from NPM:

npm install vitessce

The following code demonstrates the <Status/> and <Scatterplot/> components.

Note the vitessce-container and vitessce-theme-light classes added to the parent div element. Vitessce component styles are scoped under these classes, which means that a parent element must apply the classes in order for child components to inherit the expected styles.

import React from 'react';
import { Scatterplot } from 'vitessce/es/production/scatterplot.min.js';
import { Status } from 'vitessce/es/production/status.min.js';
import 'vitessce/es/production/static/css/index.css';

export default function App() {
    const view = { target: [0, 0, 0], zoom: 0.75 };
    const mapping = "PCA";
    const cells = {
        1: { mappings: { [mapping]: [0, 0] } },
        2: { mappings: { [mapping]: [1, 1] } },
        3: { mappings: { [mapping]: [1, 2] } }
    };
    const selectedCellIds = new Set();
    const dimensions = { width: '400px', height: '400px', margin: '10px' };

    return (
        <div className="vitessce-container vitessce-theme-light">
            <div className="card card-body bg-secondary" style={dimensions}>
                <Status
                    info="Hello world"
                    removeGridComponent={() => {}}
                />
            </div>
            <div className="card card-body bg-secondary" style={dimensions}>
                <Scatterplot
                    uuid="my-vitessce-scatterplot"
                    view={view}
                    mapping={mapping}
                    cells={cells}
                    selectedCellIds={selectedCellIds}
                    cellColors={null}
                    updateStatus={(message) => {}}
                    updateCellsSelection={(selectedIds) => {}}
                    updateCellsHover={(hoverInfo) => {}}
                    updateViewInfo={(viewInfo) => {}}
                    clearPleaseWait={(layerName) => {}}
                />
            </div>
        </div>
    );
}

If you are interested in using Vitessce in the browser as part of a script tag or the like, we also export a umd build (the above snippet uses an es bundle). Note that our es bundles contain none of the dependencies, all of which should be installed by npm automatically when it reads the package.json file that our package ships with. The advanatage of not bundling everything is that we can keep the size of our bundle down and avoid any upstream compilation issues or the like.

Development

First check your NodeJS version: It should work with NodeJS 8, 10, 12, 13, or 14.

$ node --version
v14.0.0

Note: NodeJS 14 may require the max_old_space_size option to be increased (apparently due to a different heap management strategy):

export NODE_OPTIONS=--max_old_space_size=4096

Checkout the project, cd, and then:

$ npm install
$ npm start

The development server will refresh the browser as you edit the code.

• To run all the Travis checks: ./test.sh
• To run just the unit tests: npm run test:watch

Deployment

Demo

To build the current branch and push to S3, first confirm that you have installed the AWS CLI and are in the appropriate AWS account:

$ aws iam list-account-aliases --query 'AccountAliases[0]'
"gehlenborglab"

and then run this script:

$ ./push-demo.sh

This will build, push to S3, and finally open the demo deployment in your browser.

Release

If you haven't already, push a fresh demo and do a last manual test of the deployment. If it looks good, copy it to vitessce.io:

$ ./copy-prod.sh https://{url returned by push-demo.sh}

The vitessce package is published to the NPM registry by Travis when the version in package.json has been updated and pushed to the master branch. To perform this update:

• Check out a new branch for the release,
  • Update the CHANGELOG.md to remove the "in progress" text from the current version heading.
  • Update the version by running npm version [major | minor | patch] (note: this will add a git commit and a git tag).
• Make a pull request to merge from the release branch into master.

Travis uses the NPM_EMAIL and NPM_TOKEN variables that can be set using the web interface (Settings -> Environment Variables).

Related Subsidiary Projects

• Viv: A library for multiscale visualization of high-resolution multiplexed tissue data on the web.
• vitessce-grid: Wrapper for react-grid-layout
• vitessce-data: Scripts to generate sample data
• ome-tiff-tiler: Docker container to generate tiles from OME-TIFF

Old Presentations

• July 2020: Ilan Gold's lab meeting update
• 2020 NLM Informatics Training Conference (Trevor)
• Trevor Manz's overview of multimodal imaging in Vitessce
• Ilan Gold's overview of IF Imagery
• Trevor Manz's wrap-up on Arrow, Zarr, and IMS
• September 2019 HuBMAP Poster
• August 2019 SIBMI Presentations
• July 2019 lab meeting: Intern progress reports and HuBMAP collaboration
• 2019 Harvard IT Summit
• Map 2019 lab meeting: Misc. tools
• April 2019 lab meeting: Software engineering