Highlights
Thank you for attending our webinar:
3D Cell Visualization Tools webinar
3D Cell Visualization Tools webinar
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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 It was recorded and will be available soon. 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. |
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New Segmenter plugin for napari available now!
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.
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New manuscript published in Cell Systems
To understand human cells, scientists look beyond genes
We recently published a manuscript in Cell Systems investigating the relationship between cell organization and gene expression in over 30,000 single cells. 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. |
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Introducing the MegaMenu for improved navigation on allencell.org
AllenCell.org MegaMenu screenshot
Introducing the Allen Institute Open for (Cell) Science Tutorials Series
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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. |
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New method featured on Protocols.io
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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Educational Resources on allencell.org
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We present the Allen Cell Structure Segmenter, a python-based, open-source toolkit that combines classic 3D image segmentation with artificial intelligence to detect cellular structures.
Read more about this new toolkit and how it can help biologists analyze their 3D images of cells and be more quantitative with their results. |
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Previous highlights
Introducing the Allen Institute Behind the Scenes of Science Series
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Behind the Scenes of Science is an upcoming webinar series providing opportunities 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 material from both the Allen Institute for Cell Science and the Allen Institute for Brain Science.
Registration for these events is free and open to entire classes. Our staff will hold a panel discussion where students can ask questions and learn about what it takes to do cutting-edge research. |
Thank you for attending our webinar:
Distance Learning for Cell Biology webinar
Distance Learning for Cell Biology webinar
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Distance Learning for Cell Biology: A virtual laboratory for teaching Mitosis (recorded April 14th, 2020)
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. |
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A visual essay on the Integrated Mitotic Stem Cell
We present the Integrated Mitotic Stem Cell as a data driven model and visualization tool that captures a holistic view of human cell division for the first time.
By enabling a deeper understanding of how healthy human cells divide, the model will further basic biology research as well as studies of cancer, a disease that often results from cell division gone awry. |
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Visual Guide to Human Cells
This visual guide organizes information about human induced pluripotent stem cells into a curated collection of interactive models. Users can rotate and zoom into 3D cells, each segmented from real data for each phase of mitosis, while learning more about individual cell structures and functions.
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Label-free Determination
As part of the Allen Integrated Cell, we have developed and implemented a label-free prediction method for determining the location of 3D structures inside the cell, directly from transmitted light images.
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Resources to access mitotic stem cell states & endogenously tagged cardiomyocytes
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The new lines include two single edited, nuclear lines and a dual edited cell line.
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Integrated Mitotic Stem Cell
A model & visualization tool to better understand how stem cells divide |
Videos & tutorials
Instructional videos provided to ensure success in your lab & to overview tools available on allencell.org
Cells & plasmids for your lab
We have created a series of gene edited human iPSCs that we use as the foundation for our image data, and that we share with the larger scientific community.
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Obtain cell lines & plasmids for your lab; quality control details
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Explore & download genomics & transcriptomics data
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Step-by-step protocols to generate & image gene-edited hiPSCs successfully
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Research Projects described
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Observations describing effects of drugs on 3D cellular organization
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Multiple cell structures visualized direct from brightfield imaging
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3D visualization of hIPS cell structure variation
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