Using allencell.orgDownload our feature analysis data for your own study.
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Cell Catalog Overview & TutorialDownload our image data for use in your favorite desktop viewer software.
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3D Cell Viewer TutorialInteractively rotate any of our 6,077 cells directly in your web browser.
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Using allencell.org
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.
The Allen Institute for Cell Science was founded in 2014 with a contribution from Paul G. Allen. To learn more about the mission and goals of the Allen Institute for Cell Science, please visit our institute website.
The Allen Institute for Cell Science was founded in 2014 with a contribution from Paul G. Allen. To learn more about the mission and goals of the Allen Institute for Cell Science, please visit our institute website.
Getting around the Allen Cell Explorer website
Research Updates
Here you will find up-to-date analyses and observations about our cells and how they are organized.
Modeling
Our data collection efforts culminate in predictive models of cells.
Tools & Data
We create and share publicly available resources for the community to interact with, analyze and download our data.
Cells
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.
Methods
We provide detailed descriptions and standard operating procedures for our activities, from the gene edited lines to assays, microscopy configurations, modeling approaches and more.
Here you will find up-to-date analyses and observations about our cells and how they are organized.
- Cell Stories. Read in-depth stories, including images and videos, that describe some of our initial observations and insights about human induced pluripotent stem cells and what we have learned by growing, manipulating and imaging them.
- Analyses. View an initial analysis of the surprising cell-to-cell variation we have encountered in the data.
- Publications. View a list of scientific publications from Allen Institute for Cell Science researchers.
Modeling
Our data collection efforts culminate in predictive models of cells.
- Integrated Cell Models. View a description and outputs from our first model that uses deep learning techniques to predict the organization of human stem cells.
Tools & Data
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 visualized in three dimensions.
- Interactive Plotting. Use the Analyses page as a launch point to create your own plots and figures based on our imaging data.
- Data Downloading. Download our image and feature analysis data for your own study.
Cells
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.
- 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.
- Cell Image Gallery. View a snapshot of each cell line and the power of the gene editing approach used to label individual structures.
Methods
We provide detailed descriptions and standard operating procedures for our activities, from the gene edited lines to assays, microscopy configurations, modeling approaches and more.
- Institute Workflow. Get an overview of our process and how our teams work together to generate and analyze our large-scale data.
- Detailed Methods. Delve into each step of the process and download our procedures so you can perform them yourself.
- FAQs. Get answers to common questions about the data and learn about how and why we made many of our scientific decisions.
Cell Catalog overview & tutorial
Video overviewing the data and features available in the Cell Catalog.
The Cell Catalog contains our completed cell lines, which are available through Coriell as part of the Allen Cell Collection, along with those that are still in our production pipeline, at the bottom of the page.
For all the completed lines that are available through Coriell we provide supplemental material (data, images, videos) related to the rigorous testing and quality control steps each line has undergone.
These data can quickly be accessed by clicking on the line of choice in the table on the first page of the Cell Catalog. This opens up a catalog page unique for each line where you can order the line, the parental line from which it was derived, the plasmid used to produce this line and view a host of images and QC data related to that line.
For all the completed lines that are available through Coriell we provide supplemental material (data, images, videos) related to the rigorous testing and quality control steps each line has undergone.
These data can quickly be accessed by clicking on the line of choice in the table on the first page of the Cell Catalog. This opens up a catalog page unique for each line where you can order the line, the parental line from which it was derived, the plasmid used to produce this line and view a host of images and QC data related to that line.
3D Cell Viewer tutorial
Open the 3D Cell Viewer in your web browser.
The 3D Cell Viewer pulls relatively large data files to your computer, tablet, or mobile phone which could use a lot of cellular data, so we recommend using wi-fi.
The 3D Cell Viewer pulls relatively large data files to your computer, tablet, or mobile phone which could use a lot of cellular data, so we recommend using wi-fi.
1. Get started
The first screen of the 3D Cell Viewer reveals the Images panel, which contains a scrollable gallery of all available cells with several methods to filter and search the gallery at the top.
The number of cells displayed will depend on your screen resolution and browser window size. Click on any cell image to get started. |
After clicking on a cell in the Images panel, the Viewer panel and Tools panel will open from the right and the cell will begin to load into the 3D viewport. You should see a spinning box that eventually gets replaced by a spinning cell or a large thin sheet of cells. Depending on the size of the data, your connection and traffic to the server, you can expect an image to load in 3 to 30 seconds. We promise it will be worth the wait, but if it takes longer than 30 seconds, try:
• to load a different cell, • to refresh the web page • or to access the tool at a less busy time. |
2. The Image panel
Filters sub-panel |
The Filters sub-panel in the upper left of the user interface (under Images) allows you to reduce the gallery below to show only cell images containing the selected filter buttons and/or key word search terms.
Tagged protein:
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3. The Viewer panel
The Viewer panel displays both 3D data and 2D slices of the 3D data. (As of April 4, 2017, the 2D mode is turned off and will be returned after further refinement later in 2017.) The Viewer panel has two operational modes that change the functionality in the window and the options available. When you click to load a cell from the gallery, the Viewer loads the cell or field of cells with a rotating version of the default 3D representation set to automatically rotate.
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4. The Tools panel
A. Viewer settings sub-panel (default open panel)
Clipping plane: clip into the viewport- along the Z-axis of your screen, either from the front or rear.
Clipping box: clip the volumetric representation by the axes xyz. Once activated, three sliders are displayed in the bottom of the Viewer panel and can be slid inward to clip the voxels in realtime. You can meet the clipping plans in the middle to create a thin cross-section. They will not be rendered/included in Viewer image file saving. |
B. Image Information sub-panel
C. Download sub-panel
D. Analysis sub-panel
E. Help sub-panel
The Help sub-panel provides brief instruction to use the Search box within the Image panel.
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