Skip to main content
Back to top
Ctrl
+
K
Search
Ctrl
+
K
Installation
Quickstart
Usage
Tutorials
General tutorials
Technology-specific advice
Scalable Spatial Transcriptomics Analysis with Harpy.
Highly-multiplexed image analysis with Harpy
Harpy support for InstanSeg segmentation model
Run FlowSOM for pixel and cell clustering
Generating single-cell representations from highly multiplexed images and integration with PyTorch
Highly-multiplexed image analysis with
Harpy
and
Kronos
.
Quality Control on IMC spatial proteomics with Harpy
Benchmark results Harpy
Advanced tutorials
Quality Control on in-silico spatial proteomics with Harpy
Interactive napari cell annotation on spatial proteomics
Interactive napari pixel annotation on spatial proteomics
Harpy distance calculations
Working with multiple samples (and coordinate systems)
Rasterize and vectorize
Shallow feature extraction using
Harpy
.
Basic Spatial Transcriptomics Analysis with Harpy
Example spatial transcriptomics (Xenium)
Understanding Dask behaviour in SpatialData
HPC tutorials
High Performance Computing
High Performance Computing on the VIB Data Core Compute.
API
harpy.io.macsima
harpy.io.merscope
harpy.io.xenium
harpy.io.visium
harpy.io.visium_hd
harpy.io.read_transcripts
harpy.io.read_resolve_transcripts
harpy.io.read_merscope_transcripts
harpy.io.read_stereoseq_transcripts
harpy.io.convert_to_zarr_2
harpy.im.add_image
harpy.im.add_labels
harpy.im.get_dataarray
harpy.im.map_image
harpy.im.tiling_correction
harpy.im.enhance_contrast
harpy.im.normalize
harpy.im.min_max_filtering
harpy.im.gaussian_filtering
harpy.im.transcript_density
harpy.im.combine
harpy.im.segment
harpy.im.segment_points
harpy.im.cellpose_callable
harpy.im.instanseg_callable
harpy.im.baysor_callable
harpy.im.add_grid_labels
harpy.im.expand_labels
harpy.im.align_labels
harpy.im.map_labels
harpy.im.filter_labels
harpy.im.merge_labels
harpy.im.match_labels_to_reference
harpy.im.rasterize
harpy.im.pixel_clustering_preprocess
harpy.im.flowsom
harpy.sh.vectorize
harpy.sh.add_shapes
harpy.sh.filter_shapes
harpy.sh.create_voronoi_boundaries
harpy.tb.add_table
harpy.tb.allocate
harpy.tb.bin_counts
harpy.tb.allocate_intensity
harpy.tb.add_regionprops
harpy.tb.add_feature_matrix
harpy.tb.extract_instances
harpy.tb.ZarrIterableInstances
harpy.tb.ZarrDataLoader
harpy.tb.featurize
harpy.tb.preprocess_transcriptomics
harpy.tb.preprocess_proteomics
harpy.tb.filter_on_size
harpy.tb.leiden
harpy.tb.kmeans
harpy.tb.score_genes
harpy.tb.score_genes_iter
harpy.tb.correct_marker_genes
harpy.tb.cluster_cleanliness
harpy.tb.nhood_enrichment
harpy.tb.nhood_kmeans
harpy.tb.cluster_intensity
harpy.tb.cluster_intensity_SOM
harpy.tb.spatial_pixel_neighbors
harpy.tb.cell_clustering_preprocess
harpy.tb.flowsom
harpy.tb.weighted_channel_expression
harpy.pt.add_points
harpy.externals.ilastik.run_object_classification
harpy.qc.image_histogram
harpy.qc.segmentation_coverage
harpy.qc.segmentation_histogram
harpy.qc.analyse_genes_left_out
harpy.qc.metric_histogram
harpy.qc.metrics_histogram
harpy.qc.obs_scatter
harpy.pl.plot_sdata
harpy.pl.plot_sdata_genes
harpy.pl.plot_instance_density
harpy.pl.cluster_intensity_heatmap
harpy.pl.pixel_clusters
harpy.pl.pixel_clusters_heatmap
harpy.pl.snr_ratio
harpy.pl.group_snr_ratio
harpy.pl.snr_clustermap
harpy.pl.signal_clustermap
harpy.pl.clustermap
harpy.pl.plot_transcript_density
harpy.utils.RasterAggregator
harpy.utils.Featurizer
harpy.utils.kronos_embedding
harpy.utils.bounding_box_query
harpy.datasets.cluster_blobs
harpy.datasets.multisample_blobs
harpy.datasets.pixie_example
harpy.datasets.macsima_example
harpy.datasets.macsima_colorectal_carcinoma
harpy.datasets.macsima_colorectal_carcinoma_course
harpy.datasets.macsima_tonsil
harpy.datasets.codex_example
harpy.datasets.mibi_example
harpy.datasets.vectra_example
harpy.datasets.resolve_example
harpy.datasets.merscope_mouse_liver
harpy.datasets.xenium_human_lung_cancer
harpy.datasets.xenium_human_ovarian_cancer
harpy.datasets.xenium_human_ovarian_cancer_course
harpy.datasets.visium_hd_example
harpy.datasets.visium_hd_example_custom_binning
harpy.datasets.get_registry
harpy.datasets.get_spatialdata_registry
Development
Repository
Open issue
Search
Error
Please activate JavaScript to enable the search functionality.
Ctrl
+
K
