Allen Cell Explorer
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Data Notebook Exploration

Explore and access our data with Jupyter Notebooks
 
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Pages below mix code and visualizations using the common Jupyter Notebook data science toolkit.
Jupyter.org provides no-installation-needed introductions to this powerful ecosystem.
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Cell shape analysis

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What shape are our hiPS Cells?

Programmatic data access

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Automating access to our cell images & other data using Quilt

Why Jupyter?   •    What is it?

​We want to improve access to powerful data analysis tools.
Let’s go into more detail on why we’ve settled on supporting the Jupyter ecosystem and how this work provides access to our data through it.
Jupyter Notebooks let us:
  • Combine code and styled text so that we can develop models, take notes, and explain our work, as we go, in the same document.
  • Share and view the same document in varied media, from development environments to web pages (such as this one).
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cellscience.alleninstitute.org
  • About
    • What We Do
    • FAQs
    • Videos & Tutorials
    • Site Updates
    • < Forum >
    • < AllenInstitute.org >
  • Animated Cell
    • Educational Resources
    • Visual Guide to Human Cells
    • Visual Guide Tutorial
    • Research Projects >
      • Pathtrace rendering
  • Cells & Biology
    • Cell Catalog
    • About our Cells >
      • hiPS Cell Biology Overview
      • Cell Structure Observations
      • Cell Catalog QuickView
    • Genomics
    • Methods & SOPs >
      • Methods for Cells in the Lab
      • Cell Methods: Videos from the Lab
      • Methods for Microscopy
    • Research Projects >
      • hiPS Cells During Mitosis
      • Drug Perturbation Pilot
      • Differentiation Into Cardiomyocytes
      • Why Endogenous Tagging?
  • Data & Tools
    • Cell Catalog
    • 3D Cell Viewer
    • Cell Feature Explorer
    • Integrated Mitotic Stem Cell Z-stack Viewer
    • Deep Cell Zoom
    • Segmenter
    • Data Downloading
    • Software & Code
    • Simularium
    • Research Projects >
      • Extracting Information
  • Modeling & Analysis
    • Integrated Mitotic Stem Cell
    • Allen Integrated Cell
    • Label-free Determination
    • Data Notebook Exploration >
      • Cell Shape Analysis
      • Programmatic Data Access
    • Research Projects >
      • 3D Probabilistic Modeling
  • News & Publications
    • News Feed
    • Publications
    • Archived Content