Allen Cell Explorer
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​ALLEN INSTITUTE FOR CELL SCIENCE

​Allen Cell Explorer

Learn about cells
Previous highlights
Videos & tutorials
Cells for your lab
Research projects
Explore our data

Highlights

Allen Cell Structure Segmenter
We present the Allen Cell Structure Segmenter, a python-based, open-source toolkit that combines classic 3D image segmentation with artificial intelligence to detect cellular structures.

​Read more about this new toolkit and how it can help biologists analyze their 3D images of cells and be more quantitative with their results.
Allen Cell Structure Segmenter
Read Release Article
Segmenter
IMSC
A visual essay on the Integrated Mitotic Stem Cell
We present the Integrated Mitotic Stem Cell as a data driven model and visualization tool that captures a holistic view of human cell division for the first time.

​By enabling a deeper understanding of how healthy human cells divide, the model will further basic biology research as well as studies of cancer, a disease that often results from cell division gone awry.
Integrated Mitotic Stem Cell
New resources to access mitotic stem cell states & endogenously tagged cardiomyocytes

Cell Feature Explorer

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Plot & view any of 39,200 3D cell images sorted by their features

Cell Catalog

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4 new fluorescently-tagged hiPSC lines available in the Allen Cell Collection

Integrated Mitotic Stem Cell

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A model & visualization tool to better understand how stem cells divide
The new lines include single tags targeting a muscle-specific actin filament, a pluripotent transcription factor, and a dual tag targeting nucleolar substructures. In addition, we released an additional cytoplasmic-expressing control line.

Previous highlights

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Visual Guide to Human Cells
This visual guide organizes information about human induced pluripotent stem cells into a curated collection of interactive models. Users can rotate and zoom into 3D cells, each segmented from real data for each phase of mitosis, while learning more about individual cell structures and functions.
Visual Guide
Read Release Article
Label-free Determination
As part of the Allen Integrated Cell, we have developed and implemented a label-free prediction method for determining the location of 3D structures inside the cell, directly from transmitted light images.
  • Read Allen Institute Press Release
  • Read Nature Method article
  • Access GitHub repository
Explore Label-free
Label-free Cell Viewer

Videos & tutorials

Instructional videos provided to ensure success in your lab & to overview tools available on allencell.org

Five Allen Methods tutorials 

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Two Allen Cell Explorer tutorials 

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Cells & plasmids for your lab

​We have created a series of gene edited human iPSCs that we use as the foundation for our image data, and that we share with the larger scientific community.

Cell catalog

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Obtain cell lines & plasmids for your lab​; quality control details

Genomics

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​Explore & download genomics & transcriptomics data

Methods for success

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Step-by-step protocols to generate & image gene-edited hiPSCs successfully

Research Projects described

Drug perturbation pilot

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Observations describing effects of drugs on 3D cellular organization

Label-free determination

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Multiple cell structures visualized direct from brightfield imaging

3D probabilistic modeling

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3D visualization of hIPS cell structure variation

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Copyright © 2019 Allen Institute. All Rights Reserved.
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
    • Deep Cell Zoom
    • Segmenter
    • Data Downloading
    • Software & Code
    • 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