Input Files
Input Files
The following table lists the input files for Cells2Stats. Parquet files are column-based files that efficiently store data. For more information, see the Apache Parquet Documentation.
| File | Directory and File Name | Description | Quantity |
|---|---|---|---|
| Run manifest, CSV | {root}/RunManifest.csv | CSV file that records biological sample information and analysis settings | One per run |
| Run manifest, JSON | {root}/RunManifest.json | JSON file reserved for Element processes | One per run |
| Run parameters | {root}/RunParameters.json | JSON file that records information about the run configuration | One per run |
| Panel | {root}/Panel.json | JSON file that records information about the targets for the run | One per run |
| Bases | {root}/BaseCalling/BaseCalls/{batch}_C{cycle}.zip | Binary files that contain the raw cytoprofiling base call data | One per batch per cycle |
| Filter | {root}/BaseCalling/Filter/{batch}/{tile}.filter | Binary files for use with future applications | One per tile per batch |
| Location | {root}/BaseCalling/Location/{batch}/{tile}.loc | Binary files that identify polony locations on the flow cell | One per tile per batch |
| Transform | {root}/BaseCalling/CellXform/{batch}/{tile}.xform | Binary files that transform polony locations onto cells | One per tile per batch |
| Projection Image | {root}/Projection/{well}/{batch}_{tile}_{target}.tif | Z-projected images of cell paint targets | One per target per tile |
| Cell Segmentation Mask | {root}/CellSegmentation/{well}/{tile}_Cell.tif | Cell segmentation masks for a well, where the value for a pixel in a cell is the cell ID | One per tile per well |
| Nuclear Segmentation Mask | {root}/CellSegmentation/{well}/{tile}_Nuclear.tif | Nuclear segmentation masks for a well, where the value for a pixel in a nucleus is 1 | One per tile per well |
| Average Normalized Well Statistics | {root}/Cytoprofiling/Instrument/AverageNormWellStats.csv | Filtered and average metrics for each well in the run | One per run |
| Versions, JSON | {root}/Cytoprofiling/Instrument/Versions.json | File that reports the version number for CSV output files and bundled software programs | One per run |
| Raw Cell Statistics, CSV | {root}/Cytoprofiling/Instrument/RawCellStats.csv | CSV file that reports values per cell for all morphology features and raw target counts in a run | One per run |
| Raw Cell Statistics, Parquet | {root}/Cytoprofiling/Instrument/RawCellStats.parquet | Parquet file that reports values per cell for all morphology features and raw target counts in a run | One per run |
| Barcodes | {root}/Cytoprofiling/Instrument/Wells/{well}/{batch}/{tile}_barcodes.parquet | Parquet files that provide barcoding information for each polony in a tile | One per tile per batch per well |
Alternative Cell Segmentation Directory
Cells2Stats accepts an alternate directory of nuclear and cell segmentation masks as an input using the --segmentation argument. For more information on generating cell segmentation masks please see the Performing Resegmentation and Cell Assignment Using Python tutorial. Cell Segmentation mask directories should be structured as follows:
Cell-Segmentation-Directory-Structure
└── CellSegmentation
└── WellXX // repeated per well
├── LXRXXCXXS1_Cell.tif // repeated per tile and cycle
└──LXRXXCXXS1_Nuclear.tif // repeated per tile and cycle