Files

Build pipeline: openpipelines-bio.openpipeline-spatial.v0.4.0-2g7tn

Source commit: e41c3a485f

Source message: update version

2026-03-05 11:19:10 +00:00

openpipeline_spatial 0.4.0

NEW FUNCTIONALITY

feature_annotation/spatial_autocorr: Added a spatial autocorrelation component (PR #45).
feature_annotation/xenium_spatial_statistics: Added a component to calculate spatial statistics on Xenium-ingested data (PR #46).
neighbors/join_graphs: Combine spatial and expression neighborhood graphs into a single graph (PR #47).

convert/from_h5mu_to_spatialdata: Added a converter component to convert from H5MU to SpatialData (PR #40)

neighbors/spatial_neighborhood_graph: Calculate the spatial neighborhood graph (PR #29).
convert/from_spaceranger_to_h5mu: Added converter component for convert Spaceranger output to H5MU files (PR #33).
workflows/ingestion/spaceranger_mapping: Added a workflow to ingest Visium data using Spaceranger and convert the count matrix to an H5MU file (PR #33).

Add scope to component and workflow configurations (PR #22).
convert/from_xenium_to_spatialexperiment: Add arrow with zstd codec support to handle I/O of zstd-compressed Xenium parquet files (PR #30).
mapping/spaceranger_count: Allow providing individual FASTQ files instead of directories (PR #32).
Bump anndata to 0.12.7 and mudata to 0.3.2 (PR #34).
Bump spatialdata to 0.6.1 and spatialdata-io to 0.5.1 (PR #24, #34).
Bump squidpy to 1.7.0 (PR #36).
Update openpipeline dependencies to v4.0.0 (PR #37).

convert/from_cosmx_to_h5mu: Fixed an issue where parent directories of the cosmx output bundle were duplicated when reading in data (PR #25).
mapping/spaceranger_count: Fixed issue with long temporary folder paths causing write failures (PR #31).

convert: Updated multiple components to accept spatial output bundles in .zip format (for CosMx, Xenium and Aviti) as input (PR #19, PR #20).
convert/from_cosmx_to_h5mu: Updated component to handle CosMx output bundles generated with AtoMx SIP versions < v1.3.2 (PR #25).

filter/subset_cosmx: Added a component to subset COSMX data (PR #3, PR #9).
convert/from_cosmx_to_h5mu: Added converter component for COSMX data (PR #3, PR #9).
mapping/spaceranger_count: Added a spaceranger count component (PR #2).
convert/from_spatialdata_to_h5mu, convert/from_xenium_to_spatialdata, convert/from_xenium_to_h5mu: Added converter components for xenium data (PR #1, #10).
convert/from_xenium_to_spatialexperiment, convert/from_cosmx_to_spatialexperiment: Added converter components for Xenium or CosMx data to SpatialExperiment objects (PR #9).
convert/from_cells2stats_to_h5mu: Added a component to convert data resulting from Aviti Teton sequencers processed by Cells2Stats into an H5MU file (PR #15).
workflows/qc/qc: Added a pipeline for calculating qc metrics of spatial omics samples (PR #5).
workflows/multiomics/spatial_process_samples: Added a pipeline to pre-process multiple spatial omics samples (PR #7).
convert/from_h5mu_to_spatialexperiment: Added converter component for H5MU data to SpatialExperiment objects (PR #15).