stitch

stitch#

Functions to assemble tiled images into fullscale mosaics. Uses out-of-memory computation for the assembly of larger than memory image mosaics.

class scportrait.tools.stitch.Stitcher(input_dir: str, slidename: str, outdir: str, stitching_channel: str, pattern: str, overlap: float = 0.1, max_shift: float = 30, filter_sigma: int = 0, do_intensity_rescale: bool | str = True, rescale_range: tuple = (1, 99), channel_order: list[str] = None, reader_type='FilePatternReaderRescale', image_dtype=None, orientation: dict | None = None, plot_QC: bool = True, overwrite: bool = False, cache: str = None)#

Class for stitching of image tiles to assemble a mosaic.

get_stitching_information()#

Print information about the configuration of the stitching process.

save_positions()#

Save the positions of the aligned image tiles.

generate_thumbnail(scale: float | None = 0.05) → None#

Generate a thumbnail of the stitched mosaic.

Parameters:

scale – Scale factor for the thumbnail.

plot_qc()#

Plot quality control (QC) figures for the alignment.

stitch()#

Generate the stitched mosaic.

write_tif(export_xml: bool = True) → None#

Write the assembled mosaic as TIFF files.

Parameters:

export_xml – Whether to export an XML file for the TIFF files. This XML file is compatible with loading the generated TIFF files into BIAS.

Returns:

The assembled mosaic are written to file as TIFF files in the specified output directory.

write_ome_zarr(downscaling_size: int = 4, n_downscaling_layers: int = 4, chunk_size: tuple[int, int, int] = (1, 1024, 1024)) → None#

Write the assembled mosaic as an OME-Zarr file.

Parameters:

  • downscaling_size – Downscaling factor for generating lower resolution layers (default is 4).

  • n_downscaling_layers – Number of downscaling layers to generate (default is 4).

  • chunk_size – Chunk size for the generated OME-Zarr file (default is (1, 1024, 1024)).

write_thumbnail()#

Write the generated thumbnail as a TIFF file.

write_spatialdata(scale_factors: list[int] | None = None) → None#

Write the assembled mosaic as a SpatialData object.

Parameters:

scale_factors – List of scale factors for the generated SpatialData object. Defaults to [2, 4, 8]. The scale factors are used to generate downsampled versions of the image for faster visualization at lower resolutions.

class scportrait.tools.stitch.ParallelStitcher(input_dir: str, slidename: str, outdir: str, stitching_channel: str, pattern: str, overlap: float = 0.1, max_shift: float = 30, filter_sigma: int = 0, do_intensity_rescale: bool | str = True, rescale_range: tuple = (1, 99), channel_order: list[str] = None, reader_type='FilePatternReaderRescale', image_dtype=None, orientation: dict | None = None, plot_QC: bool = True, overwrite: bool = False, cache: str = None, threads: int = 20)#

Class for parallel stitching of image tiles and generating a mosaic. For applicable steps multi-threading is used for faster processing.

write_tif_parallel(export_xml: bool = True)#

Parallelized version of the write_tif method to write the assembled mosaic as TIFF files.

Parameters:

export_xml – Whether to export an XML file for the TIFF files. This XML file is compatible with loading the generarted TIFF files into BIAS.

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