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Installation
Usage
Tutorials
General tutorials
How to start
Analyzing MERFISH Data from the MERSCOPE Platform
Analysis of NanoString CosMx data
Tutorial for the Analysis of Visium HD Data
Advanced tutorials
Working with multiple samples and coordinate systems
Using SPArrOW with a retrained Cellpose model
Using multiple stains on Xenium data
HPC tutorials
High Performance Computing
High Performance Computing on the VIB Data Core Compute
API
sparrow.io.merscope
sparrow.io.xenium
sparrow.io.visium_hd
sparrow.io.read_transcripts
sparrow.io.read_resolve_transcripts
sparrow.io.read_merscope_transcripts
sparrow.io.read_stereoseq_transcripts
sparrow.io.create_sdata
sparrow.im.add_image_layer
sparrow.im.add_labels_layer
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.cellpose_callable
sparrow.im.baysor_callable
sparrow.im.add_grid_labels_layer
sparrow.im.expand_labels_layer
sparrow.im.align_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.sh.vectorize
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.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
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.utils.RasterAggregator
sparrow.datasets.resolve_example
sparrow.datasets.visium_hd_example
sparrow.datasets.get_registry
sparrow.datasets.get_spatialdata_registry
Development
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.rst
.pdf
sparrow.pl.clustermap
Contents
clustermap()
sparrow.pl.clustermap
#
sparrow.pl.
clustermap
(
*
args
,
**
kwargs
)
#
Contents
clustermap()
