| { |
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| "checkpoint_sha256": "4228704493c9da794ed7be5c6f98194f36eeb7c05d9ed618f69109091cf2a537", |
| "stage2_checkpoint_sha256": "130d8c61ca9607827c220e1e51b6d5a6a49deac0f66c0178302303545ffd944c", |
| "gene_space_sha256": "87ac6eb3e95da658e2993ea54b8043f4bb60604fa48100aeea8697c4b84bd938", |
| "cache_fingerprint": "b8f5acc5c0956c2661fe021d06a42404b424a7e7fe45923c9c35b4a5aa41a1fe", |
| "retrieval_method": "cluster_retrieval", |
| "K": 50, |
| "tau": 0.03, |
| "target_size": 100, |
| "reference_objects": [ |
| "110", |
| "120", |
| "221", |
| "222", |
| "231", |
| "232", |
| "242", |
| "COAD", |
| "HCC", |
| "OV", |
| "TID1_scene2", |
| "TID1_scene3", |
| "TID1_scene4", |
| "benchmark_ovary_io_Xenium_V1_Human_Ovarian_Cancer_Addon_FFPE", |
| "bone_bone_marrow_bone_bone_marrow_xenium_Xenium_V1_hBoneMarrow_acute_lymphoid_leukemia_section", |
| "bone_bone_marrow_bone_bone_marrow_xenium_Xenium_V1_hBoneMarrow_nondiseased_section", |
| "bone_bone_marrow_bone_bone_marrow_xenium_Xenium_V1_hBone_nondiseased_section", |
| "breast_cancer_sample3_xenium_Xenium_V1_FFPE_Human_Breast_IDC_With_Addon", |
| "breast_cancer_sample4_xenium_Xenium_V1_FFPE_Human_Breast_IDC_With_Addon", |
| "breast_cancer_sample5_xenium_Xenium_V1_FFPE_Human_Breast_ILC_With_Addon", |
| "breast_cancer_sample6_xenium_Xenium_V1_FFPE_Human_Breast_IDC", |
| "breast_cancer_sample7_xenium_Xenium_V1_FFPE_Human_Breast_ILC", |
| "breast_cancer_sample8_xenium_replicate1_Xenium_V1_FFPE_Human_Breast_IDC_Big_1", |
| "breast_cancer_sample8_xenium_replicate2_Xenium_V1_FFPE_Human_Breast_IDC_Big_2", |
| "cervilla_Breast", |
| "colon_cancer_addon", |
| "colon_colon_preview_xenium_Xenium_V1_hColon_Non_diseased_Base_FFPE", |
| "colorectal_cancer_colorectal_cancer_xenium_Xenium_V1_Human_Colorectal_Cancer_Addon_FFPE", |
| "heart_heart_sample1_xenium_Xenium_V1_hHeart_nondiseased_section_FFPE", |
| "hest_NCBI856", |
| "hest_NCBI857", |
| "hest_NCBI860", |
| "hest_NCBI861", |
| "hest_NCBI864", |
| "hest_NCBI865", |
| "hest_NCBI867", |
| "hest_NCBI870", |
| "hest_NCBI881", |
| "hest_NCBI882", |
| "hest_NCBI885", |
| "hest_NCBI886", |
| "hest_NCBI887", |
| "hest_NCBI888", |
| "hest_TENX115", |
| "hest_TENX138", |
| "hest_TENX141", |
| "hest_TENX147", |
| "hest_TENX148", |
| "hest_TENX149", |
| "hest_TENX158", |
| "hest_TENX188", |
| "hest_TENX191", |
| "hest_TENX192", |
| "hest_TENX193", |
| "hest_TENX194", |
| "hest_TENX195", |
| "hest_TENX196", |
| "hest_TENX197", |
| "hest_TENX198", |
| "hest_TENX199", |
| "hest_TENX200", |
| "hest_TENX201", |
| "hest_TENX202", |
| "kidney_kidney_preview_xenium_Xenium_V1_hKidney_nondiseased_section", |
| "kidney_protein", |
| "liver_liver_xenium_Xenium_V1_hLiver_cancer_section_FFPE", |
| "liver_liver_xenium_Xenium_V1_hLiver_nondiseased_section_FFPE", |
| "lung_cancer_lung_cancer_post_xenium_technote_Xenium_V1_Human_Lung_Cancer_FFPE", |
| "lung_prime", |
| "lymph_node_prime", |
| "ovary_ovary_cross_platform_fresh_frozen_xenium_Xenium_V1_Human_Ovary_Cancer_FF", |
| "ovary_prime_cancer_ff", |
| "pancreas_pancreas_multimodal_xenium_Xenium_V1_human_Pancreas_FFPE", |
| "pancreas_pancreatic_cancer_xenium_Xenium_V1_hPancreas_Cancer_Add_on_FFPE", |
| "prostate_prostate_prime_ffpe_xenium_Xenium_Prime_Human_Prostate_FFPE", |
| "skin_skin_normal_xenium_Xenium_V1_hSkin_nondiseased_section_1_FFPE", |
| "skin_skin_normal_xenium_Xenium_V1_hSkin_nondiseased_section_2_FFPE", |
| "tonsil_follicular", |
| "tonsil_reactive" |
| ], |
| "reference_exclusions": { |
| "110": [ |
| "110" |
| ], |
| "120": [ |
| "120" |
| ], |
| "221": [ |
| "221" |
| ], |
| "222": [ |
| "222" |
| ], |
| "231": [ |
| "231" |
| ], |
| "232": [ |
| "232" |
| ], |
| "242": [ |
| "242" |
| ], |
| "COAD": [ |
| "COAD" |
| ], |
| "HCC": [ |
| "HCC" |
| ], |
| "OV": [ |
| "OV" |
| ], |
| "TID1_scene2": [ |
| "TID1_scene2" |
| ], |
| "TID1_scene3": [ |
| "TID1_scene3" |
| ], |
| "TID1_scene4": [ |
| "TID1_scene4" |
| ], |
| "benchmark_ovary_io_Xenium_V1_Human_Ovarian_Cancer_Addon_FFPE": [ |
| "benchmark_ovary_io_Xenium_V1_Human_Ovarian_Cancer_Addon_FFPE" |
| ], |
| "bone_bone_marrow_bone_bone_marrow_xenium_Xenium_V1_hBoneMarrow_acute_lymphoid_leukemia_section": [ |
| "bone_bone_marrow_bone_bone_marrow_xenium_Xenium_V1_hBoneMarrow_acute_lymphoid_leukemia_section" |
| ], |
| "bone_bone_marrow_bone_bone_marrow_xenium_Xenium_V1_hBoneMarrow_nondiseased_section": [ |
| "bone_bone_marrow_bone_bone_marrow_xenium_Xenium_V1_hBoneMarrow_nondiseased_section" |
| ], |
| "bone_bone_marrow_bone_bone_marrow_xenium_Xenium_V1_hBone_nondiseased_section": [ |
| "bone_bone_marrow_bone_bone_marrow_xenium_Xenium_V1_hBone_nondiseased_section" |
| ], |
| "breast_cancer_sample3_xenium_Xenium_V1_FFPE_Human_Breast_IDC_With_Addon": [ |
| "breast_cancer_sample3_xenium_Xenium_V1_FFPE_Human_Breast_IDC_With_Addon" |
| ], |
| "breast_cancer_sample4_xenium_Xenium_V1_FFPE_Human_Breast_IDC_With_Addon": [ |
| "breast_cancer_sample4_xenium_Xenium_V1_FFPE_Human_Breast_IDC_With_Addon" |
| ], |
| "breast_cancer_sample5_xenium_Xenium_V1_FFPE_Human_Breast_ILC_With_Addon": [ |
| "breast_cancer_sample5_xenium_Xenium_V1_FFPE_Human_Breast_ILC_With_Addon" |
| ], |
| "breast_cancer_sample6_xenium_Xenium_V1_FFPE_Human_Breast_IDC": [ |
| "breast_cancer_sample6_xenium_Xenium_V1_FFPE_Human_Breast_IDC" |
| ], |
| "breast_cancer_sample7_xenium_Xenium_V1_FFPE_Human_Breast_ILC": [ |
| "breast_cancer_sample7_xenium_Xenium_V1_FFPE_Human_Breast_ILC" |
| ], |
| "breast_cancer_sample8_xenium_replicate1_Xenium_V1_FFPE_Human_Breast_IDC_Big_1": [ |
| "breast_cancer_sample8_xenium_replicate1_Xenium_V1_FFPE_Human_Breast_IDC_Big_1", |
| "breast_cancer_sample8_xenium_replicate2_Xenium_V1_FFPE_Human_Breast_IDC_Big_2" |
| ], |
| "breast_cancer_sample8_xenium_replicate2_Xenium_V1_FFPE_Human_Breast_IDC_Big_2": [ |
| "breast_cancer_sample8_xenium_replicate1_Xenium_V1_FFPE_Human_Breast_IDC_Big_1", |
| "breast_cancer_sample8_xenium_replicate2_Xenium_V1_FFPE_Human_Breast_IDC_Big_2" |
| ], |
| "cervilla_Breast": [ |
| "cervilla_Breast" |
| ], |
| "colon_cancer_addon": [ |
| "colon_cancer_addon" |
| ], |
| "colon_colon_preview_xenium_Xenium_V1_hColon_Non_diseased_Base_FFPE": [ |
| "colon_colon_preview_xenium_Xenium_V1_hColon_Non_diseased_Base_FFPE" |
| ], |
| "colorectal_cancer_colorectal_cancer_xenium_Xenium_V1_Human_Colorectal_Cancer_Addon_FFPE": [ |
| "colorectal_cancer_colorectal_cancer_xenium_Xenium_V1_Human_Colorectal_Cancer_Addon_FFPE" |
| ], |
| "heart_heart_sample1_xenium_Xenium_V1_hHeart_nondiseased_section_FFPE": [ |
| "heart_heart_sample1_xenium_Xenium_V1_hHeart_nondiseased_section_FFPE" |
| ], |
| "hest_NCBI856": [ |
| "hest_NCBI856", |
| "hest_NCBI857" |
| ], |
| "hest_NCBI857": [ |
| "hest_NCBI856", |
| "hest_NCBI857" |
| ], |
| "hest_NCBI860": [ |
| "hest_NCBI860", |
| "hest_NCBI861" |
| ], |
| "hest_NCBI861": [ |
| "hest_NCBI860", |
| "hest_NCBI861" |
| ], |
| "hest_NCBI864": [ |
| "hest_NCBI864" |
| ], |
| "hest_NCBI865": [ |
| "hest_NCBI865" |
| ], |
| "hest_NCBI867": [ |
| "hest_NCBI867" |
| ], |
| "hest_NCBI870": [ |
| "hest_NCBI870" |
| ], |
| "hest_NCBI881": [ |
| "hest_NCBI881", |
| "hest_NCBI882" |
| ], |
| "hest_NCBI882": [ |
| "hest_NCBI881", |
| "hest_NCBI882" |
| ], |
| "hest_NCBI885": [ |
| "hest_NCBI885" |
| ], |
| "hest_NCBI886": [ |
| "hest_NCBI886", |
| "hest_NCBI887" |
| ], |
| "hest_NCBI887": [ |
| "hest_NCBI886", |
| "hest_NCBI887" |
| ], |
| "hest_NCBI888": [ |
| "hest_NCBI888" |
| ], |
| "hest_TENX115": [ |
| "hest_TENX115" |
| ], |
| "hest_TENX138": [ |
| "hest_TENX138" |
| ], |
| "hest_TENX141": [ |
| "hest_TENX141" |
| ], |
| "hest_TENX147": [ |
| "hest_TENX147" |
| ], |
| "hest_TENX148": [ |
| "hest_TENX148" |
| ], |
| "hest_TENX149": [ |
| "hest_TENX149" |
| ], |
| "hest_TENX158": [ |
| "hest_TENX158" |
| ], |
| "hest_TENX188": [ |
| "hest_TENX188" |
| ], |
| "hest_TENX191": [ |
| "hest_TENX191", |
| "hest_TENX192", |
| "hest_TENX193" |
| ], |
| "hest_TENX192": [ |
| "hest_TENX191", |
| "hest_TENX192", |
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| ], |
| "hest_TENX193": [ |
| "hest_TENX191", |
| "hest_TENX192", |
| "hest_TENX193" |
| ], |
| "hest_TENX194": [ |
| "hest_TENX194", |
| "hest_TENX195", |
| "hest_TENX196" |
| ], |
| "hest_TENX195": [ |
| "hest_TENX194", |
| "hest_TENX195", |
| "hest_TENX196" |
| ], |
| "hest_TENX196": [ |
| "hest_TENX194", |
| "hest_TENX195", |
| "hest_TENX196" |
| ], |
| "hest_TENX197": [ |
| "hest_TENX197", |
| "hest_TENX198", |
| "hest_TENX199" |
| ], |
| "hest_TENX198": [ |
| "hest_TENX197", |
| "hest_TENX198", |
| "hest_TENX199" |
| ], |
| "hest_TENX199": [ |
| "hest_TENX197", |
| "hest_TENX198", |
| "hest_TENX199" |
| ], |
| "hest_TENX200": [ |
| "hest_TENX200", |
| "hest_TENX201", |
| "hest_TENX202" |
| ], |
| "hest_TENX201": [ |
| "hest_TENX200", |
| "hest_TENX201", |
| "hest_TENX202" |
| ], |
| "hest_TENX202": [ |
| "hest_TENX200", |
| "hest_TENX201", |
| "hest_TENX202" |
| ], |
| "kidney_kidney_preview_xenium_Xenium_V1_hKidney_nondiseased_section": [ |
| "kidney_kidney_preview_xenium_Xenium_V1_hKidney_nondiseased_section" |
| ], |
| "kidney_protein": [ |
| "kidney_protein" |
| ], |
| "liver_liver_xenium_Xenium_V1_hLiver_cancer_section_FFPE": [ |
| "liver_liver_xenium_Xenium_V1_hLiver_cancer_section_FFPE" |
| ], |
| "liver_liver_xenium_Xenium_V1_hLiver_nondiseased_section_FFPE": [ |
| "liver_liver_xenium_Xenium_V1_hLiver_nondiseased_section_FFPE" |
| ], |
| "lung_cancer_lung_cancer_post_xenium_technote_Xenium_V1_Human_Lung_Cancer_FFPE": [ |
| "lung_cancer_lung_cancer_post_xenium_technote_Xenium_V1_Human_Lung_Cancer_FFPE" |
| ], |
| "lung_prime": [ |
| "lung_prime" |
| ], |
| "lymph_node_prime": [ |
| "lymph_node_prime" |
| ], |
| "ovary_ovary_cross_platform_fresh_frozen_xenium_Xenium_V1_Human_Ovary_Cancer_FF": [ |
| "ovary_ovary_cross_platform_fresh_frozen_xenium_Xenium_V1_Human_Ovary_Cancer_FF", |
| "ovary_prime_cancer_ff" |
| ], |
| "ovary_prime_cancer_ff": [ |
| "ovary_ovary_cross_platform_fresh_frozen_xenium_Xenium_V1_Human_Ovary_Cancer_FF", |
| "ovary_prime_cancer_ff" |
| ], |
| "pancreas_pancreas_multimodal_xenium_Xenium_V1_human_Pancreas_FFPE": [ |
| "pancreas_pancreas_multimodal_xenium_Xenium_V1_human_Pancreas_FFPE" |
| ], |
| "pancreas_pancreatic_cancer_xenium_Xenium_V1_hPancreas_Cancer_Add_on_FFPE": [ |
| "pancreas_pancreatic_cancer_xenium_Xenium_V1_hPancreas_Cancer_Add_on_FFPE" |
| ], |
| "prostate_prostate_prime_ffpe_xenium_Xenium_Prime_Human_Prostate_FFPE": [ |
| "prostate_prostate_prime_ffpe_xenium_Xenium_Prime_Human_Prostate_FFPE" |
| ], |
| "skin_skin_normal_xenium_Xenium_V1_hSkin_nondiseased_section_1_FFPE": [ |
| "skin_skin_normal_xenium_Xenium_V1_hSkin_nondiseased_section_1_FFPE" |
| ], |
| "skin_skin_normal_xenium_Xenium_V1_hSkin_nondiseased_section_2_FFPE": [ |
| "skin_skin_normal_xenium_Xenium_V1_hSkin_nondiseased_section_2_FFPE" |
| ], |
| "tonsil_follicular": [ |
| "tonsil_follicular" |
| ], |
| "tonsil_reactive": [ |
| "tonsil_reactive" |
| ] |
| }, |
| "R_dtype": "float32", |
| "tissue_casefold": true, |
| "min_refs": 1, |
| "panel_cut": 1000, |
| "fallback": "same_tissue" |
| } |
|
|
