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Test dataset for the spatialxe pipeline - xeniumranger modules

.gitattributes

@@ -53,3 +53,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.jpg filter=lfs diff=lfs merge=lfs -text
 *.jpeg filter=lfs diff=lfs merge=lfs -text
 *.webp filter=lfs diff=lfs merge=lfs -text
+morphology.ome.tif filter=lfs diff=lfs merge=lfs -text

analysis.zarr.zip

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cell_feature_matrix.zarr.zip

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cells.zarr.zip

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experiment.xenium

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+{
+    "major_version": 2,
+    "minor_version": 0,
+    "run_name": "morphology_focus",
+    "region_name": "cell_circles",
+    "experiment_uuid": "",
+    "panel_tissue_type": "N/A",
+    "run_start_time": "N/A",
+    "preservation_method": "N/A",
+    "num_cells": 36602,
+    "transcripts_per_cell": 0,
+    "transcripts_per_100um": 0,
+    "cassette_name": "N/A",
+    "slide_id": "N/A",
+    "panel_design_id": "N/A",
+    "panel_name": "N/A",
+    "panel_organism": "Human",
+    "panel_num_targets_predesigned": 0,
+    "panel_num_targets_custom": 0,
+    "pixel_size": 0.2125,
+    "instrument_sn": "N/A",
+    "instrument_sw_version": "N/A",
+    "analysis_sw_version": "xenium-1.3.0.5",
+    "cassette_uuid": "",
+    "roi_uuid": "",
+    "z_step_size": 3.0,
+    "well_uuid": "",
+    "calibration_uuid": "N/A",
+    "images": {
+        "morphology_filepath": "morphology.ome.tif",
+        "morphology_mip_filepath": "morphology_mip.ome.tif",
+        "morphology_focus_filepath": "morphology_focus.ome.tif"
+    },
+    "xenium_explorer_files": {
+        "transcripts_zarr_filepath": "transcripts.zarr.zip",
+        "cells_zarr_filepath": "cells.zarr.zip",
+        "cell_features_zarr_filepath": "cell_feature_matrix.zarr.zip",
+        "analysis_zarr_filepath": "analysis.zarr.zip",
+        "analysis_summary_filepath": "analysis_summary.html"
+    }
+}

metrics_summary.csv

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+run_name,cassette_name,region_name,panel_name,region_area,total_cell_area,fraction_transcripts_decoded_q20,fraction_predesigned_transcripts_decoded_q20,fraction_custom_transcripts_decoded_q20,decoded_transcripts_per_100um2,negative_control_probe_rate,negative_control_codeword_rate,num_cells_detected,fraction_non_empty_cells,fraction_transcripts_assigned,median_genes_per_cell,median_predesigned_genes_per_cell,median_custom_genes_per_cell,median_transcripts_per_cell,median_predesigned_transcripts_per_cell,median_custom_transcripts_per_cell
+mouse_brain_ff,sim2,Xenium_V1_FF_Mouse_Brain_Coronal_Subset_CTX+HP,xenium_mouse_brain_gene_expression_panel,17002130.5515625,11828573.97671875,0.8050196906082923,,,79.86883303595566,0.0037133732775907,0.0005343731189619,36602,0.9986612753401454,0.9556307042487284,71.0,,,211.0,,

transcripts.zarr.zip

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