Prepare data and open a workspace

Prepare your Cells2Stats output files and open a dataset in CytoCanvas™.

CytoCanvas 1.5.3 supports AVITI24™ output files from AVITI OS 4.1.0 and later. CytoCanvas is also backward compatible with run outputs from earlier AVITI OS versions, which require preprocessing by Cells2Stats.

The cyto.viz file is required to open any dataset in CytoCanvas. The cells, targets, and .zarr files and their accompanying index files are also required to visualize the data output.

Files must be in the same directory path as the cyto.viz manifest file. The default output of AVITI24 or Cells2Stats is compatible with this format.

Caution:

Do not modify or rename the contents of the cyto.viz file, the multiscale_flowcell.zarr folder, the cells folder, or the targets folder. The directory structure and file contents must remain consistent for CytoCanvas to successfully visualize data.

Workspaces

When you open a dataset in CytoCanvas, the application automatically creates a workspace alongside your data. A workspace captures your session state, including the loaded data source, view position, and any other session-specific settings. You can close CytoCanvas and reopen the workspace later to resume your session without reconfiguring your setup.

To reopen a saved session, open the workspace file from the home screen or from your filesystem instead of opening the cyto.viz file directly.

Load data

CytoCanvas supports loading data locally, directly from Amazon S3, or from demo datasets that Element Biosciences hosts. After selecting a data source, CytoCanvas prompts you to complete two steps before opening the viewer:

1. Name the workspace — enter a name for this session.
2. Confirm the workspace save location — choose where the workspace file is saved on your local machine. The default location is your Documents/CytoCanvas Workspaces folder.

Load from a local filesystem

1. Open the CytoCanvas application.
2. Select Open from files to browse the local filesystem.
3. Navigate to the folder containing the cyto.viz file.
4. Select and open the cyto.viz file.
5. Enter a name for the workspace and select Continue.
6. Confirm or update the local save path for the workspace and select Open.

   CytoCanvas loads the dataset and opens it in the viewer.

Load from Amazon S3

Data can be loaded directly from any Amazon S3 bucket using a saved credential profile. To create a credential profile before loading, see Manage AWS credential profiles.

1. Open the CytoCanvas application.
2. Select Open from Cloud.
3. On the Load Data from AWS page, complete the following:
   • Enter the S3 URI location to the cyto.viz file (for example, s3://example_bucket-name/DemoInstrument/20240821_DemoInstrument_Example_Run/SpatialData/cyto.viz).
   • Select a saved credential profile from the dropdown menu, or select Manage Credentials to add a new profile.
4. Select Submit.
5. Enter a name for the workspace and select Continue.
6. Confirm or update the local save path for the workspace and select Open.

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

Load a demo dataset

Element hosts demo cell screening datasets that can be loaded directly from CytoCanvas without any credentials or local data files. Demo datasets are a quick way to explore CytoCanvas features using real run data.

1. Open the CytoCanvas application.
2. Select Open Demo Data.
3. Browse the available demo datasets and select one to load.
4. Enter a name for the workspace and select Continue.
5. Confirm or update the local save path for the workspace and select Open.

   CytoCanvas downloads and loads the demo dataset and opens it in the viewer.