ALLEN CELL EXPLORER

New article published in Nature Methods

4/5/2022

The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models
The Simularium Viewer makes it easy to share and interrogate interactive 3D visualizations of biological simulation trajectories and related plots directly in a web browser. Its primary goal is to facilitate collaborations among experimental and computational biologists by removing major challenges to sharing, accessing, and comparing simulation results.

Try the Simularium Viewer

Nature Methods article

Interview article

New protocol for Illumination stability & linearity measurement available on protocols.io

2/15/2022

The QUAREP-LiMi Working Group has published a first version of the collaborative protocol on Illumination stability & linearity measurement in Protocols.io.

View on protocols.io

In addition to step-by-step instructions, the protocol provides:

endorsement (authorship) by 36 people representing research institutions, academia, and industry from around the world.
a link to a public database with measurements made by members of the authorship group and to which you can contribute by uploading your own measurements.
a link to a GitHub repository with scripts to automate the measurements with some scopes and power meters.
links to tutorial videos.

Watch the Seattle Cell Science Symposium 2022, recorded Jan 27-28

1/31/2022

Recorded presentations on YouTube

Thank you for attending the sixth annual Seattle Cell Science Symposium!

The 2022 Symposium was hosted virtually and featured two half-days of presentations from leaders in the field of cell biology. The overarching theme of the event was "Data integration from multiomics to imaging".

Presentations highlighted new technologies that combine high throughput imaging and omics data to create a multifaceted perspective of cell biology and that contribute to understanding cell states and identities in a spatiotemporal manner.

Each day also included a panel discussion on the future of the field and team talks from the Allen Institute for Cell Science.

Recorded January 27–28, 2022

New article published in Nature Cell Biology

11/29/2021

It’s time to incorporate diversity into our basic science and disease models
Leaders in cell biology share their perspectives including our Rick Horwitz, and Ru Gunawardane.

Read the article

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

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.

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News Feed

New article published in Nature Methods

New protocol for Illumination stability & linearity measurement available on protocols.io

Watch the Seattle Cell Science Symposium 2022, recorded Jan 27-28

New article published in Nature Cell Biology

Thank you for attending our 3D Cell Visualization Tools webinar

New Segmenter plugin for napari available now!

New manuscript published in Cell Systems

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

Introducing the MegaMenu on allencell.org for improved navigation

Protocols.io features newly posted method

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