Skip to main content

Prepare data and create a canvas

Learn how to prepare input data, navigate the dashboard, and create a canvas in CytoCanvas Studio™.

Understand the canvas workspace​

A canvas is a workspace to visually inspect and analyze a multiomic run. Each canvas points to a set of visualization input files that are the top-level entity for all exploration activity. Once a canvas is created, you can:

  • Save flow cell visualization states as a view.
  • Share a canvas with your team members in your organization, or share an anonymous read-only view.

Understand the input data file format​

CytoCanvas Studio uses a Spatial Data Object and visualization outputs as its input dataset. The cyto.viz file in the visualization output instructs the visualizer how to load visualization files and targets.

How and when visualization files are generated depends on your run type and where your data is stored. Visualization files are generated automatically for all AVITI24 runs onboard and can be visualized in CytoCanvas as soon as the run is complete. For 3′ Transcriptome or Multimodal Pooled Screening (MPS) runs, off instrument secondary analysis is required to translate raw 3' transcriptome counts into assigned cellxgene counts.

  • ElemBio Catalyst™ customers: For 3′ Transcriptome or Multimodal Pooled Screening (MPS) runs, a configured Cytos Cell Screening flow launches automatically when the run completes and generates the full 3′ transcriptome Spatial Data Object including cellxgene counts.
  • AWS or local storage customers: For 3′ Transcriptome or MPS runs, manually launch the Multiomics workflow on each completed run in your managed compute environment to generate the visualization files.

Dashboard overview​

CytoCanvas Studio opens the dashboard on login. The dashboard organizes your canvases into three tabs:

TabDescription
My CanvasesCanvases that you created.
Shared CanvasesCanvases shared with your ElemBio Cloud team members by yourself and other ElemBio Cloud team members.
DemoDemo datasets to explore CytoCanvas Studio features and multiomic datasets.

Each canvas card displays the canvas name, creator, access level, number of saved views, and number of cell groups. From a canvas card, you can favorite, clone, manage, share, or delete the canvas.

Use the search bar to filter canvases by name, run name, or execution ID. Select the star filter to display only your favorited canvases.

Dashboard

CytoCanvas Studio supports three ways to open AVITI24™ multiomic datasets into a canvas:

  1. Open from ElemBio Catalyst: Automatic access to ElemBio Catalyst-managed visualization output.
  2. AWS S3 storage connection in ElemBio Cloud: Access data in your own AWS S3 bucket through an ElemBio Cloud storage connection.
  3. Anonymous AWS access: Access any AWS S3 location by entering credentials directly at canvas creation time.

Start a canvas from ElemBio Catalyst​

If your multiomic data is processed through ElemBio Catalyst, visualization output is stored in Catalyst™-managed buckets. CytoCanvas Studio can access this data automatically.

Start from ElemBio Cloud

  1. Select an ElemBio Cloud navigation path then select View in CytoCanvas™.

    You will be navigated to CytoCanvas Studio with a canvas created for you.

Start from CytoCanvas

  1. From the Dashboard, select Start a Canvas.
  2. Select ElemBio Cloud.
  3. Search for and select the multiomic run that you want to visualize.
  4. Select Start Canvas.

    CytoCanvas Studio validates the visualization data and opens the canvas in the viewer.

Start a canvas from an AWS storage connection in ElemBio Cloud​

If your visualization data is stored in your own Amazon S3 bucket, you can make it available to CytoCanvas Studio by connecting the bucket as a storage connection in ElemBio Cloud. If you have multiple runs in the same bucket, this allows you to reuse a credential across team members in a secure manner.

  1. Follow the instructions to setup an AWS storage connection in ElemBio Cloud.
  2. Ensure the CORS configuration to your AWS S3 bucket so that CytoCanvas Studio can load data in the browser.
  3. From the Dashboard, select Start a Canvas.
  4. Select AWS.
  5. Select an ElemBio Cloud Provider from the dropdown.
  6. Select the AWS region the bucket is located in.
  7. Enter the path to visualization as the S3 URI to the visualization data (for example, s3://your-bucket-name/path/to/visualization/).
  8. Enter a canvas name and an optional description.
  9. Select Start Canvas.

    CytoCanvas Studio validates the visualization data and opens the canvas in the viewer.

Start a canvas from any AWS bucket with credentials​

Multiomic data in any AWS bucket may be visualized in CytoCanvas Studio without having to login, provided that you have a credential with access to the data. To load any generic AWS location:

  1. From the Dashboard, select Start a Canvas.
  2. Select AWS.
  3. Select Enter new credentials.
  4. Provide the Role ARN, or the AWS Access Key and Secret Key and optional Session Token if provided.
  5. Select the AWS region the bucket is located in.
  6. Enter the path to visualization as the S3 URI to the visualization data (for example, s3://your-bucket-name/path/to/visualization/).
  7. Enter a canvas name and an optional description.
  8. Select Start Canvas.

    CytoCanvas Studio validates the visualization data and opens the canvas in the viewer.

Last updated on