Using allencell.org

Download our feature analysis data for your own study.

Cell Catalog Overview & Tutorial

Download our image data for use in your favorite desktop viewer software.

3D Cell Viewer Tutorial

Interactively rotate any of our 6,077 cells directly in your web browser.  
​No plugins required!

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.

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.​
  • 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.

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.

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:
  • Only cells containing the selected Tagged protein will be shown in the gallery below. The All/None button toggles the full set of Tagged protein buttons on or off.
Image:
  • Images available are either individual cells, i.e. single cells that have been segmented out from full field images, or the Full field images themselves. All reveals both types in the gallery below.
Scroll bar
  • There are thousands of cells in the gallery, but only a few are visible at a time depending on the size of your screen.  You can scroll through pages of cells by dragging the slider or clicking the arrows
Search
  • Click in the search box to get instructions for cell name and metadata keyword searching options.
    • Limitation: On very small screens, e.g. smart phones and some tablets, the search box may be cut off, but you can still enter text and hit return to execute a search.

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.
  • Click anywhere on the screen will stop the auto-rotation. 
  • Click & drag to manually rotate the cell in the window.
  • On-screen scroll (mouse) or two-finger pinch/pan (touch screen devices) to zoom in/out. There is also a vertical zoom slider in the top left corner. 
    • Known limitation: on some Windows computers and tablets, the rotation may feel like it moves at half-speed compared to the motion of your finger gesture.  We are working to resolve this for these devices.
  • A small scale bar and set to auto-dim, a 3D orientation icon is shown in the lower left corner. 
  • The lower right displays buttons to:
    • Download the current viewing file as ome.tiff
    • Load the field of cells that contains the current viewing cell, i.e. see all of the neighboring cells of the isolated cell.
    • Get link to the currently viewed cell that you can cut-n-paste to share that cell.

4. The Tools panel

A. Viewer settings sub-panel (default open panel)

  • Default: 3D representation on black background
  • Optional 2D representation: show single layer of the z-stack. 
    • Known issue: as of April 4, 2017, the 2D viewer feature and all associated tools are turned off. This functionality will return later in 2017 after refinement.
Channels section:
  • Toggle on/off for each channel's visibility in the window
  • Click on color square to change the default color.
  • OBS_*: observed
  • SEG_*: segmented
  • LIN_*: line
  • Adjust cell mask slider to reveal neighbor cells
Data Representation section: 
  • Brightness: Slide to the right to brighten the intensity of all voxels.
  • Density: Slide to the right to ~ increase the opacity of all voxels. 
  • Fusion:
    • ​Average:
    • Maximum:
  • Enhancement:
    • Data range:
    • Full range:
    • Data + tolerance:
    • Equalized:
Render Style section:
  • Click on icon to select/highlight it - hover over an icon will show its label.
Intensity levels: Slide to adjust the values of all of the voxels, which affects how each voxel contributes to the scene (brightness, apparent opacity, etc.
Transfer function (LUT): once activated, this panel expands under the Viewer panel. Click to add knots to remap the voxels, which are distributed by frequency along the X-axis, to new Y values.
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. 
Render settings:
  • Autorotate camera: reactivate the initial autorotation around an independent vertical axis.
  • Rendering quality: minimal, low, medium, high. Lower quality allows better speed for manipulation and autorotation. Higher quality is recommend for saving or recording scene files. 

B. Image Information sub-panel

The Image Information sub-panel provides the related metadata of the current viewing file.

C. Download sub-panel

The Download sub-panel offers several ways to save the current viewing file:
  • PNG
  • Embed Code
  • Cell Volume as ome.tif: to be opened in other microscopy or 3D data viewer softwares. 
  • Cell Field Volume as ome.tif

D. Analysis sub-panel

The Analysis sub-panel is coming soon.  In the meantime, it provides a link to the interactive plotting tool where you can graph several cell features calculated for the entire data-set against one another.

E. Help sub-panel

The Help sub-panel provides brief instruction to use the Search box within the Image panel.
  • Report a bug so we can improve the experience in the future.
  • Request a feature: we are interested in the various possibilities to explore our large cell data collection, if there is anything you'd like to see in future iterations of the 3D Cell Viewer, please submit a request to be consider. 
  • Help Page: this will link to this page which shows the step-by-step instructions to familiarize yourself with the Cell Viewer web application and other helpful information.