Exploring Visualizations

Load Demo Data

CytoCanvas provides demo datasets for you to explore.

1. Open the CytoCanvas application.
2. Select Explore Demo Data.
3. Identify the demo dataset that you want to explore, and then Select Open.

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 Amazon S3 cloud location

For both options, CytoCanvas first identifies the dataset by pointing 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 that contains the cyto.viz file.
4. Select and open the cyto.viz file.

Load Data from AWS S3

Data can be loaded directly from any Amazon S3 bucket.

Prerequisites

1. For CytoCanvas version 1.0.0-beta only, the Amazon S3 bucket must have the following CORS policy added:

   [
      {
         "AllowedHeaders": [],
         "AllowedMethods": [
               "GET",
               "HEAD"
         ],
         "AllowedOrigins": [
               "*"
         ],
         "ExposeHeaders": [],
         "MaxAgeSeconds": 3000
      }
   ]
2. For all CytoCanvas versions, the user must have Amazon S3 storage credentials to this bucket with read access.

Loading Data

1. Identify the S3 URI location of the cyto.viz file (For example, s3://example_bucket-name/DemoInstrument/20240821_DemoInstrument_Example_Run/visualization/cyto.viz).
2. Open the CytoCanvas application.
3. Select Open from Cloud.
4. On the Load Data from AWS page, complete the following:
   • Enter the S3 URI location to the cyto.viz file.
   • Enter the AWS Access Key ID.
   • Enter the AWS Secret Key.
   • (Optional) If you use temporary credentials, enter the AWS Session Token.
   • Enter the AWS Region of the bucket, or select a region from the drop-down menu.
5. Select Submit.

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

After the data is loaded, CytoCanvas displays a visualization of the cell culture samples. Each grid represents one of the wells on the flow cell for the run. To control the data types that appear, use the collapsible panels for Imaging, Protein, and Transcript. To zoom in and out of the target, use the zoom bar. To lock or unlock the zoom, toggle the lock icon next to the zoom bar.

Imaging Panel

The Imaging panel contains toggles that control the visibility of cell features, such as cell boundaries and nuclear boundaries. Also, you can modify the appearance settings of the cell paint targets, such as:

• Target Visibility: To toggle the target visibility on or off, select or unselect the checkbox.
• Target Color: To customize the target color, select the color indicator circle, and then update the color.
• Color Contrast: To modify the target color contrast, set the [begin, end] values of the slider function for that imaging channel.

Protein and Transcript Panels

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.

You can modify the appearance of protein and transcript targets as follows:

• Target Visibility: A checkbox toggles the protein or transcript visibility on or off.
• Target Color: To customize the protein or transcript color, select the color indicator circle, and then update the color.

Location Controls Panel

The Location Controls panel allows you to set, copy, or paste X and Y coordinates and the zoom level.

View and Undo Selections

Current selections are displayed in a bar at the top of the screen. To clear selections and revert to the default view, select the reverse arrow icon.

Export Image

To export the view on the screen as a JPEG, use the Export Image button.