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SPArrOW quickstart
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Work with multiple samples (and coordinate systems)
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High Performance Computing on the VIB Data Core Compute.
API
sparrow.io.create_sdata
sparrow.io.read_transcripts
sparrow.io.read_resolve_transcripts
sparrow.io.read_vizgen_transcripts
sparrow.io.read_stereoseq_transcripts
sparrow.im.add_image_layer
sparrow.im.add_labels_layer
sparrow.im.map_channels_zstacks
sparrow.im.tiling_correction
sparrow.im.enhance_contrast
sparrow.im.normalize
sparrow.im.min_max_filtering
sparrow.im.gaussian_filtering
sparrow.im.transcript_density
sparrow.im.combine
sparrow.im.segment
sparrow.im.segment_points
sparrow.im.add_grid_labels_layer
sparrow.im.expand_labels_layer
sparrow.im.align_labels_layers
sparrow.im.apply_labels_layers
sparrow.im.filter_labels_layer
sparrow.im.merge_labels_layers
sparrow.im.merge_labels_layers_nuclei
sparrow.im.rasterize
sparrow.im.mask_to_original
sparrow.im.pixel_clustering_preprocess
sparrow.im.flowsom
sparrow.sh.add_shapes_layer
sparrow.sh.filter_shapes_layer
sparrow.sh.create_voronoi_boundaries
sparrow.tb.add_table_layer
sparrow.tb.allocate
sparrow.tb.allocate_intensity
sparrow.tb.preprocess_transcriptomics
sparrow.tb.preprocess_proteomics
sparrow.tb.filter_on_size
sparrow.tb.leiden
sparrow.tb.kmeans
sparrow.tb.score_genes
sparrow.tb.score_genes_iter
sparrow.tb.correct_marker_genes
sparrow.tb.cluster_cleanliness
sparrow.tb.nhood_enrichment
sparrow.tb.add_regionprop_features
sparrow.tb.cluster_intensity
sparrow.tb.cell_clustering_preprocess
sparrow.tb.flowsom
sparrow.tb.weighted_channel_expression
sparrow.pt.add_points_layer
sparrow.pl.plot_image
sparrow.pl.plot_shapes
sparrow.pl.plot_labels
sparrow.pl.tiling_correction
sparrow.pl.flatfield
sparrow.pl.segment
sparrow.pl.snr_ratio
sparrow.pl.group_snr_ratio
sparrow.pl.snr_clustermap
sparrow.pl.signal_clustermap
sparrow.pl.clustermap
sparrow.pl.segmentation_coverage
sparrow.pl.segmentation_size_boxplot
sparrow.pl.segments_per_area
sparrow.pl.sanity_plot_transcripts_matrix
sparrow.pl.analyse_genes_left_out
sparrow.pl.transcript_density
sparrow.pl.preprocess_transcriptomics
sparrow.pl.cluster
sparrow.pl.score_genes
sparrow.pl.cluster_cleanliness
sparrow.pl.nhood_enrichment
sparrow.utils.bounding_box_query
sparrow.datasets.cluster_blobs
sparrow.datasets.multisample_blobs
sparrow.datasets.pixie_example
sparrow.datasets.macsima_example
sparrow.datasets.mibi_example
sparrow.datasets.vectra_example
sparrow.datasets.resolve_example
sparrow.datasets.get_registry
sparrow.datasets.get_spatialdata_registry
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.rst
.pdf
sparrow.pl.clustermap
Contents
clustermap()
sparrow.pl.clustermap
#
sparrow.pl.
clustermap
(
*
args
,
**
kwargs
)
#
Contents
clustermap()
