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Overview of our processes to generate & analyze our large-scale data
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Track all changes made to data & other information on allencell.org
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A comprehensive list of written tutorials & instructional videos collected from each menu category
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Find answers to common questions about the data & scientific decisions
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Overview of the Allen Cell Explorer website
The Allen Cell Explorer is the data portal for the Allen Institute for Cell Science, where you can explore our publicly available data, tools and models. The portal provides an unprecedented view into the organizational diversity of human stem cells by combining large-scale 3D imaging data, predictive models, observations of cells, detailed methods, and cell lines that can be purchased for use in labs around the world.
Getting around the Allen Cell Explorer website
The allencell.org website has undergone a major reorganization to improve usability.
The site is now organized into four categories that more closely mirror our scientific approaches to understanding cells. These new categories– Animated Cell, Cells & Biology, Microscopy, and Modeling & Analysis– have a similar structure with major "products" of different types that you can use listed first, followed by Research Projects, and then a More... subcategory with Videos & Tutorials, Methods, and Software & Code categories. In these More... sub category pages, we provide detailed descriptions and standard operating procedures for our activities, from the gene edited lines to assays, microscopy configurations, modeling approaches and more. Delve into each step of the process and download our procedures so you can perform them yourself.
The Home page announces new or updated content you can find deeper in the site of allencell.org, while the About and News categories house more general content.
The site is now organized into four categories that more closely mirror our scientific approaches to understanding cells. These new categories– Animated Cell, Cells & Biology, Microscopy, and Modeling & Analysis– have a similar structure with major "products" of different types that you can use listed first, followed by Research Projects, and then a More... subcategory with Videos & Tutorials, Methods, and Software & Code categories. In these More... sub category pages, we provide detailed descriptions and standard operating procedures for our activities, from the gene edited lines to assays, microscopy configurations, modeling approaches and more. Delve into each step of the process and download our procedures so you can perform them yourself.
The Home page announces new or updated content you can find deeper in the site of allencell.org, while the About and News categories house more general content.
Here we list a summary of each page found in the menu. Please visit the pages for the full experience.
Home (Click the Allen Cell Explorer logo)
The Home page at allencell.org has sections describing new or updated content you can find deeper in the site of allencell.org. Page descriptions on the Home page are often organized into different categories compared to the categories already provided by the top level menu.
About
Animated Cell
This new menu category summarizes what we are learning about cells at the Allen Institute for Cell Science with engaging tools. Research projects and methods for developing visual analysis software and code used across various pages of the site will be provided in this category as well.
Cells & Biology
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.
Microscopy
We create and share publicly available resources for the community to interact with, analyze and download our data.
Modeling & Analysis
Our data collection efforts culminate in predictive models of cells and more.
News
Home (Click the Allen Cell Explorer logo)
The Home page at allencell.org has sections describing new or updated content you can find deeper in the site of allencell.org. Page descriptions on the Home page are often organized into different categories compared to the categories already provided by the top level menu.
About
- What we do. Get an overview of our process and how our teams work together to generate and analyze our large-scale data.
- Site updates. Track all changes made to data & other information on allencell.org.
- FAQs. Get answers to common questions about the data and learn about how and why we made many of our scientific decisions.
Animated Cell
This new menu category summarizes what we are learning about cells at the Allen Institute for Cell Science with engaging tools. Research projects and methods for developing visual analysis software and code used across various pages of the site will be provided in this category as well.
- Visual Guide to Human Cells. An online interactive overview of hiPSC structure and function.
- Animated Cell Research Projects. Coming soon.
- More...
- Videos & Tutorials. Instructional Videos & Tutorials for Animated Cell Tools
- Methods. Methods for the visual analysis of cells
- Software & Code. Visualization software and code
- Publications. Animated cell related publications
Cells & Biology
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.
- About our Cells. This subcategory of pages provides an hiPS cell biology overview with cell structure observations.
- hiPS Cell Biology Overview has short articles describing hIPS cells & what we have learned by growing, manipulating & imaging them.
- The Cell Structure Observations blog includes images and videos, that describe some of our initial observations and insights about human induced pluripotent stem cells.
- Cell Catalog QuickView provides a visual snapshot of each cell line with Z-stack movies of the 3D microscopy image data.
- Cell Catalog. View detailed information and quality control measures for our genome edited human cell lines, and find out how to obtain the lines and plasmids for use in your lab.
- Genomics. Explore & download genomics & transcriptomics data.
- Cell Research Projects. This subcategory of growing pages collects observations we've made during human induced pluripotent stem cell biology experiments.
- More...
- Videos & Tutorials. Instructional Videos & Tutorials for Cell Methods
- Methods. Methods for cells in the lab
- Software & Code. Laboratory software and code
- Publications. Cell biology publications
Microscopy
We create and share publicly available resources for the community to interact with, analyze and download our data.
- 3D Cell Viewer. Explore our high replicate collection of human stem cells by viewing any of our 31,987 3D cell images directly in a web browser with this online visual analysis tool. Use the interactive plotting tool panel of the 3D Cell Viewer to explore relationships or to create your own plots and figures based on our imaging data.
- Deep Cell Zoom. Zoom & scroll around an image showing 24,928 segmented cells.
- Data Downloading. Download our image and feature analysis data for your own study.
- Microscopy Research Projects. This subcategory of growing pages describes outcomes of projects developed to improve cell imaging.
- More...
- Videos & Tutorials. Instructional Videos & Tutorials for microscopy and cell image visual analysis tools
- Methods. Methods for microscopy
- Software & Code. Microscopy software and code
- Publications. Microscopy related publications
Modeling & Analysis
Our data collection efforts culminate in predictive models of cells and more.
- Allen Integrated Cell. This new page describes 2 projects that use deep learning to illuminate cell structure.
- Data Notebook Exploration. Explore and access our data with guided walkthroughs of programmatic tools using Jupyter Notebooks.
- Modeling & Analysis Research Projects. This subcategory of growing pages describes the outcomes of various projects designed to improve our understanding of cell structure and behavior.
- More...
- Videos & Tutorials. Instructional Videos & Tutorials for modeling & analysis tools
- Methods. Methods for modeling and analysis
- Software & Code. Modeling & analysis software and code
- Publications. Modeling & analysis related publications
News
- News Feed. Catch up on recent scientific news from the Allen Institute for Cell Science.
- Publications. View a list of scientific publications from Allen Institute for Cell Science researchers.
- Collected Content. Content from retired pages remains available here.
- Tutorials & Videos Collected. A comprehensive list of written tutorials & instructional videos collected from each menu category.
- Archived Content. Content from retired pages remains available here.