Outputs

After running this preprocessing module, you will have:

Tissue Region Files

• OME-TIFF tissue crops: {OUT_DIR}/{EXP_ID}/{base_name}_tissue_{i}.ome.tiff

  • Each crop is a multi-channel image representing a distinct tissue region
  • Images are saved in OME-TIFF format (C,H,W) with LZW compression
  • If skip_roi_crop is enabled, a single full image will be saved as {base_name}_full.ome.tiff

• Visualization (optional): {OUT_DIR}/{EXP_ID}/tissue_masks_preview.png

  • Visual representation of detected tissue regions if visualize is enabled

Antibody Data

• Antibody mapping: {OUT_DIR}/extras/antibodies.tsv

  • Tab-separated file with columns: version, channel_id, and antibody_name
  • Maps each channel to its corresponding antibody marker

• OME-XML metadata: {data_path}/{base_name}.xml

  • Extracted OME-XML metadata from the original QPTIFF file
  • Contains detailed information about channels, dimensions, etc.

Log Files

• Detailed logs for each experiment are saved to {LOG_DIR}/{EXP_ID}.log
• Contains timing information, processing steps, and any errors/warnings