Inputs

AVITI24 output files require pre-processing by Cells2Stats to be used with CytoCanvas. Preprocessing includes tiling images and building a visualization manifest.

Generating Visualization Data

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

Representative view of Cells2Stats 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 Cell2Stats 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.