stitch

stitch#

Contains 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._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 = None, reader_type=<class 'scportrait.tools.stitch._utils.filereaders.FilePatternReaderRescale'>, orientation: dict | None = None, plot_QC: bool = True, overwrite: bool = False, cache: str | None = None)#

Class for stitching of image tiles to assemble a mosaic.

Parameters:

input_dir (str) – Directory containing the input image tiles.
slidename (str) – Name of the slide.
outdir (str) – Output directory to save the stitched mosaic.
stitching_channel (str) – Name of the channel to be used for stitching.
pattern (str) – File pattern to match the image tiles.
overlap (float, optional) – Overlap between adjacent image tiles (default is 0.1).
max_shift (float, optional) – Maximum allowed shift during alignment (default is 30).
filter_sigma (int, optional) – Sigma value for Gaussian filter applied during alignment (default is 0).
do_intensity_rescale (bool or "full_image", optional) – Flag to indicate whether to rescale image intensities (default is True). Alternatively, set to “full_image” to rescale the entire image.
rescale_range (tuple or dict, optional) – If all channels should be rescaled to the same range pass a tuple with the percentiles for rescaling (default is (1, 99)). Alternatively, a dictionary can be passed with the channel names as keys and the percentiles as values if each channel should be rescaled to a different range.
channel_order (list, optional) – Order of channels in the generated output mosaic. If none (default value) the order of the channels is left unchanged.
reader_type (class, optional) – Type of reader to use for reading image tiles (default is FilePatternReaderRescale).
orientation (dict, optional) – Dictionary specifying which dimensions of the slide to flip (default is {‘flip_x’: False, ‘flip_y’: True}).
plot_QC (bool, optional) – Flag to indicate whether to plot quality control (QC) figures (default is True).
overwrite (bool, optional) – Flag to indicate whether to overwrite the output directory if it already exists (default is False).
cache (str, optional) – Directory to store temporary files during stitching (default is None). If set to none this directory will be created in the outdir.

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=0.05)#

Generate a thumbnail of the stitched mosaic.

Parameters:: scale (float, optional) – Scale factor for the thumbnail. Defaults to 0.05.

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 (bool, optional) – Flag to indicate whether to export an XML file for the TIFF files (default is True). 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=4, n_downscaling_layers=4, chunk_size=(1, 1024, 1024))#

Write the assembled mosaic as an OME-Zarr file.

Parameters:

downscaling_size (int, optional) – Downscaling factor for generating lower resolution layers (default is 4).
n_downscaling_layers (int, optional) – Number of downscaling layers to generate (default is 4).
chunk_size (tuple, optional) – Chunk size for the generated OME-Zarr file (default is (1, 1024, 1024)).

Returns:

None

write_thumbnail()#: Write the generated thumbnail as a TIFF file.

write_spatialdata(scale_factors=None)#

Write the assembled mosaic as a SpatialData object.

Parameters:: scale_factors (list, optional) – List of scale factors for the generated SpatialData object. Default is [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._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 = True, rescale_range: tuple = (1, 99), plot_QC: bool = True, WGAchannel: str | None = None, channel_order: list[str] | None = None, overwrite: bool = False, reader_type=<class 'scportrait.tools.stitch._utils.filereaders.FilePatternReaderRescale'>, orientation=None, cache: str | None = 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.

Parameters:

input_dir (str) – Directory containing the input image tiles.
slidename (str) – Name of the slide.
outdir (str) – Output directory to save the stitched mosaic.
stitching_channel (str) – Name of the channel to be used for stitching.
pattern (str) – File pattern to match the image tiles.
overlap (float, optional) – Overlap between adjacent image tiles (default is 0.1).
max_shift (float, optional) – Maximum allowed shift during alignment (default is 30).
filter_sigma (int, optional) – Sigma value for Gaussian filter applied during alignment (default is 0).
do_intensity_rescale (bool or "full_image", optional) – Flag to indicate whether to rescale image intensities (default is True). Alternatively, set to “full_image” to rescale the entire image.
rescale_range (tuple or dict, optional) – If all channels should be rescaled to the same range pass a tuple with the percentiles for rescaling (default is (1, 99)). Alternatively, a dictionary can be passed with the channel names as keys and the percentiles as values if each channel should be rescaled to a different range.
channel_order (list, optional) – Order of channels in the generated output mosaic. If none (default value) the order of the channels is left unchanged.
reader_type (class, optional) – Type of reader to use for reading image tiles (default is FilePatternReaderRescale).
orientation (dict, optional) – Dictionary specifying which dimensions of the slide to flip (default is {‘flip_x’: False, ‘flip_y’: True}).
plot_QC (bool, optional) – Flag to indicate whether to plot quality control (QC) figures (default is True).
overwrite (bool, optional) – Flag to indicate whether to overwrite the output directory if it already exists (default is False).
cache (str, optional) – Directory to store temporary files during stitching (default is None). If set to none this directory will be created in the outdir.
threads (int, optional) – Number of threads to use for parallel processing (default is 20).

write_tif_parallel(export_xml=True)#

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

Parameters:: export_xml (bool, optional) – Flag to indicate whether to export an XML file for the TIFF files (default is True). This XML file is compatible with loading the generarted TIFF files into BIAS.

stitch

Contents

stitch#