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Inputs and Outputs

Input files for Cells2Stats 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, including cell assignment statistics, and subfolders. The subfolders include a Wells folder, a Logs folder, a CellSegmentation folder, and an optional visualization folder.

Example Output Directories​

Regenerating AVITI24 Output​

The following file structure is a representative example of an output directory from a Cells2Stats run that regenerated the AVITI24 output files and folders. Optional arguments can change the structure of output files.

output
├── AverageNormWellStats.csv
├── CellSegmentation
│   ├── WellA1
│   │   ├── L1R02C01S1_Cell.tif
│   │   ├── L1R02C01S1_Nuclear.tif
│   │   └── ... for n tiles in the well
│   └── ... for n wells
├── Logs
│   └── Cells2Stats.log
├── Panel.json
├── RawCellStats.csv
├── RawCellStats.parquet
├── RunManifest.json
├── RunParameters.json
├── RunStats.json
├── Versions.json
└── Wells
    ├── WellA1
    │   ├── B01
    │   │   ├── L1R02C01S1_barcodes.parquet
    │   │   └── ... for n tiles
    │   └── ... for n batches
    └── ... for n wells

Preparing Run Output for Visualization in CytoCanvas​

The following file structure is a representative example of an output directory from a Cells2Stats run that prepared the run output for visualization using the CytoCanvas tool with the optional --visualization-only argument. Optional arguments can change the structure of output files.

output
├── CellSegmentation
│   ├── WellA1
│   │   ├── L1R02C01S1_Cell.tif
│   │   ├── L1R02C01S1_Nuclear.tif
│   │   └── ... for n tiles in the well
│   └── ... for n wells
├── Logs
│   ├── Cells2Stats.log
│   └── Visualization.log
├── Panel.json
├── RunManifest.json
├── RunParameters.json
└── visualization
    ├── cells
    ├── cyto.viz
    ├── locations
    ├── multiscale_flowcell.zarr
    └── targets

Regenerating AVITI24 Output and Preparing the Run Output for Visualization in CytoCanvas​

The following file structure is a representative example of an output directory from a Cells2Stats run using the optional --visualization argument. Optional arguments can change the structure of output files.

output
├── AverageNormWellStats.csv
├── CellSegmentation
│   ├── WellA1
│   │   ├── L1R02C01S1_Cell.tif
│   │   ├── L1R02C01S1_Nuclear.tif
│   │   └── ... for n tiles in the well
│   └── ... for n wells
├── Logs
│   ├── Cells2Stats.log
│   └── Visualization.log
├── Panel.json
├── RawCellStats.csv
├── RawCellStats.parquet
├── RunManifest.json
├── RunParameters.json
├── RunStats.json
├── Versions.json
├── Wells
│   ├── WellA1
│   │   ├── B01
│   │   │   ├── L1R02C01S1_barcodes.parquet
│   │   │   └── ... for n tiles
│   │   └── ... for n batches
│   └── ... for n wells
└── visualization
    ├── cells
    ├── cyto.viz
    ├── locations
    ├── multiscale_flowcell.zarr
    └── targets

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

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