Visual Integration Tool for Exploration of Spatial Single-Cell Experiments
Vitessce consists of reusable interactive views including a scatterplot, spatial+imaging plot, genome browser tracks, statistical plots, and control views, built on web technologies such as WebGL.
Vitessce enables visual analysis of multi-modal assay types which probe biological systems through techniques such as microscopy, genomics, and transcriptomics.
Visualize large datasets stored in static cloud object stores such as AWS S3. No need to manage or pay for expensive compute infrastructure for visualization purposes.
Vitessce can be used in React projects by installing the package from NPM:
npm install vitessce
For more details, please visit the documentation.
First install PNPM v7. We develop and test against NodeJS v18.6.0
and NPM 8.13.2
.
Note NodeJS may require the
max_old_space_size
value to be increased.
. ./set-node-options.sh
Checkout the project, cd
, and then:
pnpm install
pnpm run build # for @vitessce/icons and @vitessce/workers
pnpm run start-demo
The development server will refresh the browser as you edit the code.
Please use one of the following naming conventions for new branches:
{github-username}/{feature-name}
{github-username}/fix-{issue-num}
We use squash merging for pull requests.
pnpm run meta-dryrun
pnpm run meta-update
For the end-to-end tests, they depend on
pnpm run build-demo
- To run all the tests, both unit and e2e:
./test.sh
- To run just the unit tests:
pnpm run test
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}
Note: if you need to obtain this URL later:
Copy dev to https://s3.amazonaws.com/vitessce-data/demos/$DATE/$HASH/index.html
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}
Note: if you need to obtain this URL later:
Copy docs to https://s3.amazonaws.com/vitessce-data/docs-root/$DATE/$HASH/index.html
From GitHub Actions:
- The
vitessce
package is published to the NPM registry by GitHub Actions when the version inpackage.json
has been updated and pushed to themain
branch. To perform this update, make a pull request to merge from the release branch intomain
.
From local machine:
pnpm run build
pnpm publish --filter='./packages/**' --no-git-checks --tag beta --access public --dry-run
In this project we try to follow semantic versioning. The following are examples of things that would require a major, minor, or patch type of bump.
Bug fixes, minor feature improvements, additional view types, additional coordination types, and additional file type implementations are possible in a patch version bump.
When a coordination type is added, it must be reflected by a new view config JSON schema with an incremented version
property, and a new view config upgrade function to enable previous view config versions to remain compatible.
The default schema version parameter of the VitessceConfig
constructor may also change to reflect the new schema version.
An exported helper function or React component for plugin views had a change in props or function signature. Major feature improvements or additions.
The exported constant values changed, such as view types and coordination types, such that previous code using these values may no longer run successfully.
React props of the main <Vitessce />
component changed.
Major behavior changes or interface updates.
Changes to the directory structure or filenames in the dist/
directory that could result in broken import statements.
- 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
- May 2022: Mark Keller's lab meeting update
- February 2022: Mark Keller's lab meeting update
- October 2021: Mark Keller's lab meeting update
- September 2021: HuBMAP Consortium Sci-Tech Webinar (Mark)
- June 2021: Mark Keller's lab meeting update
- April 2021: Spatial Biology Europe (Mark)
- 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