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​ALLEN INSTITUTE FOR CELL SCIENCE

​Allen Cell Explorer

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

Black Lives Matter. 

We, the Allen Institute, stand with our Black employees. 
We want to be more than allies. We want to further our commitment as accomplices. 
We are in this together.

Highlights

Introducing the Allen Institute Behind the Scenes of Science Series
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Behind the Scenes of Science is an upcoming webinar series providing opportunities for educators and students to meet the professionals who make our research possible and get a glimpse of the many different careers in science. The series includes material from both the Allen Institute for Cell Science and the Allen Institute for Brain Science.

Registration for these events is free and open to entire classes. Our staff will hold a panel discussion where students can ask questions and learn about what it takes to do cutting-edge research.
Find additional resources in Behind the Scenes of Science
Educational Resources on allencell.org
Many educators have incorporated data, tools, and information they found on allencell.org into how they teach biology.

Learn how three educators use these resources, and incorporate a step-by-step virtual laboratory on cell division, published in CourseSource, into your classroom.
Educational Resources for Cell Biology
Cytiva licenses Allen Institute’s advanced machine learning technology to develop new cell imaging techniques
Strategic license to advance the field of 3D & live cell imaging

Cytiva and the Allen Institute have entered into a license agreement to integrate the Allen Institute’s machine learning technology with Cytiva’s microscopy and image analysis systems to advance the development of cell imaging innovations....
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Read full story
Label free tool
Thank you for attending our webinar:
Distance Learning for Cell Biology webinar
​Distance Learning for Cell Biology: A virtual laboratory for teaching Mitosis (recorded April 14th, 2020)

As part of our mission to support open science, the Allen Institute shares all of the data we generate freely for anyone to use in research or teaching. This enables students to conduct online experiments for distance learning. In this webinar, you’ll learn how to run a ready-to-use, fully online virtual lab experiment with your students.
Discuss on our forum
Educational Resources
COVID-19 update
To minimize risk of transmission of COVID-19 among employees and to meet Washington state mandates, we activated a work from home policy for non-essential employees, effective March 6th. 

While our experimental program is compromised, all of our other activities continue uninhibited and we remain open for science. Our cell lines and plasmids are still available from Coriell and Addgene, respectively.  Our computational analysis tools and visualization platforms can be viewed and utilized by researchers and educators here on allencell.org.  

If your laboratory is working on COVID-19 research, and you think any of our resources might help you, please let us know at cells@alleninstitute.org.
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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2 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 cell lines are single-edited, nuclear lines in which the polycomb repressive complex 2 and RNA polymerase II are labeled. 
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

Previous highlights

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
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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 © 2020 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
    • 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