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  • Data & Digital Tools
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      1. Tools and resources overview
      2. Download cell data: images, genomics, features
      3. Code repositories & software
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      1. AGAVE 3D pathtrace image viewer
      2. Allen Cell & Structure Segmenter
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      2. Cell Feature Explorer
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      Web tools (con't)
      1. Simularium viewer
      2. Timelapse Feature Explorer
      3. Visual Guide to Human Cells
      4. Vol-E (Web Volume Viewer)
      5. 3D Cell Viewer
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
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      6. └ 3D Probabilistic Modeling
      7. └ Label-free Determination
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News feed

For general news from the Allen Institute, visit alleninstitute.org

Thank you for attending our 3D Cell Visualization Tools webinar

10/20/2021

 
Thanks for joining us for the webinar: Visualizing 3D cellular images and simulations: learn about AGAVE, Cell Feature Explorer, and Simularium
The webinar occurred on Tuesday, October 19, 2021 at 10AM PT
In this webinar we described our open-source visualization software, Advanced GPU Accelerated Volume Explorer (AGAVE), which can be downloaded to use on your image files. We also showed how you can explore, sort, and download our imaging data in our Cell Feature Explorer for your own modeling, analysis, or machine learning tasks. In addition, we showed you how you can explore cell models in our online Simularium, a tool to share, visualize, and interrogate biological simulations.
Continue the discussion on our forum

New Segmenter plugin for napari available now!

6/30/2021

 
Picture
Access the 3D segmentation power of the Allen Cell & Structure Segmenter via an intuitive graphical user interface, newly available as a plugin for the popular open source image analysis software napari.
Learn more about the plugin
Try the plugin now

New manuscript published in Cell Systems

6/18/2021

 
Cell states beyond transcriptomics: Integrating structural organization & gene expression in hiPSC-derived cardiomyocytes
A team of scientists at the Allen Institute for Cell Science recently published a manuscript in Cell Systems investigating the relationship between cell organization and gene expression in over 30,000 single cells. In this study, the team studied heart muscle cells generated from human stem cells, and developed a method to automatically classify how organized the contractile machinery in single cells was. When they compared this to expression levels of key cardiac developmental genes, they found very little correlation, suggesting that a cell’s state cannot be determined by either measurement alone. This manuscript was featured on the cover of Cell Systems for the 5-year anniversary special edition and highlighted in the corresponding editorial. Read more about the project here. ​
Picture
View the manuscript

Introducing theĀ Allen InstituteĀ Open for (Cell) Science TutorialsĀ Series

6/11/2021

 
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Open for (Cell) Science Tutorials is an upcoming webinar series showcasing open resources from our Allen Cell Explorer. At these tutorials, learn how and why to integrate Allen Institute for Cell Science open cell lines and software tools into your research. Team members who worked on each resource will discuss the development process, use cases, and more.

Registration for these events is free and open to anyone who is interested. 
​
More information about the Open for (Cell) Science Tutorials series

Introducing the MegaMenu on allencell.org for improved navigation

5/18/2021

 
We made major upgrades to your website navigation experience on allencell.org!
​
The navigation menu has been reorganized and categorized,
​with many pages renamed (old URLs will automatically redirect).
Picture
A screenshot of the MegaMenu navigation used on allencell.org as of May 2021.
This website, allencell.org has grown to over 50 pages in recent years, which makes it challenging to find what you want efficiently. To address this issue, we have recently upgraded the navigation menu, which lives at the top all pages on allencell.org, to a newer MegaMenu style. The MegaMenu expands to display our site's structure in a more informative and easy-to-explore way. The 50+ pages are now grouped into descriptive subcategories and some pages have links in multiple categories to make them easy to find for different users (based on the results of user experience studies). We hope you can find useful or interesting pages at a glance as the site continues to grow.

This diagram shows a sitemap for allencell.org prior to May 17, 2021 on the left, the new sitemap on the right, and arrows to help you understand where the old pages moved.
menu mapping
Click to enlarge

Protocols.io features newly posted method

4/24/2021

 
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Access the protocol
As we migrate many of our written methods and standard operating procedures to protocols.io, the service has highlighted the protocol Maintenance of Undifferentiated hiPSC Cultures and Differentiation to Cardiomyocytes on Glass Surfaces on the Featured protocols section of their website, Twitter and Facebook accounts. 

Nature article on AICS Label-Free technology

4/6/2021

 
Amber Dance published a Technology Feature article in the March 30, 2021 edition of Nature entitled:
AI spots cell structures that humans can’t
Models can predict the location of cell structures from light-microscopy images alone, without the need for harmful fluorescence labelling.
Read article in Nature

MiTOSSis VR learning game available for download

3/9/2021

 
MiTOSSis game
Pick up and throw 3D cells generated from real microscopy data. Sort them by the stages of cell division, mitosis, to test your biology knowledge!
Download on STEAM
Learn more

Don't miss the last twoĀ 2020 Scientist of Color Speaker Series seminars & mark your calendars for 2021

11/7/2020

 
Picture
Omar Quintero is an associate professor of biology at the University of Richmond who sits on a Project Advisory Council for the Allen Institute for Cell Science that is focused on developing cutting edged tools for education. In the period directly after the killing of George Floyd and the nationwide protests against systemic racism that followed, Quintero, considered how he might find a way to support the work and careers of Black scientists. He decided to develop a seminar, the 2020 Scientist of Color Speaker Series. (–paraphrased from the article below)

Read the full article on the University of Richmond website: 

Professor brings together scientists of color in speaker series

Upcoming speakers 2020–2021
Recorded seminars on YouTube

New cell line lets researchers use CRISPR to reversibly switch off genes

10/23/2020

 
​CRISPR interference technique enables study of basic cell biology and disease in human stem cells​
Picture
The CRISPR interference technique allows new explorations of human cells. Here, Allen Distinguished Investigator Martin Kampmann, Ph.D., and his colleagues used the method to reduce levels of a dementia-associated protein known as progranulin, shown in green on the left, in human neurons by dialing down the progranulin gene in the cells on the right. (Image adapted from Tian et al (2019) Neuron 104:239)
Read full article on alleninstitute.org
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  • About
      Institute
      1. Our science
      2. Past foundational projects
      3. News feed
      4. About us
      5. Careers
  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
      2. Disease Collection Cell Catalog
      3. Cell video shorts
      Lab methods
      1. Video protocols
      2. Written protocols
      3. Our methodology
      4. Support forum
      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
      General
      1. Tools and resources overview
      2. Download cell data: images, genomics, features
      3. Code repositories & software
      Desktop tools
      1. AGAVE 3D pathtrace image viewer
      2. Allen Cell & Structure Segmenter
      Web tools
      1. BioFile Finder
      2. Cell Feature Explorer
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      Web tools (con't)
      1. Simularium viewer
      2. Timelapse Feature Explorer
      3. Visual Guide to Human Cells
      4. Vol-E (Web Volume Viewer)
      5. 3D Cell Viewer
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Allen Integrated Cell
      6. └ 3D Probabilistic Modeling
      7. └ Label-free Determination
      4D biology models
      1. Simularium viewer
      Methodologies
      1. Drug perturbation pilot study
      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
  • Publications
      Articles
      1. Publications
      2. Preprints
      Presentations
      1. Talks & posters
  • Education
      Educational resources
      1. All resources
      2. Teaching materials
      Online tools popular with teachers
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. 3D Cell Feature Explorer
      4. 3D Cell Viewer
      5. hiPS cell structure overview
  • Support
      Questions
      1. FAQs
      2. Forum
      Tutorials for digital tools
      1. Video tutorials
      2. Visual Guide tutorial
      3. AGAVE documentation
      Lab methods
      1. Video protocols
      2. Written protocols
      3. Our methodology
  • šŸ”
      SEARCHBAR