API Reference

This section contains the reference documentation for all modules in the pipeline.

CoreCutter(margin=0, mask_value=0)

Extract rectangular or polygonal regions from images.

Create a new cutter.

Parameters:

Name	Type	Description	Default
margin	int	Padding to apply around each core.	0
mask_value	int	Value used outside polygon masks.	0

extract_core(array, row)

Extract a single core from the given image.

Parameters:

Name	Type	Description	Default
array	ndarray | Array	Source image.	required
row	Series	Metadata describing the core. Required fields include row_start, row_stop, column_start, column_stop and poly_type.	required

Returns:

Type	Description
ndarray	numpy.ndarray: The extracted core image.

CoreAssembler(temp_dir, output_dir, max_pyramid_levels=4, downscale=2, allowed_channels=None, cleanup=False)

Assemble per-channel TIFFs into a SpatialData object.

Initialize the assembler.

Parameters:

Name	Type	Description	Default
temp_dir	str	Directory containing temporary per-core folders.	required
output_dir	str	Location where .zarr outputs are written.	required
max_pyramid_levels	int	Maximum number of multiscale levels. 0 disables pyramid creation.	4
downscale	int	Downsampling factor per level.	2
allowed_channels	list[str] | None	Restrict processing to these channels. If None all channels are used.	None
cleanup	bool	Remove intermediate TIFFs when True.	False

assemble_core(core_id)

Assemble a single core from its per-channel TIFF images.

Parameters:

Name	Type	Description	Default
core_id	str	Identifier of the core's temporary folder.	required

Returns:

Name	Type	Description
str	str	Path to the written .zarr dataset.

Raises:

Type	Description
FileNotFoundError	If the temporary core folder is missing.
ValueError	If no TIFF files are found in the folder.

CorePreparationController(metadata_df, image_paths, temp_dir, output_dir, file_strategy, margin=0, mask_value=0, max_pyramid_levels=3, core_cleanup_enabled=True)

Coordinate cutting and assembly of cores from multiplex images.

Initialize the controller.

Parameters:

Name	Type	Description	Default
metadata_df	DataFrame	Table describing each core.	required
image_paths	dict[str, str]	Mapping of channel names to image paths.	required
temp_dir	str	Directory for temporary core files.	required
output_dir	str	Destination for assembled .zarr outputs.	required
file_strategy	FileAvailabilityStrategy	Strategy used to obtain image files.	required
margin	int	Pixels of padding around each core.	0
mask_value	int	Fill value for masked regions.	0
max_pyramid_levels	int	Number of pyramid levels.	3
core_cleanup_enabled	bool	Remove intermediate TIFFs after assembly.	True

cut_channel(channel, file_path)

Cut all cores from a single channel image.

Parameters:

Name	Type	Description	Default
channel	str	Name of the channel being processed.	required
file_path	str | Path	Path to the OME-TIFF file.	required

run()

Process all channels and assemble cores.

This method blocks until all channels have been processed and the corresponding cores have been assembled.

try_assemble_ready_cores()

Assemble any cores whose channels are complete.