Blog Posts

New Segmenter plugin for napari available now!

6/30/2021

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.

View the manuscript

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

6/11/2021

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).

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.

Click to enlarge

Protocols.io features newly posted method

4/24/2021

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

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

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

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.

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