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openproblems-bio / task_ist_preprocessing Public

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Update spatialdata#130

Merged

dariarom94 merged 23 commits into

mainopenproblems-bio/task_ist_preprocessing:mainfrom

update_spatialdataopenproblems-bio/task_ist_preprocessing:update_spatialdataCopy head branch name to clipboard

Jun 1, 2026

Conversation Commits23 (23)Checks Files changed

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Update spatialdata#130
dariarom94 merged 23 commits into
mainfrom
update_spatialdata

Claude dask/pandas correction

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Test on: pull_request 37

build / List components to test

build / Test (binning, methods_segmentation, src/methods_segmentation/binning/config.vsh.yaml, src/method...

build / Test (watershed, methods_segmentation, src/methods_segmentation/watershed/config.vsh.yaml, src/me...

build / Test (stardist, methods_segmentation, src/methods_segmentation/stardist/config.vsh.yaml, src/meth...

build / Test (custom_segmentation, methods_segmentation, src/methods_segmentation/custom_segmentation/con...

build / Test (cellpose, methods_segmentation, src/methods_segmentation/cellpose/config.vsh.yaml, src/meth...

build / Test (comseg, methods_transcript_assignment, src/methods_transcript_assignment/comseg/config.vsh....

build / Test (proseg, methods_transcript_assignment, src/methods_transcript_assignment/proseg/config.vsh....

build / Test (baysor, methods_transcript_assignment, src/methods_transcript_assignment/baysor/config.vsh....

build / Test (clustermap, methods_transcript_assignment, src/methods_transcript_assignment/clustermap/con...

build / Test (pciseq, methods_transcript_assignment, src/methods_transcript_assignment/pciseq/config.vsh....

build / Test (basic_transcript_assignment, methods_transcript_assignment, src/methods_transcript_assignme...

build / Test (alpha_shapes, methods_calculate_cell_volume, src/methods_calculate_cell_volume/alpha_shapes...

build / Test (aggregate_spatial_data, methods_data_aggregation, src/methods_data_aggregation/aggregate_sp...

build / Test (tacco, methods_cell_type_annotation, src/methods_cell_type_annotation/tacco/config.vsh.yaml...

build / Test (moscot, methods_cell_type_annotation, src/methods_cell_type_annotation/moscot/config.vsh.ya...

build / Test (singler, methods_cell_type_annotation, src/methods_cell_type_annotation/singler/config.vsh....

build / Test (mapmycells, methods_cell_type_annotation, src/methods_cell_type_annotation/mapmycells/confi...

build / Test (ssam, methods_cell_type_annotation, src/methods_cell_type_annotation/ssam/config.vsh.yaml, ...

build / Test (tangram, methods_cell_type_annotation, src/methods_cell_type_annotation/tangram/config.vsh....

build / Test (rctd, methods_cell_type_annotation, src/methods_cell_type_annotation/rctd/config.vsh.yaml, ...

build / Test (quality, metrics, src/metrics/quality/config.vsh.yaml, src/metrics/quality/, python_script,...

build / Test (similarity, metrics, src/metrics/similarity/config.vsh.yaml, src/metrics/similarity/, pytho...

build / Test (basic_count_aggregation, methods_count_aggregation, src/methods_count_aggregation/basic_cou...

build / Test (no_correction, methods_expression_correction, src/methods_expression_correction/no_correcti...

build / Test (gene_efficiency_correction, methods_expression_correction, src/methods_expression_correctio...

build / Test (resolvi_correction, methods_expression_correction, src/methods_expression_correction/resolv...

build / Test (split, methods_expression_correction, src/methods_expression_correction/split/config.vsh.ya...

build / Test (normalize_by_volume, methods_normalization, src/methods_normalization/normalize_by_volume/c...

build / Test (normalize_by_counts, methods_normalization, src/methods_normalization/normalize_by_counts/c...

build / Test (spanorm, methods_normalization, src/methods_normalization/spanorm/config.vsh.yaml, src/meth...

build / Test (tenx_xenium, datasets/loaders, src/datasets/loaders/tenx_xenium/config.vsh.yaml, src/datase...

build / Test (allen_brain_cell_atlas, datasets/loaders, src/datasets/loaders/allen_brain_cell_atlas/confi...

build / Test (identity, control_methods, src/control_methods/identity/config.vsh.yaml, src/control_method...

build / Test (permute_celltype_annotations, control_methods, src/control_methods/permute_celltype_annotat...

build / Test (process_dataset, data_processors, src/data_processors/process_dataset/config.vsh.yaml, src/...

build / Test (basic_qc_filter, methods_qc_filter, src/methods_qc_filter/basic_qc_filter/config.vsh.yaml, ...

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