ALLEN CELL EXPLORER
  • 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

News Feed

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

Introducing the Allen Institute Open for (Cell) Science Tutorials Series

6/11/2021

 
Picture
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

 
Picture
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 two 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

Cytiva licenses Allen Institute’s advanced machine learning technology to develop new cell imaging techniques

8/7/2020

 
Strategic license to advance the field of 3D and live cell imaging.
Picture
Figure 1. Images from our collection of cells can be used to generate models that produce integrated images of 3D subcellular structures—all from an input brightfield image of a field of cells. Cell segmentations can then be applied to the predictions to determine structure localization for individual cells.
​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....
Read full story
Label-free tool

Article: WSU professors create virtual lab on cell development

4/24/2020

 
Washington State University News wrote a followup article to a webinar, Distance Learning for Cell Biology: A virtual laboratory for teaching mitosis, hosted on April 14th, 2020.

The article begins:
Hundreds of Biology 107 students have taken part in a virtual laboratory exercise developed by two WSU professors [Eric Sheldon and 
Erika Offerdahl] in collaboration with the Allen Institute for Cell Science....
Picture
Read full article from RJ Wolcott on WSU News

Distance Learning for Cell Biology. Webinar Today April 14

4/13/2020

 
Join us Tuesday, April 14, at 10am PT for this free webinar:
​Distance Learning for Cell Biology: A virtual laboratory for teaching Mitosis

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.
Picture
Register by 10am PST April 14, 2020
<<Previous
Forward>>

    Overview

    To receive the Allen Institute e-newsletter, sign up here.

    Archives

    January 2023
    December 2022
    October 2022
    April 2022
    February 2022
    January 2022
    November 2021
    October 2021
    June 2021
    May 2021
    April 2021
    March 2021
    November 2020
    October 2020
    August 2020
    April 2020
    September 2019
    August 2019
    May 2019
    February 2019
    December 2018
    September 2018
    June 2018
    May 2018
    March 2018
    February 2018
    January 2018
    December 2017
    November 2017
    October 2017
    September 2017
    August 2017
    June 2017
    May 2017
    April 2017
    March 2017
    February 2017
    December 2016
    November 2016
    August 2016
    June 2016

    Categories

    All

    RSS Feed

Home

Terms of Use

Citation Policy

Privacy Policy

FAQs

Help

Send us a message

Our diversity, equity & inclusion commitment
Copyright © 2023 Allen Institute. All Rights Reserved.
cellscience.alleninstitute.org
  • 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