Exploring Visualizations

Load Demo Data

CytoCanvas provides demo datasets to explore.

1. Open the CytoCanvas application.
2. Select Explore Demo Data.
3. Select Open for the demo dataset of choice.

Load a Cell Dataset for Visualization

CytoCanvas provides two options to load your cytoprofiling data for exploration.

• Load data from a local filesystem
• Load data from an AWS S3 cloud location

For both situations, CytoCanvas first identifies the dataset via being pointed at a cyto.viz manifest file.

Load Data Locally

1. Open the CytoCanvas application.
2. Select Open from files to browse the local filesystem.
3. Navigate to the visualization output folder containing the cyto.viz file.
4. Select and open the cyto.viz file.

Load Data from AWS S3

Data may be loaded directly from any AWS S3 bucket.

Prerequisites

1. The AWS bucket must have the following CORS policy added:

   [
      {
         "AllowedHeaders": [],
         "AllowedMethods": [
               "GET",
               "HEAD"
         ],
         "AllowedOrigins": [
               "*"
         ],
         "ExposeHeaders": [],
         "MaxAgeSeconds": 3000
      }
   ]
2. The user must have AWS S3 storage credentials to this bucket with read access.

Loading Data

1. Open the CytoCanvas application.
2. Locate the location of the cyto.viz file.
3. Open the CytoCanvas application.
4. Select Open from Cloud.
5. In the cyto.viz S3 URI field, enter the S3 URI to the cyto.viz file

   For example, s3://example_bucket-name/DemoInstrument/20240821_DemoInstrument_Example_Run/visualization/cyto.viz

6. Enter the AWS Access Key.
7. Enter the AWS Secret Access Key.
8. If using temporary credentials, enter a session token.
9. Enter the region of the bucket.
10. Select Submit.

The visualization data loads and is ready to explore in CytoCanvas.

After loading the data, CytoCanvas displays a visualization of the cell culture samples. The 12 grids each represent one of the 12 wells on the flow cell for the run. Use the collapsible panels for Imaging, Protein, and Transcript to control the types of data that appear.

Imaging Panel

The Imaging panel contains toggles that control the visibility of cell features, such as cell boundaries and nuclear boundaries. The panel also lets you modify the appearance of cell paint targets, including the following controls:

• A checkbox to control the visibility of a target
• A color indicator circle to update the color for a target
• A slider to control the color contrast for a target by setting the [begin, end] values of the ramp function for that imaging channel

Protein and Transcript Panel

The Protein and Transcript panels contain controls to view locations of proteins and transcripts. Circles on the visualization indicate the locations of the proteins and transcripts. The panels contain a Marker Size tool to adjust the size of the circles. Search bars let you filter to find specific proteins and transcripts.

The panels let you modify the appearance of protein and transcript targets, including the following controls:

• A checkbox to control the visibility of a protein or transcript
• A color indicator circle to update the color for a protein or transcript

View and Undo Selections

Current selections are displayed in a bar at the top of the screen. Click the back arrow icon to clear selections and go back to the default state.

Export Image

Use the Export Image button to export the view on the screen as a JPEG.