![Vitessce Vitessce logo](https://raw.githubusercontent.com/mukundraj/vitessce/master/./img/logo-transparent.png)
Visual Integration Tool for Exploration of Spatial Single-Cell Experiments
You can also use the demo website for visualizing your own data via view configs passed in as url parameters. If you are storing a json
view configuration on a remote server, the url will look something like http://vitessce.io/?url=https://example.com/my_config.json
. Otherwise, if you have a view configuration that is not stored somewhere that can be accessed via a web server, you can do something like http://vitessce.io/?url=data:,{"name":"FAKE", "version": "0.1.0", "description":"fake dataset", "layers":[], "staticLayout":[{"component":"description", "props":{"description": "Hello World"}, "x":0, "y": 0, "w": 2, "h": 2}]}
where data:
prepends the actual view config.
Vitessce components can be used in React projects by installing the package from NPM:
npm install vitessce
For more details, please visit the documentation.
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
Before running any of the deployment scripts, confirm that you have installed the AWS CLI and are in the appropriate AWS account:
$ aws iam list-account-aliases --query 'AccountAliases[0]'
"gehlenborglab"
To build the current branch and push the "minimal" demo and docs sites to S3, run this script:
$ ./push-demos.sh
This will build the demo and docs, push both to S3, and finally open the docs deployment in your browser.
To make a release of the dev site, docs site, and NPM package:
$ ./create-release.sh patch
This script does the following:
- Checks out a new branch for the release
- Runs
npm version (major | minor | patch)
(depending on the first argument passed to the script) - Pushes staging demos via
./push-demos.sh
- Updates the CHANGELOG.md
- Makes a pull request using the GitHub CLI
gh pr create
After doing a manual test of the deployment of the dev site, if it looks good, copy it to dev.vitessce.io:
$ ./copy-dev.sh https://{url returned by create-release.sh or push-demos.sh}
After doing a manual test of the deployment of the docs, if it looks good, copy it to vitessce.io:
$ ./copy-docs.sh https://{url returned by create-release.sh or push-demos.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, 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).
Vitessce provides a pure ESM export intended for bundlers (e.g. Vite, Webpack, Rollup).
Most modern bundlers should work out of the box, however bundling with legacy Webpack (<5.0)
requires adding the following resolution alias
to your webpack.config.js
.
module.exports = {
//...
resolve: {
alias: {
'txml/txml': 'txml/dist/txml'
},
},
};
This fix is temporary and will no longer be necessary after the next release of Viv.
- Viv: A library for multiscale visualization of high-resolution multiplexed tissue data on the web.
- HiGlass: A library for multiscale visualization of genomic data on the web.
- vitessce-python: Python API and Jupyter widget.
- vitessce-r: R API and R htmlwidget.
- vitessce-data: Scripts to generate sample data
- January 2021: Ilan Gold's lab meeting update
- December 2020: Mark Keller's lab meeting update
- November 2020: Ilan Gold's lab meeting update
- October 2020: Mark Keller's lab meeting update
- July 2020: Ilan Gold's lab meeting update
- June 2020: NLM Informatics Training Conference (Trevor)
- May 2020: Trevor Manz's overview of multimodal imaging in Vitessce
- January 2020: Ilan Gold's overview of IF Imagery
- January 2020: Trevor Manz's wrap-up on Arrow, Zarr, and IMS
- September 2019: HuBMAP Poster
- August 2019: SIBMI Presentations
- July 2019: Intern progress reports and HuBMAP collaboration
- May 2019: Harvard IT Summit
- May 2019: Misc. tools
- April 2019: Software engineering