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hschryverhschryver
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added alignment functions
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‎src/xenium_analysis_tools/alignment/align_sections.py‎

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‎src/xenium_analysis_tools/alignment/format_for_napari.py‎

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‎src/xenium_analysis_tools/example_notebooks/combine_sections.ipynb‎

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‎src/xenium_analysis_tools/example_notebooks/datasets_names_dict.json‎

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{
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"726465": {
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"xenium_name": "Xenium_726465_2024-09-18",
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"genotype": "Slc32a1-IRES-Cre;Oi1",
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"sectioning_depth": 450,
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"sections_thickness": 20
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},
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"738168": {
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"xenium_name": "Xenium_738168_2025-03-12",
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"genotype": "Slc32a1-IRES-Cre;Oi1",
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"sectioning_depth": 450,
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"sections_thickness": 20,
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"confocal_name": "confocal-thick-tissue_748168_2025-02-13_processed_2026-01-07_01-02-54",
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"raw_confocal_name": "confocal-thick-tissue_748168_2025-02-13",
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"zstack_name": "ophys-z-stacks_748168_registered",
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"zstack_masks_name": "ophys-z-stacks_748168_segmented"
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},
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"748168": {
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"xenium_name": "Xenium_738168_2025-03-12",
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"genotype": "Slc32a1-IRES-Cre;Oi1",
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"sectioning_depth": 450,
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"sections_thickness": 20,
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"confocal_name": "confocal-thick-tissue_748168_2025-02-13_processed_2026-01-07_01-02-54",
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"zstack_name": "ophys-z-stacks_748168_registered",
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"zstack_masks_name": "ophys-z-stacks_748168_segmented"
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},
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"760970": {
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"xenium_name": "Xenium_760970_2025-04-25",
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"genotype": "Slc32a1-IRES-Cre;Oi1",
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"sectioning_depth": 450,
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"sections_thickness": 20
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},
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"756772": {
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"xenium_name": "Xenium_756772_2025-04-23",
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"genotype": "Slc32a1-IRES-Cre;Oi1",
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"sectioning_depth": 450,
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"sections_thickness": 20,
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"confocal_name": "confocal-thick-tissue_756772_2025-04-09_processed_2026-01-07_00-36-19",
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"raw_confocal_name": "confocal-thick-tissue_756772_2025-04-09",
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"zstack_name": "ophys-z-stacks_756772_registered",
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"zstack_masks_name": "ophys-z-stacks_756772_segmented"
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},
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"759003": {
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"xenium_name": "Xenium_759003_2025-04-23",
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"genotype": "Slc32a1-IRES-Cre;Oi1",
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"sectioning_depth": 450,
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"sections_thickness": 20
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},
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"778174": {
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"xenium_name": "Xenium_778174_2025-05-07",
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"genotype": "Snap25-IRES2-Cre;Oi4",
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"sectioning_depth": 450,
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"sections_thickness": 20
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},
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"770057": {
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"xenium_name": "Xenium_770057_2025-07-17",
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"genotype": "Slc32a1-IRES-Cre;Oi1",
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"sectioning_depth": 450,
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"sections_thickness": 20
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},
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"786297": {
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"xenium_name": "Xenium_786297_2025-07-16",
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"genotype": "Snap25-IRES2-Cre;Oi4",
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"sectioning_depth": 450,
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"sections_thickness": 20
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},
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"775682": {
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"xenium_name": "Xenium_775682_2025-10-03",
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"genotype": "Slc32a1-IRES-Cre;Oi1",
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"sectioning_depth": 450,
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"sections_thickness": 20
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},
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"779891": {
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"xenium_name": "Xenium_779891_2025-10-03",
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"genotype": "Slc32a1-IRES-Cre;Oi1",
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"sectioning_depth": 450,
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"sections_thickness": 20
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},
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"797371": {
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"xenium_name": "Xenium_797371_2025-10-22",
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"genotype": "Snap25-IRES2-Cre;Oi4",
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"sectioning_depth": 600,
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"sections_thickness": 20,
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"confocal_name": "confocal-thick-tissue_797371_2025-09-25_processed_2026-01-06_23-00-58",
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"raw_confocal_name": "confocal-thick-tissue_797371_2025-09-25",
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"zstack_name": "ophys-z-stacks_797371_registered",
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"zstack_masks_name": "ophys-z-stacks_797371_segmented"
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},
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"806644": {
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"xenium_name": "Xenium_806644_2025-12-18",
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"genotype": "Snap25-IRES2-Cre;Oi4",
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"sectioning_depth": 600,
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"sections_thickness": 20
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},
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"804670": {
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"xenium_name": "Xenium_804670_2025-12-18",
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"genotype": "Slc32a1-IRES-Cre;Oi1",
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"sectioning_depth": 600,
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"sections_thickness": 20
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},
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"810976": {
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"xenium_name": "Xenium_810976_2026-02-07",
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"genotype": "Snap25-IRES2-Cre;Oi4",
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"sectioning_depth": 600,
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"sections_thickness": 20
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},
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"816462": {
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"xenium_name": "Xenium_816462_2026-02-07",
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"genotype": "Snap25-IRES2-Cre;Oi4",
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"sectioning_depth": 600,
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"sections_thickness": 20
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}
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}
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‎src/xenium_analysis_tools/example_notebooks/map_dataset.ipynb‎

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‎src/xenium_analysis_tools/example_notebooks/params.json‎

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{
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"zarr_settings": {
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"default_format": 3
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},
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"paths": {
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"data_root": "/root/capsule/data",
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"scratch_root": "/root/capsule/scratch",
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"results_root": "/root/capsule/results",
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"abc_path": "/root/capsule/data/abc_atlas",
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"mmc_path": "/root/capsule/data/abc_atlas/mapmycells"
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},
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"sdata_reader_params": {
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"n_jobs": "max",
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"cells_as_circles": true,
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"gex_only": false
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},
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"processing_control": {
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"save_initial_data_parent_folder": "results",
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"save_processed_data_parent_folder": "results",
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"save_mapped_data_parent_folder": "results",
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"save_initial_dataset_suffix": "_slides",
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"save_mapped_dataset_suffix": "_mapped",
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"save_processed_dataset_suffix": "_processed",
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"save_initial_dataset_prefix": "slide_",
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"save_processed_dataset_prefix": "section_",
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"check_data_folder_slides": false,
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"check_data_folder_sections": false,
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"check_data_folder_mapped": true
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},
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"validation_params": {
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"test_loading_data": false,
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"test_sizes": true,
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"plot_bboxes": true
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},
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"mapping_config": {
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"input_data_folder_name": "input_data",
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"input_h5ad_name": "input_cellxgene.h5ad",
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"mapped_data_folder_name": "mapped_data",
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"mapped_data_h5ad_name": "mapped_cellxgene.h5ad",
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"basic_results_name": "basic_results.csv",
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"extended_results_name": "extended_results.json",
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"overwrite_all_steps": false,
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"overwrite_input_data": false,
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"overwrite_running_mapping": false,
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"overwrite_formatting": false,
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"overwrite_merge": false,
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"validate_input": true,
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"filter_mapping_v1_types": {
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"enabled": true,
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"h_level": "subclass",
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"min_cells": 6,
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"saved_df_name": "v1_merfish_cells.csv"
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},
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"drop_nodes_dict": null,
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"var_filters": {
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"feature_types": {
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"eq": "Gene Expression"
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},
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"tag_feature": {
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"eq": false
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}
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},
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"mapping_params": {
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"normalization": "raw",
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"drop_level": "supertype",
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"mapping_type": "hrc",
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"bootstrap_iteration": 100,
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"bootstrap_factor": 0.5,
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"n_runner_ups": 2,
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"clobber": "1",
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"chunk_size": 15000,
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"num_workers": 8,
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"rng_seed": 42
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}
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}
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}

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