Input files
The input files Cells2Stats reads
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 Biosciences 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 cell screening 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 |
| Raw Projection Image | {root}/Projection/{well}/{batch}_{tile}_{target}_Raw.tif | Uncorrected raw projection TIFFs. Present only when the Raw Projections advanced run setting is enabled (RawProjections). Required input for process_imaging_targets. | One per target per tile when enabled |
| Cell Segmentation Mask | {root}/CellSegmentation/{well}/{tile}_Cell.tif or {tile}_Cell.zarr | Cell segmentation masks for a well, where the value for a pixel in a cell is the cell ID. TIFF and Zarr are both accepted, as described in Segmentation mask formats | One per tile per well |
| Nuclear Segmentation Mask | {root}/CellSegmentation/{well}/{tile}_Nuclear.tif or {tile}_Nuclear.zarr | Nuclear segmentation masks for a well, where the value for a pixel in a nucleus is 1. TIFF and Zarr are both accepted, as described in Segmentation mask formats | One per tile per well |
By default, Cells2Stats reads projection images from {root}/Projection and segmentation masks from {root}/CellSegmentation. Options are available to read projection images or segmentation masks from alternate directories instead. For more information, see the CLI reference.
Segmentation mask formats
Cells2Stats accepts cell and nuclear segmentation masks as either TIFF or Zarr files, in both the run directory and an alternate directory. The format a run carries depends on the AVITI OS version that produced it:
| AVITI OS version | Cell mask | Nuclear mask |
|---|---|---|
| 4.1.0 and later | {tile}_Cell.zarr | {tile}_Nuclear.zarr |
| Earlier than 4.1.0 | {tile}_Cell.tif | {tile}_Nuclear.tif |
No configuration is required to select a format. Cells2Stats detects the format a run carries and reads it, so a run from either AVITI OS version analyzes with the same command. Cells2Stats also copies masks to its output without converting them, so the output carries whichever format the run used. For the output paths, see Segmentation mask formats.