ALLEN CELL EXPLORER
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      1. Instructional videos for success in the lab
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      About our hiPS cells
      1. hiPS Cell Structure Overview
      2. Visual Guide to Human Cells
      3. Cell structure observations
      4. Why endogenous tagging?
      5. Differentiation into cardiomyocytes
      6. Genomics
      7. Download cell data (images, genomics, features)
  • Data & Digital Tools
      Online image analysis
      1. Cell Feature Explorer (plotting & 3D viewer)
      2. 3D cell viewer (pre2018)
      3. Deep cell zoom (216,016 cells)
      Online modeling viewers
      1. Visual Guide to Human Cells
      2. Simularium (4D visual analysis)
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      6. Allen Integrated Cell viewer
      7. Label-free examples viewer
      8. 3D probabilistic model viewer
      Desktop tools
      1. Allen Cell & Structure Segmenter
      2. AGAVE 3D pathtrace image viewer
      Data & code
      1. Download cell data (images, genomics, features)
      2. Code repositories & software
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Overview
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Label-free Determination
      6. └ 3D viewer
      7. 3D Probabilistic Modeling
      8. └ 3D viewer
      9. Visual Guide to Human Cells
      4D biology models
      1. Simularium (online 4D viewer)
      Methodologies
      1. Drug perturbation pilot study
      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
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      2. Preprints (biorxiv, arxiv)
      Posters
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  • Education
      Education resources
      1. All Resources
      2. Teaching materials
      Online tools popular with teachers
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. Cell Feature Explorer (interactive plotting & 3D viewer)
      4. 3D cell viewer (pre2018 data)
      5. hiPS cell structure overview
  • Support
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      1. Digital tool tutorials with videos
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      3. Illustrated overviews
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Educational Resources

Research data, tools, & information available now that can can be used for teaching
Teaching materials
How teachers use our resources (videos)
Popular online tools

Introduction

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In our research, the Allen Institute for Cell Science collects thousands of 3D microscopy images and movies of our fluorescently tagged human induced pluripotent stem cells (hiPS cells). We analyze these images to uncover and study underlying mechanisms that drive the complex multi-scale organization and dynamics of the cells.

​Many educators have incorporated data, tools, and information they found on allencell.org into how they teach biology. Below, you’ll find ready-to-use lesson plans that use allencell.org data and tools in lessons for high school and college students, as well as quick-start guides for some of our datasets and tools that are most popular with educators.
Teaching materials
Popular online tools

Teaching materials

Lesson plans
Learn about principles of cell biology with these short, ready-to-use, fully online activities by Allen Institute staff.  
  • Healthy Cells, Healthy Bodies introduces middle school students to the link between cellular health and human health. Includes materials needed for a teacher to give the prepared presentation and a video of a scientist giving the presentation that can be played in class.
  • Introduction to Microscopy in Biology introduces principles of cell image analysis, with two levels of an interactive activity available for early or advanced high school students. Includes materials needed for a teacher to give the prepared presentation and a video of a scientist giving the presentation that can be played in class.
  • Mitosis and Microscopy introduces principles of mitosis and image analysis to advanced high school to early college students. This lesson includes all virtual lab activity materials, as well as a webinar for teachers demonstrating the lesson. 
  • Visit the Education outreach page on allen institute.org to find additional resources for teaching cell biology, posters for your classroom, and materials for teaching neuroscience and immunology.

A virtual laboratory on cell division using a publicly-available image database

This ready-to-use, fully online virtual lab experiment teaches principles of mitosis, aimed towards college students. 
A virtual laboratory on cell division using a publicly-available image database. Shelden EA, Offerdahl EG, Johnson GT. CourseSource: Evidence-based teaching resources for undergraduate biology education, May 2019.
CourseSource Virtual Lab
Continue the discussion on our forum

How teachers use our resources (videos)

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Three educators who use various resources from allencell.org in their classrooms presented their curricula and data applications to an audience at the American Society for Cell Biology's 2018 ASCB | EMBO Annual Meeting. The speakers present their applications of these data, tools, and approaches in classrooms ranging from high school to advanced college levels. 
Read more

Career perspectives: Behind the Scenes of Science 

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Behind the Scenes of Science is a webinar series 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 interviews with team members from the Allen Institute for Cell Science and other divisions of the Allen Institute. ​
Read more

Online tools popular with teachers

Get started with some of our engaging resources that are particularly popular with educators.  For a brief overview of our research goals, process, and cells, see What We Do.

Quickstart Guide for Teachers  
In-depth tips for new users, detailed information on how to view and interact with the data and online tools highlighted in this section, and use cases for each resource in classrooms and curricula.

Visual guide to human cells
This interactive resource designed specifically for students demonstrates major cell structures and their functions in an illustrated model of a real human cell. The illustrated cell model is accompanied by microscope images and videos, written explanations of each structure's function, and illustrations and explanations for each cell structure in each stage of mitosis.  

Integrated Mitotic Stem Cell
This visual essay introduces an advanced data-driven model and visualization tool that captures human cell division. This model and the visualizations in the essay follow 15 cell structures through the whole cell cycle. 

Cell Feature Explorer 
Plot measurements of cell features (e.g. surface area vs volume of various organelles) on an interactive graph and interactively view 3D images of over 200,000 individual human cells including cardiomyocytes. 
For a ready-to-use activity applying the Cell Feature Explorer, try the Mitosis and Microscopy (high school level) lesson.  

3D Cell Viewer 
Browse and view this collection of almost 25,000 individual human cells, as well as over 7,000 cell colony sections (fields of view). 
For a ready-to-use activity using the 3D Cell Viewer, try our Introduction to Microscopy in Biology (high school level) or A virtual laboratory on cell division using a publicly-available image dataset (college level) lesson. 

About our cells
Observations about cell behavior seen in select cell lines, through both images and video, demonstrate the function of cell structures through vivid visualizations. 

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  • About
      Institute
      1. News feed
      2. What we do
      3. Publications
      4. Allen Institute | allenInstitute.org
      5. Careers
      Site
      1. Home page
      2. Site updates
      3. Archived content
  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
      2. Cell Catalog quickview
      3. Cell Shorts (documentaries on labs using our cells)
      4. Support forum
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
      About our hiPS cells
      1. hiPS Cell Structure Overview
      2. Visual Guide to Human Cells
      3. Cell structure observations
      4. Why endogenous tagging?
      5. Differentiation into cardiomyocytes
      6. Genomics
      7. Download cell data (images, genomics, features)
  • Data & Digital Tools
      Online image analysis
      1. Cell Feature Explorer (plotting & 3D viewer)
      2. 3D cell viewer (pre2018)
      3. Deep cell zoom (216,016 cells)
      Online modeling viewers
      1. Visual Guide to Human Cells
      2. Simularium (4D visual analysis)
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      6. Allen Integrated Cell viewer
      7. Label-free examples viewer
      8. 3D probabilistic model viewer
      Desktop tools
      1. Allen Cell & Structure Segmenter
      2. AGAVE 3D pathtrace image viewer
      Data & code
      1. Download cell data (images, genomics, features)
      2. Code repositories & software
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Overview
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Label-free Determination
      6. └ 3D viewer
      7. 3D Probabilistic Modeling
      8. └ 3D viewer
      9. Visual Guide to Human Cells
      4D biology models
      1. Simularium (online 4D viewer)
      Methodologies
      1. Drug perturbation pilot study
      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
  • Publications
      Articles
      1. All journal publications
      2. Preprints (biorxiv, arxiv)
      Posters
      1. Select posters
  • Education
      Education resources
      1. All Resources
      2. Teaching materials
      Online tools popular with teachers
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. Cell Feature Explorer (interactive plotting & 3D viewer)
      4. 3D cell viewer (pre2018 data)
      5. hiPS cell structure overview
  • Support
      Questions
      1. FAQs
      2. Forum
      Tutorials for digital tools
      1. Digital tool tutorials with videos
      2. Visual Guide tutorial
      3. AGAVE user guide
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
  • 🔍
      SEARCHBAR