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Input Data

File Naming Convention

The pipeline expects OME-TIFF files to follow a specific naming convention (typical of processed CellDive data). The filename is parsed to extract the round number and marker name.

Format: [Prefix]_[Round].0.4_R000_[Dye]_[Marker]-[Suffix].ome.tif

  • Round: Extracted from the second segment (e.g., 001 from ..._1.0.4_...).
  • Marker:
    • If the [Dye] segment contains "DAPI", the marker is set to DAPI.
    • Otherwise, the marker is extracted from the [Marker] segment (everything before the first hyphen -).

Example:

  • File: BLCA-1_1.0.4_R000_Cy3_pH2AX-AF555_FINAL_AFR_F.ome.tif
  • Round: 1
  • Marker: pH2AX
  • Channel Name: 001_pH2AX

Sourcing Image Files

Original tiff files are required to divide into separate SpatialData objects in the ROI Cutting step.

These files can be sourced differently resulting in the ROI cutting step supporting two modes of operation:

  • Local mode: Tiff files are available on the local filesystem.
  • Globus mode: Tiff files are accessed remotely using Globus endpoints.

For details of setting up Globus see Globus Setup.

All downstream steps are performed on locally available SpatialData object.