iST Preprocessing
in developmentBenchmarking approaches for preprocessing imaging-based spatial transcriptomics
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Contributors
Leaderboard
Methods ranked by scaled overall mean. Each cell encodes a score from 0 to 1 by size and intensity.
QC: Normalisation Visualisation 17 plots
Per metric: points placed by control-anchored scaled score (x); dashed lines mark scaled 0 and 1 (worst/best control); the lower axis shows the raw score. Points beyond [-0.2, 1.2] are clamped to the edge as triangles. Hover a dot or line to highlight it and read details.
- Annotated cellshigher better
- Assigned readshigher better
- Co-expr. sim.higher better
- Co-expr. sim. (CT)higher better
- Co-expr. sim. (CT) (QC)higher better
- Co-expr. sim. (QC)higher better
- kNN mixinghigher better
- kNN mixing (QC)higher better
- Neg. marker purity (cells)higher better
- Neg. marker purity (cells) (QC)higher better
- Neg. marker purity (reads)higher better
- Neg. marker purity (reads) (QC)higher better
- No. of cellshigher better
- Rel. CT expr. sim.higher better
- Rel. CT expr. sim. (QC)higher better
- Rel. gene expr. sim.higher better
- Rel. gene expr. sim. (QC)higher better
QC: Indicator table 106 errors18 warnings
Automated checks on the benchmark run and its results: missing values, score scaling, metric ranges and similar. Errors are high-severity issues that usually need a maintainer's attention; warnings are lower-severity signals. Findings that are expected for this task are listed separately as silenced.
106 high-severity issues need review. 279 of 403 checks passed.
- error Dataset info Info field 'references' % missing
Dataset info field 'references' should be defined Task: ist_preprocessing Field: references Percentage missing: 58
- error Method info Info field 'references' % missing
Method info field 'references' should be defined Task: ist_preprocessing Field: references Percentage missing: 71
- error Raw results Task number of results
Number of results should be equal to #datasets × #methods × #metrics Task: ist_preprocessing Number of results: 13819 Number of datasets: 31 Number of methods: 7 Number of metrics: 17 Expected number of results: 3689
- error Raw results Dataset 'bruker_human_lung_cancer_cosmx_combined/lung6' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: bruker_human_lung_cancer_cosmx_combined/lung6 Number of results: 453 Expected number of results: 119 Percentage missing: -281%
- error Raw results Dataset '2023_10x_mouse_brain_xenium_combined/rep3' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2023_10x_mouse_brain_xenium_combined/rep3 Number of results: 453 Expected number of results: 119 Percentage missing: -281%
- error Raw results Dataset '2023_10x_human_lung_xenium_combined' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2023_10x_human_lung_xenium_combined Number of results: 470 Expected number of results: 119 Percentage missing: -295%
- error Raw results Dataset '2022_vizgen_human_lung_cancer_merfish_combined/rep2' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2022_vizgen_human_lung_cancer_merfish_combined/rep2 Number of results: 453 Expected number of results: 119 Percentage missing: -281%
- error Raw results Dataset '2022_vizgen_human_colon_cancer_merfish_combined/rep1' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2022_vizgen_human_colon_cancer_merfish_combined/rep1 Number of results: 436 Expected number of results: 119 Percentage missing: -266%
- error Raw results Dataset 'mpii_human_lung_xenium_combined/978_reg1' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: mpii_human_lung_xenium_combined/978_reg1 Number of results: 487 Expected number of results: 119 Percentage missing: -309%
- error Raw results Dataset '2023_10x_mouse_brain_xenium_combined/rep2' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2023_10x_mouse_brain_xenium_combined/rep2 Number of results: 453 Expected number of results: 119 Percentage missing: -281%
- error Raw results Dataset '2022_vizgen_human_lung_cancer_merfish_combined/rep1' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2022_vizgen_human_lung_cancer_merfish_combined/rep1 Number of results: 453 Expected number of results: 119 Percentage missing: -281%
- error Raw results Dataset 'ltx_human_lung_xenium_combined/B_AK-16-12103' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: ltx_human_lung_xenium_combined/B_AK-16-12103 Number of results: 470 Expected number of results: 119 Percentage missing: -295%
- error Raw results Dataset 'kuppe_kidney_healthy_merfish_combined/rep1' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: kuppe_kidney_healthy_merfish_combined/rep1 Number of results: 453 Expected number of results: 119 Percentage missing: -281%
- error Raw results Dataset 'bruker_human_lung_cancer_cosmx_combined/lung13' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: bruker_human_lung_cancer_cosmx_combined/lung13 Number of results: 419 Expected number of results: 119 Percentage missing: -252%
- error Raw results Dataset 'bruker_human_lung_cancer_cosmx_combined/lung5_rep2' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: bruker_human_lung_cancer_cosmx_combined/lung5_rep2 Number of results: 436 Expected number of results: 119 Percentage missing: -266%
- error Raw results Dataset '2023_10x_human_lung_cancer_xenium_combined' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2023_10x_human_lung_cancer_xenium_combined Number of results: 470 Expected number of results: 119 Percentage missing: -295%
- error Raw results Dataset '2023_10x_human_colon_cancer_xenium_combined' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2023_10x_human_colon_cancer_xenium_combined Number of results: 470 Expected number of results: 119 Percentage missing: -295%
- error Raw results Dataset '2024_10x_human_liver_xenium_combined' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2024_10x_human_liver_xenium_combined Number of results: 487 Expected number of results: 119 Percentage missing: -309%
- error Raw results Dataset '2022_vizgen_human_liver_cancer_merfish_combined/rep2' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2022_vizgen_human_liver_cancer_merfish_combined/rep2 Number of results: 453 Expected number of results: 119 Percentage missing: -281%
- error Raw results Dataset '2024_10x_human_liver_cancer_xenium_combined' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2024_10x_human_liver_cancer_xenium_combined Number of results: 470 Expected number of results: 119 Percentage missing: -295%
- error Raw results Dataset '2026_10x_human_breast_cancer_atera_combined' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2026_10x_human_breast_cancer_atera_combined Number of results: 209 Expected number of results: 119 Percentage missing: -76%
- error Raw results Dataset 'bruker_human_lung_cancer_cosmx_combined/lung9_rep2' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: bruker_human_lung_cancer_cosmx_combined/lung9_rep2 Number of results: 419 Expected number of results: 119 Percentage missing: -252%
- error Raw results Dataset 'kuppe_kidney_cancer_merfish_combined/rep1' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: kuppe_kidney_cancer_merfish_combined/rep1 Number of results: 473 Expected number of results: 119 Percentage missing: -297%
- error Raw results Dataset 'ltx_human_lung_xenium_combined/L_AK14_14254' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: ltx_human_lung_xenium_combined/L_AK14_14254 Number of results: 453 Expected number of results: 119 Percentage missing: -281%
- error Raw results Dataset '2022_vizgen_human_colon_cancer_merfish_combined/rep2' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2022_vizgen_human_colon_cancer_merfish_combined/rep2 Number of results: 436 Expected number of results: 119 Percentage missing: -266%
- error Raw results Dataset 'bruker_human_liver_cosmx_combined' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: bruker_human_liver_cosmx_combined Number of results: 470 Expected number of results: 119 Percentage missing: -295%
- error Raw results Dataset 'bruker_human_lung_cancer_cosmx_combined/lung9_rep1' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: bruker_human_lung_cancer_cosmx_combined/lung9_rep1 Number of results: 436 Expected number of results: 119 Percentage missing: -266%
- error Raw results Dataset '2024_10x_human_skin_xenium_combined' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2024_10x_human_skin_xenium_combined Number of results: 419 Expected number of results: 119 Percentage missing: -252%
- error Raw results Dataset '2022_vizgen_human_liver_cancer_merfish_combined/rep1' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2022_vizgen_human_liver_cancer_merfish_combined/rep1 Number of results: 470 Expected number of results: 119 Percentage missing: -295%
- error Raw results Dataset '2023_10x_human_breast_cancer_xenium_combined' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2023_10x_human_breast_cancer_xenium_combined Number of results: 470 Expected number of results: 119 Percentage missing: -295%
- error Raw results Dataset 'bruker_human_lung_cancer_cosmx_combined/lung12' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: bruker_human_lung_cancer_cosmx_combined/lung12 Number of results: 436 Expected number of results: 119 Percentage missing: -266%
- error Raw results Dataset 'bruker_human_lung_cancer_cosmx_combined/lung5_rep1' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: bruker_human_lung_cancer_cosmx_combined/lung5_rep1 Number of results: 436 Expected number of results: 119 Percentage missing: -266%
- error Raw results Dataset '2022_vizgen_human_breast_cancer_merfish_combined/rep1' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2022_vizgen_human_breast_cancer_merfish_combined/rep1 Number of results: 453 Expected number of results: 119 Percentage missing: -281%
- error Raw results Dataset '2023_10x_mouse_brain_xenium_combined/rep1' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Dataset: 2023_10x_mouse_brain_xenium_combined/rep1 Number of results: 453 Expected number of results: 119 Percentage missing: -281%
- error Raw results Method 'segmentation' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Method: segmentation Number of results: 3093 Expected number of results: 527 Percentage missing: -487%
- error Raw results Method 'assignment' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Method: assignment Number of results: 3315 Expected number of results: 527 Percentage missing: -529%
- error Raw results Method 'normalization' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Method: normalization Number of results: 1514 Expected number of results: 527 Percentage missing: -187%
- error Raw results Method 'cell_type_assignment' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Method: cell_type_assignment Number of results: 3499 Expected number of results: 527 Percentage missing: -564%
- error Raw results Method 'expression_correction' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Method: expression_correction Number of results: 1530 Expected number of results: 527 Percentage missing: -190%
- error Raw results Metric 'negative_marker_purity_reads' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: negative_marker_purity_reads Number of results: 824 Expected number of results: 217 Percentage missing: -280%
- error Raw results Metric 'negative_marker_purity_cells' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: negative_marker_purity_cells Number of results: 824 Expected number of results: 217 Percentage missing: -280%
- error Raw results Metric 'coexpr_similarity' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: coexpr_similarity Number of results: 824 Expected number of results: 217 Percentage missing: -280%
- error Raw results Metric 'coexpr_similarity_celltype' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: coexpr_similarity_celltype Number of results: 824 Expected number of results: 217 Percentage missing: -280%
- error Raw results Metric 'rel_pairwise_ct_expr_sim' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: rel_pairwise_ct_expr_sim Number of results: 824 Expected number of results: 217 Percentage missing: -280%
- error Raw results Metric 'rel_pairwise_gene_expr_sim' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: rel_pairwise_gene_expr_sim Number of results: 824 Expected number of results: 217 Percentage missing: -280%
- error Raw results Metric 'knn_mixing' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: knn_mixing Number of results: 824 Expected number of results: 217 Percentage missing: -280%
- error Raw results Metric 'negative_marker_purity_reads_qc_filtered' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: negative_marker_purity_reads_qc_filtered Number of results: 824 Expected number of results: 217 Percentage missing: -280%
- error Raw results Metric 'negative_marker_purity_cells_qc_filtered' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: negative_marker_purity_cells_qc_filtered Number of results: 824 Expected number of results: 217 Percentage missing: -280%
- error Raw results Metric 'coexpr_similarity_qc_filtered' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: coexpr_similarity_qc_filtered Number of results: 824 Expected number of results: 217 Percentage missing: -280%
- error Raw results Metric 'coexpr_similarity_celltype_qc_filtered' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: coexpr_similarity_celltype_qc_filtered Number of results: 824 Expected number of results: 217 Percentage missing: -280%
- error Raw results Metric 'rel_pairwise_ct_expr_sim_qc_filtered' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: rel_pairwise_ct_expr_sim_qc_filtered Number of results: 824 Expected number of results: 217 Percentage missing: -280%
- error Raw results Metric 'rel_pairwise_gene_expr_sim_qc_filtered' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: rel_pairwise_gene_expr_sim_qc_filtered Number of results: 824 Expected number of results: 217 Percentage missing: -280%
- error Raw results Metric 'knn_mixing_qc_filtered' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: knn_mixing_qc_filtered Number of results: 824 Expected number of results: 217 Percentage missing: -280%
- error Raw results Metric 'proportion_of_assigned_reads' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: proportion_of_assigned_reads Number of results: 757 Expected number of results: 217 Percentage missing: -249%
- error Raw results Metric 'proportion_of_annotated_cells' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: proportion_of_annotated_cells Number of results: 763 Expected number of results: 217 Percentage missing: -252%
- error Raw results Metric 'number_of_cells' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Metric: number_of_cells Number of results: 763 Expected number of results: 217 Percentage missing: -252%
- error Raw results Metric component 'similarity' % failed
Percentage of failed processes should be less than 10% Task: ist_preprocessing Metric component: similarity Succeeded processes: 42 Attempted processes: 62 Percentage failed: 32%
- error Raw results Metric 'proportion_of_assigned_reads' number of control methods
Number of metric scores for control methods should be equal to #datasets × #control_methods Task: ist_preprocessing Metric: proportion_of_assigned_reads Control method scores: 0 Expected control method scores: 62 Percentage succeeded: 0%
- error Raw results Metric 'proportion_of_annotated_cells' number of control methods
Number of metric scores for control methods should be equal to #datasets × #control_methods Task: ist_preprocessing Metric: proportion_of_annotated_cells Control method scores: 0 Expected control method scores: 62 Percentage succeeded: 0%
- error Raw results Metric 'number_of_cells' number of control methods
Number of metric scores for control methods should be equal to #datasets × #control_methods Task: ist_preprocessing Metric: number_of_cells Control method scores: 0 Expected control method scores: 62 Percentage succeeded: 0%
- error Scaling Metric 'negative_marker_purity_cells' % outside range
Percentage of scaled scores outside control range should be less than 10% Task: ist_preprocessing Metric: negative_marker_purity_cells Inside range: 0 Scaled scores: 824 Percentage outside: 100%
- error Scaling Metric 'negative_marker_purity_cells' worst score % outside range
The worst scaled score should be less than 10% outside the control range Task: ist_preprocessing Metric: negative_marker_purity_cells Worst score: -2.39915966386554 Percentage outside range: 240%
- error Scaling Metric 'coexpr_similarity' % outside range
Percentage of scaled scores outside control range should be less than 10% Task: ist_preprocessing Metric: coexpr_similarity Inside range: 0 Scaled scores: 824 Percentage outside: 100%
- error Scaling Metric 'coexpr_similarity' worst score % outside range
The worst scaled score should be less than 10% outside the control range Task: ist_preprocessing Metric: coexpr_similarity Worst score: -Inf Percentage outside range: Inf%
- error Scaling Worst 'coexpr_similarity' score for 'assignment'
Method 'assignment' performs much worse than controls for metric' coexpr_similarity' Task: ist_preprocessing Method: assignment Metric: coexpr_similarity Worst score: -Inf Percentage outside range: Inf%
- error Scaling Worst 'coexpr_similarity' score for 'cell_type_assignment'
Method 'cell_type_assignment' performs much worse than controls for metric' coexpr_similarity' Task: ist_preprocessing Method: cell_type_assignment Metric: coexpr_similarity Worst score: -Inf Percentage outside range: Inf%
- error Scaling Worst 'coexpr_similarity' score for 'expression_correction'
Method 'expression_correction' performs much worse than controls for metric' coexpr_similarity' Task: ist_preprocessing Method: expression_correction Metric: coexpr_similarity Worst score: -Inf Percentage outside range: Inf%
- error Scaling Worst 'coexpr_similarity' score for 'identity'
Method 'identity' performs much worse than controls for metric' coexpr_similarity' Task: ist_preprocessing Method: identity Metric: coexpr_similarity Worst score: -Inf Percentage outside range: Inf%
- error Scaling Worst 'coexpr_similarity' score for 'normalization'
Method 'normalization' performs much worse than controls for metric' coexpr_similarity' Task: ist_preprocessing Method: normalization Metric: coexpr_similarity Worst score: -Inf Percentage outside range: Inf%
- error Scaling Worst 'coexpr_similarity' score for 'permute_celltype_annotations'
Method 'permute_celltype_annotations' performs much worse than controls for metric' coexpr_similarity' Task: ist_preprocessing Method: permute_celltype_annotations Metric: coexpr_similarity Worst score: -Inf Percentage outside range: Inf%
- error Scaling Worst 'coexpr_similarity' score for 'segmentation'
Method 'segmentation' performs much worse than controls for metric' coexpr_similarity' Task: ist_preprocessing Method: segmentation Metric: coexpr_similarity Worst score: -Inf Percentage outside range: Inf%
- error Scaling Metric 'coexpr_similarity_celltype' % outside range
Percentage of scaled scores outside control range should be less than 10% Task: ist_preprocessing Metric: coexpr_similarity_celltype Inside range: 0 Scaled scores: 824 Percentage outside: 100%
- error Scaling Metric 'coexpr_similarity_celltype' worst score % outside range
The worst scaled score should be less than 10% outside the control range Task: ist_preprocessing Metric: coexpr_similarity_celltype Worst score: -3.2689075630252 Percentage outside range: 327%
- error Scaling Worst 'coexpr_similarity_celltype' score for 'assignment'
Method 'assignment' performs much worse than controls for metric' coexpr_similarity_celltype' Task: ist_preprocessing Method: assignment Metric: coexpr_similarity_celltype Worst score: -3.2689075630252 Percentage outside range: 327%
- error Scaling Worst 'coexpr_similarity_celltype' score for 'cell_type_assignment'
Method 'cell_type_assignment' performs much worse than controls for metric' coexpr_similarity_celltype' Task: ist_preprocessing Method: cell_type_assignment Metric: coexpr_similarity_celltype Worst score: -3.2689075630252 Percentage outside range: 327%
- error Scaling Worst 'coexpr_similarity_celltype' score for 'expression_correction'
Method 'expression_correction' performs much worse than controls for metric' coexpr_similarity_celltype' Task: ist_preprocessing Method: expression_correction Metric: coexpr_similarity_celltype Worst score: -3.2689075630252 Percentage outside range: 327%
- error Scaling Worst 'coexpr_similarity_celltype' score for 'identity'
Method 'identity' performs much worse than controls for metric' coexpr_similarity_celltype' Task: ist_preprocessing Method: identity Metric: coexpr_similarity_celltype Worst score: -3.2689075630252 Percentage outside range: 327%
- error Scaling Worst 'coexpr_similarity_celltype' score for 'normalization'
Method 'normalization' performs much worse than controls for metric' coexpr_similarity_celltype' Task: ist_preprocessing Method: normalization Metric: coexpr_similarity_celltype Worst score: -3.2689075630252 Percentage outside range: 327%
- error Scaling Worst 'coexpr_similarity_celltype' score for 'permute_celltype_annotations'
Method 'permute_celltype_annotations' performs much worse than controls for metric' coexpr_similarity_celltype' Task: ist_preprocessing Method: permute_celltype_annotations Metric: coexpr_similarity_celltype Worst score: -3.2689075630252 Percentage outside range: 327%
- error Scaling Worst 'coexpr_similarity_celltype' score for 'segmentation'
Method 'segmentation' performs much worse than controls for metric' coexpr_similarity_celltype' Task: ist_preprocessing Method: segmentation Metric: coexpr_similarity_celltype Worst score: -3.2689075630252 Percentage outside range: 327%
- error Scaling Metric 'rel_pairwise_gene_expr_sim' % outside range
Percentage of scaled scores outside control range should be less than 10% Task: ist_preprocessing Metric: rel_pairwise_gene_expr_sim Inside range: 0 Scaled scores: 824 Percentage outside: 100%
- error Scaling Metric 'rel_pairwise_gene_expr_sim' worst score % outside range
The worst scaled score should be less than 10% outside the control range Task: ist_preprocessing Metric: rel_pairwise_gene_expr_sim Worst score: -0.398274987316083 Percentage outside range: 40%
- error Scaling Metric 'knn_mixing' % outside range
Percentage of scaled scores outside control range should be less than 10% Task: ist_preprocessing Metric: knn_mixing Inside range: 0 Scaled scores: 824 Percentage outside: 100%
- error Scaling Metric 'negative_marker_purity_cells_qc_filtered' % outside range
Percentage of scaled scores outside control range should be less than 10% Task: ist_preprocessing Metric: negative_marker_purity_cells_qc_filtered Inside range: 0 Scaled scores: 824 Percentage outside: 100%
- error Scaling Metric 'negative_marker_purity_cells_qc_filtered' worst score % outside range
The worst scaled score should be less than 10% outside the control range Task: ist_preprocessing Metric: negative_marker_purity_cells_qc_filtered Worst score: -2.62605042016806 Percentage outside range: 263%
- error Scaling Metric 'coexpr_similarity_qc_filtered' % outside range
Percentage of scaled scores outside control range should be less than 10% Task: ist_preprocessing Metric: coexpr_similarity_qc_filtered Inside range: 0 Scaled scores: 824 Percentage outside: 100%
- error Scaling Metric 'coexpr_similarity_qc_filtered' worst score % outside range
The worst scaled score should be less than 10% outside the control range Task: ist_preprocessing Metric: coexpr_similarity_qc_filtered Worst score: -Inf Percentage outside range: Inf%
- error Scaling Worst 'coexpr_similarity_qc_filtered' score for 'assignment'
Method 'assignment' performs much worse than controls for metric' coexpr_similarity_qc_filtered' Task: ist_preprocessing Method: assignment Metric: coexpr_similarity_qc_filtered Worst score: -Inf Percentage outside range: Inf%
- error Scaling Worst 'coexpr_similarity_qc_filtered' score for 'cell_type_assignment'
Method 'cell_type_assignment' performs much worse than controls for metric' coexpr_similarity_qc_filtered' Task: ist_preprocessing Method: cell_type_assignment Metric: coexpr_similarity_qc_filtered Worst score: -Inf Percentage outside range: Inf%
- error Scaling Worst 'coexpr_similarity_qc_filtered' score for 'expression_correction'
Method 'expression_correction' performs much worse than controls for metric' coexpr_similarity_qc_filtered' Task: ist_preprocessing Method: expression_correction Metric: coexpr_similarity_qc_filtered Worst score: -Inf Percentage outside range: Inf%
- error Scaling Worst 'coexpr_similarity_qc_filtered' score for 'identity'
Method 'identity' performs much worse than controls for metric' coexpr_similarity_qc_filtered' Task: ist_preprocessing Method: identity Metric: coexpr_similarity_qc_filtered Worst score: -Inf Percentage outside range: Inf%
- error Scaling Worst 'coexpr_similarity_qc_filtered' score for 'normalization'
Method 'normalization' performs much worse than controls for metric' coexpr_similarity_qc_filtered' Task: ist_preprocessing Method: normalization Metric: coexpr_similarity_qc_filtered Worst score: -Inf Percentage outside range: Inf%
- error Scaling Worst 'coexpr_similarity_qc_filtered' score for 'permute_celltype_annotations'
Method 'permute_celltype_annotations' performs much worse than controls for metric' coexpr_similarity_qc_filtered' Task: ist_preprocessing Method: permute_celltype_annotations Metric: coexpr_similarity_qc_filtered Worst score: -Inf Percentage outside range: Inf%
- error Scaling Worst 'coexpr_similarity_qc_filtered' score for 'segmentation'
Method 'segmentation' performs much worse than controls for metric' coexpr_similarity_qc_filtered' Task: ist_preprocessing Method: segmentation Metric: coexpr_similarity_qc_filtered Worst score: -Inf Percentage outside range: Inf%
- error Scaling Metric 'coexpr_similarity_celltype_qc_filtered' % outside range
Percentage of scaled scores outside control range should be less than 10% Task: ist_preprocessing Metric: coexpr_similarity_celltype_qc_filtered Inside range: 0 Scaled scores: 824 Percentage outside: 100%
- error Scaling Metric 'coexpr_similarity_celltype_qc_filtered' worst score % outside range
The worst scaled score should be less than 10% outside the control range Task: ist_preprocessing Metric: coexpr_similarity_celltype_qc_filtered Worst score: -3.07142857142856 Percentage outside range: 307%
- error Scaling Worst 'coexpr_similarity_celltype_qc_filtered' score for 'assignment'
Method 'assignment' performs much worse than controls for metric' coexpr_similarity_celltype_qc_filtered' Task: ist_preprocessing Method: assignment Metric: coexpr_similarity_celltype_qc_filtered Worst score: -3.07142857142856 Percentage outside range: 307%
- error Scaling Worst 'coexpr_similarity_celltype_qc_filtered' score for 'cell_type_assignment'
Method 'cell_type_assignment' performs much worse than controls for metric' coexpr_similarity_celltype_qc_filtered' Task: ist_preprocessing Method: cell_type_assignment Metric: coexpr_similarity_celltype_qc_filtered Worst score: -3.07142857142856 Percentage outside range: 307%
- error Scaling Worst 'coexpr_similarity_celltype_qc_filtered' score for 'expression_correction'
Method 'expression_correction' performs much worse than controls for metric' coexpr_similarity_celltype_qc_filtered' Task: ist_preprocessing Method: expression_correction Metric: coexpr_similarity_celltype_qc_filtered Worst score: -3.07142857142856 Percentage outside range: 307%
- error Scaling Worst 'coexpr_similarity_celltype_qc_filtered' score for 'identity'
Method 'identity' performs much worse than controls for metric' coexpr_similarity_celltype_qc_filtered' Task: ist_preprocessing Method: identity Metric: coexpr_similarity_celltype_qc_filtered Worst score: -3.07142857142856 Percentage outside range: 307%
- error Scaling Worst 'coexpr_similarity_celltype_qc_filtered' score for 'normalization'
Method 'normalization' performs much worse than controls for metric' coexpr_similarity_celltype_qc_filtered' Task: ist_preprocessing Method: normalization Metric: coexpr_similarity_celltype_qc_filtered Worst score: -3.07142857142856 Percentage outside range: 307%
- error Scaling Worst 'coexpr_similarity_celltype_qc_filtered' score for 'permute_celltype_annotations'
Method 'permute_celltype_annotations' performs much worse than controls for metric' coexpr_similarity_celltype_qc_filtered' Task: ist_preprocessing Method: permute_celltype_annotations Metric: coexpr_similarity_celltype_qc_filtered Worst score: -3.07142857142856 Percentage outside range: 307%
- error Scaling Worst 'coexpr_similarity_celltype_qc_filtered' score for 'segmentation'
Method 'segmentation' performs much worse than controls for metric' coexpr_similarity_celltype_qc_filtered' Task: ist_preprocessing Method: segmentation Metric: coexpr_similarity_celltype_qc_filtered Worst score: -3.07142857142856 Percentage outside range: 307%
- error Scaling Metric 'rel_pairwise_gene_expr_sim_qc_filtered' % outside range
Percentage of scaled scores outside control range should be less than 10% Task: ist_preprocessing Metric: rel_pairwise_gene_expr_sim_qc_filtered Inside range: 0 Scaled scores: 824 Percentage outside: 100%
- error Scaling Metric 'rel_pairwise_gene_expr_sim_qc_filtered' worst score % outside range
The worst scaled score should be less than 10% outside the control range Task: ist_preprocessing Metric: rel_pairwise_gene_expr_sim_qc_filtered Worst score: -0.398274987316083 Percentage outside range: 40%
- error Scaling Metric 'knn_mixing_qc_filtered' % outside range
Percentage of scaled scores outside control range should be less than 10% Task: ist_preprocessing Metric: knn_mixing_qc_filtered Inside range: 0 Scaled scores: 824 Percentage outside: 100%
Show 18 warnings
- warning Scaling Worst 'negative_marker_purity_cells' score for 'assignment'
Method 'assignment' performs much worse than controls for metric' negative_marker_purity_cells' Task: ist_preprocessing Method: assignment Metric: negative_marker_purity_cells Worst score: -2.39915966386554 Percentage outside range: 240%
- warning Scaling Worst 'negative_marker_purity_cells' score for 'cell_type_assignment'
Method 'cell_type_assignment' performs much worse than controls for metric' negative_marker_purity_cells' Task: ist_preprocessing Method: cell_type_assignment Metric: negative_marker_purity_cells Worst score: -2.39915966386554 Percentage outside range: 240%
- warning Scaling Worst 'negative_marker_purity_cells' score for 'expression_correction'
Method 'expression_correction' performs much worse than controls for metric' negative_marker_purity_cells' Task: ist_preprocessing Method: expression_correction Metric: negative_marker_purity_cells Worst score: -2.39915966386554 Percentage outside range: 240%
- warning Scaling Worst 'negative_marker_purity_cells' score for 'identity'
Method 'identity' performs much worse than controls for metric' negative_marker_purity_cells' Task: ist_preprocessing Method: identity Metric: negative_marker_purity_cells Worst score: -2.39915966386554 Percentage outside range: 240%
- warning Scaling Worst 'negative_marker_purity_cells' score for 'normalization'
Method 'normalization' performs much worse than controls for metric' negative_marker_purity_cells' Task: ist_preprocessing Method: normalization Metric: negative_marker_purity_cells Worst score: -2.39915966386554 Percentage outside range: 240%
- warning Scaling Worst 'negative_marker_purity_cells' score for 'permute_celltype_annotations'
Method 'permute_celltype_annotations' performs much worse than controls for metric' negative_marker_purity_cells' Task: ist_preprocessing Method: permute_celltype_annotations Metric: negative_marker_purity_cells Worst score: -2.39915966386554 Percentage outside range: 240%
- warning Scaling Worst 'negative_marker_purity_cells' score for 'segmentation'
Method 'segmentation' performs much worse than controls for metric' negative_marker_purity_cells' Task: ist_preprocessing Method: segmentation Metric: negative_marker_purity_cells Worst score: -2.39915966386554 Percentage outside range: 240%
- warning Scaling Metric 'knn_mixing' worst score % outside range
The worst scaled score should be less than 10% outside the control range Task: ist_preprocessing Metric: knn_mixing Worst score: -0.263718484562492 Percentage outside range: 26%
- warning Scaling Worst 'negative_marker_purity_cells_qc_filtered' score for 'assignment'
Method 'assignment' performs much worse than controls for metric' negative_marker_purity_cells_qc_filtered' Task: ist_preprocessing Method: assignment Metric: negative_marker_purity_cells_qc_filtered Worst score: -2.62605042016806 Percentage outside range: 263%
- warning Scaling Worst 'negative_marker_purity_cells_qc_filtered' score for 'cell_type_assignment'
Method 'cell_type_assignment' performs much worse than controls for metric' negative_marker_purity_cells_qc_filtered' Task: ist_preprocessing Method: cell_type_assignment Metric: negative_marker_purity_cells_qc_filtered Worst score: -2.62605042016806 Percentage outside range: 263%
- warning Scaling Worst 'negative_marker_purity_cells_qc_filtered' score for 'expression_correction'
Method 'expression_correction' performs much worse than controls for metric' negative_marker_purity_cells_qc_filtered' Task: ist_preprocessing Method: expression_correction Metric: negative_marker_purity_cells_qc_filtered Worst score: -2.62605042016806 Percentage outside range: 263%
- warning Scaling Worst 'negative_marker_purity_cells_qc_filtered' score for 'identity'
Method 'identity' performs much worse than controls for metric' negative_marker_purity_cells_qc_filtered' Task: ist_preprocessing Method: identity Metric: negative_marker_purity_cells_qc_filtered Worst score: -2.62605042016806 Percentage outside range: 263%
- warning Scaling Worst 'negative_marker_purity_cells_qc_filtered' score for 'normalization'
Method 'normalization' performs much worse than controls for metric' negative_marker_purity_cells_qc_filtered' Task: ist_preprocessing Method: normalization Metric: negative_marker_purity_cells_qc_filtered Worst score: -2.62605042016806 Percentage outside range: 263%
- warning Scaling Worst 'negative_marker_purity_cells_qc_filtered' score for 'permute_celltype_annotations'
Method 'permute_celltype_annotations' performs much worse than controls for metric' negative_marker_purity_cells_qc_filtered' Task: ist_preprocessing Method: permute_celltype_annotations Metric: negative_marker_purity_cells_qc_filtered Worst score: -2.62605042016806 Percentage outside range: 263%
- warning Scaling Worst 'negative_marker_purity_cells_qc_filtered' score for 'segmentation'
Method 'segmentation' performs much worse than controls for metric' negative_marker_purity_cells_qc_filtered' Task: ist_preprocessing Method: segmentation Metric: negative_marker_purity_cells_qc_filtered Worst score: -2.62605042016806 Percentage outside range: 263%
- warning Scaling Metric 'knn_mixing_qc_filtered' worst score % outside range
The worst scaled score should be less than 10% outside the control range Task: ist_preprocessing Metric: knn_mixing_qc_filtered Worst score: -0.260482674935958 Percentage outside range: 26%
- warning Raw results Method 'identity' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Method: identity Number of results: 434 Expected number of results: 527 Percentage missing: 18%
- warning Raw results Method 'permute_celltype_annotations' % missing
Percentage of missing results should be less than 10% Task: ist_preprocessing Method: permute_celltype_annotations Number of results: 434 Expected number of results: 527 Percentage missing: 18%
Method info 5
Pipeline variants that differ from the baseline only in the cell_type_assignment step.
Each parameter set is a full preprocessing pipeline in which only the cell_type_assignment step is swapped (mapmycells, moscot, rctd, singler, ssam, tacco, tangram). All other steps are fixed to the baseline: segmentation: custom_segmentation → assignment: basic_transcript_assignment → count_aggregation: basic_count_aggregation → qc_filter: basic_qc_filter → calculate_cell_volume: alpha_shapes → normalization: normalize_by_volume → cell_type_assignment: tacco → expression_correction: no_correction → gene_efficiency_correction: no_correction.
Pipeline variants that differ from the baseline only in the expression_correction step.
Each parameter set is a full preprocessing pipeline in which only the expression_correction step is swapped (no_correction, resolvi_correction, split). All other steps are fixed to the baseline: segmentation: custom_segmentation → assignment: basic_transcript_assignment → count_aggregation: basic_count_aggregation → qc_filter: basic_qc_filter → calculate_cell_volume: alpha_shapes → normalization: normalize_by_volume → cell_type_assignment: tacco → expression_correction: no_correction → gene_efficiency_correction: no_correction.
Pipeline variants that differ from the baseline only in the normalization step.
Each parameter set is a full preprocessing pipeline in which only the normalization step is swapped (normalize_by_counts, normalize_by_volume, spanorm). All other steps are fixed to the baseline: segmentation: custom_segmentation → assignment: basic_transcript_assignment → count_aggregation: basic_count_aggregation → qc_filter: basic_qc_filter → calculate_cell_volume: alpha_shapes → normalization: normalize_by_volume → cell_type_assignment: tacco → expression_correction: no_correction → gene_efficiency_correction: no_correction.
Pipeline variants that differ from the baseline only in the segmentation step.
Each parameter set is a full preprocessing pipeline in which only the segmentation step is swapped (binning, cellpose, cellposev4, custom_segmentation, stardist, watershed). All other steps are fixed to the baseline: segmentation: custom_segmentation → assignment: basic_transcript_assignment → count_aggregation: basic_count_aggregation → qc_filter: basic_qc_filter → calculate_cell_volume: alpha_shapes → normalization: normalize_by_volume → cell_type_assignment: tacco → expression_correction: no_correction → gene_efficiency_correction: no_correction.
Pipeline variants that differ from the baseline only in the assignment step.
Each parameter set is a full preprocessing pipeline in which only the assignment step is swapped (basic_transcript_assignment, baysor, clustermap, comseg, fastreseg, proseg, segger). All other steps are fixed to the baseline: segmentation: custom_segmentation → assignment: basic_transcript_assignment → count_aggregation: basic_count_aggregation → qc_filter: basic_qc_filter → calculate_cell_volume: alpha_shapes → normalization: normalize_by_volume → cell_type_assignment: tacco → expression_correction: no_correction → gene_efficiency_correction: no_correction.
Control method info 2
Positive control: uses the ground-truth single-cell reference.
Negative control: cell type annotations are randomly permuted.
Metric info 17
The proportion of cells that are annotated with cell types.
The proportion of assigned reads.
The similarity between the co-expression patterns of spatial and scRNA-seq data.
The similarity is calculated as the absolute difference between the correlation matrices of spatial and scRNA-seq data. The correlation matrices contain pair-wise correlations between all genes in the dataset.
The similarity between the within cell type co-expression patterns of spatial and scRNA-seq data.
The similarity is calculated as the absolute difference between the correlation matrices of spatial and scRNA-seq data for each cell type. The final score is the mean over cell types. The correlation matrices contain pair-wise correlations between all genes in the dataset.
The similarity between the within cell type co-expression patterns of spatial and scRNA-seq data. Computed on QC-filtered cells.
The similarity is calculated as the absolute difference between the correlation matrices of spatial and scRNA-seq data for each cell type. The final score is the mean over cell types. The correlation matrices contain pair-wise correlations between all genes in the dataset.
The similarity between the co-expression patterns of spatial and scRNA-seq data. Computed on QC-filtered cells.
The similarity is calculated as the absolute difference between the correlation matrices of spatial and scRNA-seq data. The correlation matrices contain pair-wise correlations between all genes in the dataset.
Measure of the modality mixing within the joint knn graph of spatial and scRNA-seq data.
todo
Measure of the modality mixing within the joint knn graph of spatial and scRNA-seq data. Computed on QC-filtered cells.
todo
The percentage of cells that do not contain counts of negative markers of their specific cell type.
The percentage of cells that do not contain counts of negative markers of their specific cell type. Computed on QC-filtered cells.
The percentage of cells that do not contain counts of negative markers of their specific cell type.
The percentage of negative marker reads assigned to the correct cell types.
The percentage of negative marker reads assigned to the correct cell types. Computed on QC-filtered cells.
The percentage of negative marker reads assigned to the correct cell types.
The number of cells in the spatial dataset.
Similarity of the mean expression difference between cell type pairs between spatial and scRNA-seq data.
todo
Similarity of the mean expression difference between cell type pairs between spatial and scRNA-seq data. Computed on QC-filtered cells.
todo
Similarity of the mean expression difference between gene pairs between spatial and scRNA-seq data.
todo
Similarity of the mean expression difference between gene pairs between spatial and scRNA-seq data. Computed on QC-filtered cells.
todo
Dataset info 31
Atera WTA FFPE Human Breast Cancer (DCIS Grade 3) + 2021 Wu scRNAseq
Bruker CosMx Human Liver + 2022 Andrews scRNAseq
Bruker CosMx Human Lung Cancer Lung12 + 2024 Zuani scRNAseq
Bruker CosMx Human Lung Cancer Lung13 + 2024 Zuani scRNAseq
Bruker CosMx Human Lung Cancer Lung5 Rep1 + 2024 Zuani scRNAseq
Bruker CosMx Human Lung Cancer Lung5 Rep2 + 2024 Zuani scRNAseq
Bruker CosMx Human Lung Cancer Lung6 + 2024 Zuani scRNAseq
Bruker CosMx Human Lung Cancer Lung9 Rep1 + 2024 Zuani scRNAseq
Bruker CosMx Human Lung Cancer Lung9 Rep2 + 2024 Zuani scRNAseq
Vizgen Human Breast Cancer MERFISH Patient1 + 2021 Wu scRNAseq
2022 Vizgen Human Colon Cancer MERFISH Patient1 + 2020 Lee scRNAseq
2022 Vizgen Human Colon Cancer MERFISH Patient2 + 2020 Lee scRNAseq
Kuppe Clear Cell Kidney Carcinoma MERFISH (Vizgen MERSCOPE, 500-gene Pan-Cancer panel) + Kuppe kidney cancer snRNAseq reference
Kuppe lab Clear Cell Kidney Carcinoma FFPE sample (MERFISH, Vizgen MERSCOPE, 500-gene Pan-Cancer panel) paired with the Kuppe kidney cancer Flex snRNA-seq reference. Note: the Pan-Cancer panel does not separate NKT vs T cells or pericytes vs vSMC.
Kuppe healthy kidney MERFISH (Vizgen MERSCOPE, 140-gene Spapros panel) + Kuppe kidney healthy snRNAseq reference
Kuppe lab healthy kidney FFPE sample (MERFISH, Vizgen MERSCOPE, 140-gene Spapros panel) paired with the Kuppe kidney healthy Flex snRNA-seq reference.
Vizgen Human Liver Cancer MERFISH Patient1 + 2022 Lu scRNAseq
Vizgen Human Liver Cancer MERFISH Patient2 + 2022 Lu scRNAseq
Vizgen Human Lung Cancer MERFISH Patient1 + 2024 Zuani scRNAseq
Vizgen Human Lung Cancer MERFISH Patient2 + 2024 Zuani scRNAseq
Xenium V1 FFPE Human Breast IDC + 2021 Wu scRNAseq
Xenium V1 hColon Cancer FFPE + 2020 Lee scRNAseq
Xenium V1 hLiver FFPE + 2022 Andrews scRNAseq
Xenium V1 hLiver cancer FFPE + 2022 Lu scRNAseq
Xenium Preview Human Non diseased Lung FFPE + 2020 Travaglini scRNAseq
Xenium Preview Human Lung Cancer FFPE + 2024 Zuani scRNAseq
LTX Xenium human lung (sample B_AK-16-12103) + LTX human lung scRNAseq reference
LTX Xenium human lung (sample B_AK-16-12103) + LTX human lung scRNAseq reference (ltx_full_annotation_2026_04_25)
LTX Xenium human lung (sample L_AK14_14254) + LTX human lung scRNAseq reference
LTX Xenium human lung (sample L_AK14_14254) + LTX human lung scRNAseq reference (ltx_full_annotation_2026_04_25)
MPII Xenium human lung (sample 978, region 1) + MPII human lung scRNAseq reference
Xenium V1 Fresh Frozen Mouse Brain rep1 + ABCA Mouse Brain scRNAseq
Xenium V1 Fresh Frozen Mouse Brain rep2 + ABCA Mouse Brain scRNAseq
Xenium V1 Fresh Frozen Mouse Brain rep3 + ABCA Mouse Brain scRNAseq
Xenium V1 hSkin nondiseased FFPE + 2024 Ganier scRNAseq
References
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- Lu, Y., Yang, A., Quan, C., Pan, Y., Zhang, H., Li, Y., Gao, C., Lu, H., Wang, X., Cao, P., Chen, H., Lu, S., & Zhou, G. (2022). A single-cell atlas of the multicellular ecosystem of primary and metastatic hepatocellular carcinoma. 10.1038/s41467-022-32283-3 ↗
- Salas, S. M., Czarnewski, P., Kuemmerle, L. B., Helgadottir, S., Matsson-Langseth, C., Tismeyer, S., Avenel, C., Rehman, H., Tiklova, K., Andersson, A., Chatzinikolaou, M., Theis, F. J., Luecken, M. D., Wählby, C., Ishaque, N., & Nilsson, M. (2023). Optimizing Xenium In Situ data utility by quality assessment and best practice analysis workflows. 10.1101/2023.02.13.528102 ↗
- Travaglini, K. J., Nabhan, A. N., Penland, L., Sinha, R., Gillich, A., Sit, R. V., Chang, S., Conley, S. D., Mori, Y., Seita, J., Berry, G. J., Shrager, J. B., Metzger, R. J., Kuo, C. S., Neff, N., Weissman, I. L., Quake, S. R., & Krasnow, M. A. (2020). A molecular cell atlas of the human lung from single-cell RNA sequencing. 10.1038/s41586-020-2922-4 ↗
- Wu, S. Z., Al-Eryani, G., Roden, D. L., Junankar, S., Harvey, K., Andersson, A., Thennavan, A., Wang, C., Torpy, J. R., Bartonicek, N., Wang, T., Larsson, L., Kaczorowski, D., Weisenfeld, N. I., Uytingco, C. R., Chew, J. G., Bent, Z. W., Chan, C.-L., Gnanasambandapillai, V., … Swarbrick, A. (2021). A single-cell and spatially resolved atlas of human breast cancers. Nature Genetics, 53(9), 1334–1347. 10.1038/s41588-021-00911-1 ↗