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Preprocessing and exploratory analysis of thalamus MERFISH data

Each new Code Ocean Capsule is a git repo. You can make a Capsule by cloning a pre-existing git repo, in a way that uses the user's credentials and maintains a connection to the original repo, or without any credentials and creates a new repo in Code Ocean. By maintaining a link to the original repo, changes can be pushed and pulled between repos.

In this section, we will:

  1. Create a Capsule from a GitHub template.
  2. Make an access token in GitHub and bring it into Code Ocean.
  3. Clone the git repo with thalamus MERFISH data and analysis notebooks so that we can sync changes.
  4. We will have to set the environment in the Capsule.
  5. Commit changes
  6. Find and attach Data Assets

You can run the notebooks in this Capsule by opening a Cloud Workstation or pressing the Reproducible Run button to run the Capsule code end-to-end, without any intervention.

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