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Core Cutting Configuration

Core cutting supports two modes of operation:

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

Shared Configuration

These fields are common to both modes:

temp_dir: "C:/path_to_temporary_directory"
output_dir: "C:/path_to_output_directory"
core_info: "C:/path_to/core_metadata.csv"
include_channels: ['002_DAPI']
exclude_channels: ['005_pRB']
use_channels: ['DAPI','CD3']
margin: 10
mask_value: 0
max_pyramid_levels: 3

transfer_cleanup_enabled: true
core_cleanup_enabled: true
Key Type Description
temp_dir str Temporary folder to store extracted TIFFs for each core
output_dir str Final destination for SpatialData (Zarr) outputs
core_info str Path to the CSV file containing core cutting metadata
include_channels list[str] Optional list of full channel names to include (e.g., 001_DAPI)
exclude_channels list[str] Optional list of full channel names to exclude
use_channels list[str] Optional list to restrict final base marker names (e.g., DAPI, CD3)
margin int Number of pixels to pad around each bounding box when cutting cores
mask_value int Value used to fill background for polygonal core masks
max_pyramid_levels int Number of downsampled pyramid levels (0 means no pyramid)
transfer_cleanup_enabled bool Whether to delete temporary files downloaded via Globus after the run
core_cleanup_enabled bool Whether to delete TIFFs from temp_dir after core assembly
  • For detailed explanation of include_channels, exclude_channels, and use_channels, see the channel selection logic.

Sourcing Image Files

Differences in local vs. Globus mode come from how OME-TIFF files are sourced.

📰 Local Mode

In local mode, image_dir should point to a folder with accessible OME-TIFF files on disk.

image_dir: "C:/path_to_image_directory"
  • On Windows, use forward slashes / in paths: C:/path/to/folder. This avoids issues with escape characters.

☁️ Globus Mode

In Globus mode, you must also specify the path to a Globus configuration directory. The image_dir field should reflect the remote directory on the Globus endpoint:

image_dir: "/my_globus/path_to_image_directory"
globus_config: "C:/path_to_globus_config_directory"

This allows the pipeline to discover and transfer files on demand via Globus.