API Reference

This section contains the reference documentation for the elements important for the user.

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RoiPreparationController(metadata_df, file_strategy, temp_dir, output_dir, margin=0, mask_value=0, max_pyramid_levels=3, chunk_size=(1, 256, 256), downscale=2, temp_roi_delete=True)

Coordinate cutting and assembly of cores from multiplex images.

Initialize the RoiPreparationController.

Parameters:

Name	Type	Description	Default
metadata_df	DataFrame	DataFrame containing ROI metadata.	required
file_strategy	FileAvailabilityStrategy	Strategy for retrieving image files.	required
temp_dir	str	Directory for temporary core files.	required
output_dir	str	Destination for assembled Zarr outputs.	required
margin	int	Padding pixels around each core.	0
mask_value	int	Fill value for masked regions.	0
max_pyramid_levels	int	Number of pyramid levels for the output.	3
chunk_size	tuple[int, int, int]	Chunk dimensions (C, Y, X) for the Zarr array.	(1, 256, 256)
downscale	int	Downsampling factor between pyramid levels.	2
temp_roi_delete	bool	Whether to delete intermediate TIFFs after assembly.	True

run()

Execute the ROI preparation pipeline.

Iterates through available channels, cuts ROIs, and assembles them into SpatialData Zarr stores.

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