Input data

AVITI24™ output files require preprocessing by Cells2Stats to be used with CytoCanvas™. CytoCanvas 1.4.9 supports two Cells2Stats output formats, which are described below.

Cells2Stats 1.3.x visualization output

Visualization output from Cells2Stats 1.3.x is fully supported in CytoCanvas 1.4.9.

Run Cells2Stats with the --visualization or --visualization-only option to generate visualization files. Make sure that these output files include a visualization folder, which contains the following artifacts and structure:

Example Cells2Stats 1.3.x visualization output

visualization
    ├── cells
    ├── cyto.viz
    ├── locations
    ├── multiscale_flowcell.zarr
    └── targets

The cyto.viz file is required to open any dataset in CytoCanvas. The cells, targets, and .zarr 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 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.

Cells2Stats spatial data output

CytoCanvas 1.4.9 introduces native support for the Cells2Stats spatial data output format, introduced in Cells2Stats 1.4.0-beta. This format enables visualization of spatially-resolved transcript locations and cell and nuclear boundaries at the full flow cell scale, in addition to the fluorescence imagery available in the standard visualization format.

Unlike the 1.3.x format, the spatial data output is written to a SpatialData/ directory within the Cells2Stats run output. The cyto.viz file is located inside this folder and serves as the entry point for CytoCanvas.

Example Cells2Stats 1.4.0-beta spatial data output

SpatialData/
├── cyto.viz
├── RunName.zarr-index.json.gz
├── RunName.zarr.zip
├── cell_shapes_global.parquet
├── nuclear_shapes_global.parquet
└── points_global.parquet

The cyto.viz file is required to open any spatial dataset in CytoCanvas. Files must remain in the same directory structure as generated by Cells2Stats.

Caution:

Do not modify or rename any files in the Cells2Stats spatial output directory. The directory structure and file contents must remain consistent for CytoCanvas to successfully visualize data.

Note:

The spatial data output format requires Cells2Stats 1.4.0-beta or later. Refer to the Cells2Stats documentation for details.