stitching

For parallel stitching with multiple threads, use the following class:

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

Parameters:

input_dirstr

Directory containing the input image tiles.

slidenamestr

Name of the slide.

outdirstr

Output directory to save the stitched mosaic.

stitching_channelstr

Name of the channel to be used for stitching.

patternstr

File pattern to match the image tiles.

overlapfloat, optional

Overlap between adjacent image tiles (default is 0.1).

max_shiftfloat, optional

Maximum allowed shift during alignment (default is 30).

filter_sigmaint, optional

Sigma value for Gaussian filter applied during alignment (default is 0).

do_intensity_rescalebool 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_rangetuple or dictionary, optional

If all channels should be rescaled to the same range pass a tuple with the percentiles for rescaleing (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_orderlist, optional

Order of channels in the generated output mosaic. If none (default value) the order of the channels is left unchanged.

reader_typeclass, optional

Type of reader to use for reading image tiles (default is FilePatternReaderRescale).

orientationdict, optional

Dictionary specifiying which dimensions of the slide to flip (default is {‘flip_x’: False, ‘flip_y’: True}).

plot_QCbool, optional

Flag to indicate whether to plot quality control (QC) figures (default is True).

overwritebool, optional

Flag to indicate whether to overwrite the output directory if it already exists (default is False).

cachestr, optional

Directory to store temporary files during stitching (default is None). If set to none this directory will be created in the outdir.

threadsint, optional

Number of threads to use for parallel processing (default is 20).