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The Integrated Mitotic Stem Cell is a data driven model and visualization tool that captures a holistic view of human cell division. This model transforms microscopy images of 15 individual organelles into an integrated representation of the undifferentiated human induced pluripotent stem cell (hIPSC) at each major stage of mitosis.

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allen-cell-animated/visual-essay-integrated-mitotic-cell

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imsc-visual-essay

Structure

src/
    components/
    constants/
    styles/


Running locally

To run this application in development, run $ npm install then $ npm start. This will start webpack-dev-server, running by default on the port specified in webpack/constants.js. To view, visit http://localhost:{PORT}. Webpack-dev-server will watch all relevant project files, and reload the browser automatically when those files change.

Note (9/13/2021)

If you run into EINTEGRITY errors and/or TypeScript errors upon npm install or npm start (before having made any local changes to the code), you may need to configure npm to install dependencies from the AICS Artifactory (in ~/.npmrc). If that doesn't work, you may also need to run the application in a node v10.5.0 environment. If we want to continue to develop this application and/or make it available for community contributions in the future, we should update the dependencies as they are rather outdated.


Build-time configuration:

Env var Default Options
DEPLOYMENT_ENV dev "dev", "staging", "production"

Differences in builds by environment:

Target Sources Maps Uglification NODE_ENV === 'production'
dev true false false
staging true false false
production false true true

Deployment

Staging deployment

Any commits to the main branch are automatically deployed to staging.

Production deployment

On main branch

  1. Make a new version: npm version [patch/minor/major]
  2. Push the new package.json version: git push origin main
  3. Push the new tag: git push origin [NEW_TAG] This will trigger a github workflow which copies the assets from the staging bucket into the production bucket.

About

The Integrated Mitotic Stem Cell is a data driven model and visualization tool that captures a holistic view of human cell division. This model transforms microscopy images of 15 individual organelles into an integrated representation of the undifferentiated human induced pluripotent stem cell (hIPSC) at each major stage of mitosis.

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