openpipeline_spatial/CHANGELOG.md

openpipeline_spatial 0.5.0

NEW FUNCTIONALITY

• dataflow/concatenate_spatialdata: Concatenate two or more SpatialData objects (PR #49).

• dataflow/move_layer_spatialdata: Move/rename a layer in a SpatialData object (PR #50).

• convert/from_h5mu_to_seurat_with_fov: Added converter component for H5MU data to Seurat objects with spatial FOV (PR #51).

MAJOR CHANGES

• Pin OpenPipeline dependency to v4.1.0 (PR #56).

MINOR CHANGES

• Pin ome-zarr to 0.13.0 to avoid a chunk shape incompatibility with zarr 3.x (PR #48).

• Bump Viash to 0.9.7 (PR #57).

• Bump anndata to 0.12.16 (PR #57).

• Bump mudata to 0.3.8 (PR #57).

• Bump scanpy to 1.11.4 (PR #57)

• Testing: bump viashpy to 0.10.0 (PR #57).

BUG FIXES

• convert/from_h5mu_to_spatialdata: Make sure the AnnData table is properly parsed before inserting into the new SpatialData object (PR #53).

• convert/from_h5mu_to_spatialexperiment: Add libuv1-dev to the test image so reticulate imports successfully (#54).

• nichecompass/gene_program_mask: Bump container base image to nvidia/cuda:12.6.3-cudnn-devel-ubuntu24.04 and pin decoupler>=2.1.6 to pick up the updated HCOP orthology download URL (PR #55).

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).

openpipeline_spatial 0.3.0

NEW FUNCTIONALITY

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

• nichecompass/gene_program_mask: Added a component to create a prior knowledge gene program mask for NicheCompass analysis (PR #27).

MINOR CHANGES

• Bump squidpy to 1.8.1 and spatialdata to 0.7.2 (PR #41).

• Update openpipeline dependencies to v4.0.3 (PR #42, PR #44).

openpipeline_spatial 0.2.0

NEW FUNCTIONALITY

• 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).

MINOR CHANGES

• 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).

BUG FIXES

• 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).

openpipeline_spatial 0.1.1

MINOR CHANGES

• Add a README (PR #21).

NEW FUNCTIONALITY

• 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).

openpipeline_spatial 0.1.0

NEW FUNCTIONALITY

• 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).