Exploring Visualizations

Load Demo Data

CytoCanvas provides demo datasets that you can 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

To load your cytoprofiling data in CytoCanvas for exploration, use one of the following methods:

• Load data from a local filesystem
• Load data from an Amazon S3 bucket

For both options, CytoCanvas first identifies the dataset through 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 Amazon 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 other 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.
   • (Optional) Select Manage Credentials to create and store new AWS credentials or manage your existing AWS credentials.
   • 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.

Visualization Types

Flow Cell View

After the data is loaded, a visualization of the cell culture samples are displayed in Flow Cell view. In this view, 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, Proteins, and Transcripts. 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. You can also add well and tile labels that are visible while you pan the flow cell. Category data can be visualized from RawCellStats.parquet in the run directory. Categories are defined as any string grouping (for example, Gene, MostAbundantTarget, etc.).

Montage View

Use Montage view to display cell groups and tile individual cell snapshots. Compare cells within a cell group or across cell groups. The Montage Controls panel allows you to reorder groups, change image size, set the number of cells per column, and adjust the zoom. You can overlay morphology features, proteins, and transcript spatial locations. You can also visually focus on individual cells by removing the background to focus on intracellular proteins and reagents. Export Montage view images as needed.

To generate a montage, select the cell groups that you want to montage from the Montage Controls panel, and then select Generate. For more information on how to create cell groups, see Cell Table and Create a Cell Group.

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.

Proteins and Transcripts Panels

The Proteins and Transcripts panels contain controls to view locations of proteins and transcripts. Dots on the visualization indicate the locations of the proteins and transcripts. The Marker Size tool allows you to adjust the size of the dots that are displayed in the view. To find specific proteins and transcripts, use the Search bars.

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

• Target Visibility: A checkbox that 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.

Cell Groups Panel

The Cell Groups panel is available in Flow Cell view only. This panel allows you to toggle which cell groups you want to view. For more information on how to create cell groups, see Cell Table and Create a Cell Group.

Cell Table

To manage cell groups, open the Cell Table from the Flow Cell or Montage view. From the Cell Table, you can create a new cell group or edit, delete, and reorder existing cell groups. Any available data column in RawCellStats.parquet can be added to the Cell Table. From the Cell Table, you can further sort and filter each data column to select specific cells for display in Montage view. Cell groups can be exported from one run and imported into another run to share group definitions across collaborators and runs.

Note:  

The Cell Table is only available when you generate visualizations with Cells2Stats v1.3.0 or later.

The Cell Table includes the following features:

• Select Columns: You can add additional columns to display. The default columns are Cell, Well, WellLabel, Tile, X, Y, Area.
• Manage Cell Groups: You can create, edit, rename, or delete a cell group.
• Show Cell Groups or Hide Cell Groups: You can toggle the Cell Group pane, which allows you to view cell groups and add or remove cells from cell groups.
• Charts: You can create a histogram, scatter plot, or box plot that allow you to visualize cell data and filter cells in the Cell Table. Data available for each chart is based on the columns selected in the Cell Table. Box plot charts can be exported as images if desired.

Create a Cell Group

1. From the Flow Cell or Montage view, select Open Cell Table in the upper-right corner.
2. Select Manage Cell Groups.
3. In the Create New Group box, complete the following:
   • Enter a group name.
   • Select a color.
   • Select Create.

After you create a cell group, you can edit the cell group to add or remove cells or modify the cell group name and color.

Add or Remove Cells from a Cell Group

Up to 100 cells can be added to an individual cell group.

1. From the Flow Cell or Montage view, select Open Cell Table in the upper-right corner.
2. Select Show Cell Groups, and then select a cell group from the Select Group drop-down menu.
3. To add or remove cells from the cell group, complete the following:
   • Add: Select the cell checkboxes in the Cell Table view. Then, select Add Selected from the Cell Groups pane. The number of Cells in Group updates based on your new selections. To select a range of cells, select a cell checkbox, and then press and hold the Shift key down while you select another cell in the table. All cells in between are selected.
   • Remove: Select the cells that you want to remove in the Cell Groups pane. Then, select Remove. The number of Cells in Group updates based on your new selections.

Edit the Cell Group Name and Color

1. From the Flow Cell or Montage view, select Open Cell Table in the upper-right corner.
2. Select Manage Cell Groups.
3. To modify the cell group name or color, select Edit and make your desired changes.
4. Select Save.

Delete a Cell Group

1. From the Flow Cell or Montage view, select Open Cell Table in the upper-right corner.
2. Select Manage Cell Groups.
3. Select Delete for the cell group that you want to delete.

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.