Overview of directory structure

Cells2Stats input files are the files output from a cytoprofiling run. AVITI24™ generates the input files and transfers them to a run folder in your storage location.

During an execution, Cells2Stats generates an output folder that contains the output files and includes cell assignment statistics and subfolders. The subfolders include a Wells folder and a SpatialData folder.

Example output directories

Preparing run output for visualization in CytoCanvas™

The following file structure is a representative example of a run directory after a Cells2Stats execution that prepares the run output for visualization. The Cells2Stats output is located in the Cytoprofiling/ folder. Optional arguments can change the structure of output files.

20260519T195105Z/
├── RunManifest.json
├── RunManifest.csv
├── RunParameters.json
├── Panel.json
├── AverageNormWellStats.csv
├── RawCellStats.csv
├── RawCellStats.parquet
├── RunStats.json
├── multiqc_report.html
├── Versions.json
├── Wells/
│   └── WellXX/BXX/
│       └── LXRXXCXXS1_barcodes.parquet
├── CellSegmentation/
│   └── WellXX/
│       ├── LXRXXCXXS1_Cell.tif
│       └── LXRXXCXXS1_Nuclear.tif
└── SpatialData/
    ├── cyto.viz
    ├── RunName.zarr-index.json.gz
    ├── RunName.zarr.zip
    ├── cell_shapes_global.parquet
    ├── nuclear_shapes_global.parquet
    └── points_global.parquet

Example input directory

The following file structure is a representative example of an input directory:

example-storage-location
└── DemoInstrumentName
    └── 20240506_DemoInstrumentName_ExampleRunName
        ├── BaseCalling
        │   ├── BaseCalls
        │   │   └── BXX_CXXX.zip ... (for n cycles)
        │   ├── CellXform
        │   │   └── BXX ... (for n batches)
        │   │       └── LXRXXCXXS1.xform ... (for n tiles)
        │   ├── Location
        │   │   └── BXX ... (for n batches)
        │   │       └── LXRXXCXXS1ZXX.loc ... (for n tiles)
        │   └── Filter
        │       └── BXX ... (for n batches)
        │           └── LXRXXCXXS1ZXX.filter ... (for n tiles)
        ├── Cell Segmentation
        │   └── WellXX ... (for n wells)
        │       ├── LXRXXCXXS1_Cell.tif ... (for n tiles)
        │       └── LXRXXCXXS1_Nuclear.tif ... (for n tiles)
        ├── Thumbnails
        │   └── WellXX_Thumbnail.png ... (for n wells)
        ├── Projection
        │   └── WellXX ... (for n wells)
        │       └──BXX_LXRXXCXXS1_Target.tif ... (for each target and n tiles)
        ├── Cytoprofiling
        │   └── Instrument
        │       ├── AverageNormWellStats.csv
        │       ├── RawCellStats.csv
        │       ├── RawCellStats.parquet
        │       ├── RunStats.json
        │       ├── Versions.json
        │       └── Wells
        │           └── WellXX ... (for n wells)
        │               └── BXX ... (for n batches)
        │                   └── LXRXXCXXS1_barcodes.parquet ... (for n tiles)
        ├── RunManifest.csv
        ├── RunManifest.json
        ├── RunParameters.json
        ├── Panel.json
        ├── RunStats.bin
        ├── RunAnalysisFilesUploaded.json
        └── RunUploaded.json