{ "format_version": 1, "release": "2026-07-27", "file_count": 112, "total_bytes": 545212946, "files": [ { "path": "README.md", "bytes": 2954, "sha256": "f99f356c12a83488d364aca5b4e3ac206c386fb95879bd2a2ed0f4facba1e83c" }, { "path": "chat/config.example.env", "bytes": 108, "sha256": "f03c107999d9e4ecf2cd0fdc52cd08a79f90f40e76a5cdb7cf69419196066ec9" }, { "path": "chat/slice_images/GSE175540_GSM5924034.jpg", "bytes": 2904278, "sha256": "eca25457369e9330b12f8be41df518e3ed3534b48fe71dc0fc8339079b038826" }, { "path": "chat/slice_images/GSE175540_GSM5924036.jpg", "bytes": 2514500, "sha256": "9536c3c64f21e1bbdde6d73df5e3eee4932f6bf3108caffc52ca7ed55bc83e23" }, { "path": "chat/slice_images/GSE175540_GSM5924039.jpg", "bytes": 2782541, "sha256": "41b65fa3c64254382799624fde1f8a2d7277b443b57cb5e35ff9935f6a080532" }, { "path": "chat/spots.jsonl", "bytes": 57736044, "sha256": "cf0a3197ecf67884741275c19d20d1240cfc393d2a4a4b67e9d0e0c344544504" }, { "path": "rankridge_pack_versions.csv", "bytes": 622, "sha256": "5b87ac8a990a900507ac5b5432f1d506efe95bedb189f67d216fc8a123da0b9f" }, { "path": "rankridge_rcc_validation.json", "bytes": 371, "sha256": "b67f8c137bc25565369937cb217ea607f31fa4348c518e7cb4745674098916f8" }, { "path": "rankridge_release_manifest.json", "bytes": 11890, "sha256": "bb3c71b3a355d15f076a22accf5df3dbf51548c2c7f44a30fd2eb200a43c7bf0" }, { "path": "rankridge_tutorial_packs/human__breast/feature_genes.txt", "bytes": 9257, "sha256": "23806ae488090aee5563be441095707bae5c01ec58063ec7b6b3ecdaa0f41f9b" }, { "path": "rankridge_tutorial_packs/human__breast/pack_manifest.json", "bytes": 792, "sha256": "2d9feb48627255cf5acbe5c8c7433258e756bf2bc243d9e8499cb63d4d720db6" }, { "path": "rankridge_tutorial_packs/human__breast/query_expression.npy", "bytes": 8544, "sha256": "f5827fa453470cf8aedfc4cc3396c507c98b8d396cd2085788c119540cd52861" }, { "path": "rankridge_tutorial_packs/human__breast/query_genes.txt", "bytes": 7, "sha256": "77acb2999ee146ba1005aadc6a304dde76836abdf579e5b811f2b21711df9d7a" }, { "path": "rankridge_tutorial_packs/human__breast/query_rank_features.npz", "bytes": 182017, "sha256": "5788637fff1db315ac35586bdd50ed153d1856b8ab6f8ee8166b6c0786a82757" }, { "path": "rankridge_tutorial_packs/human__breast/query_rows.csv", "bytes": 93588, "sha256": "c701526d1dac7596636704ec8acb08853276d7f6f6aa2ffd5282467acdb1a086" }, { "path": "rankridge_tutorial_packs/human__breast/reference_expression_targets.npz", "bytes": 85550, "sha256": "58e8e02b725dda681541202b848c7f8e1d832c41b5014cb9f0a504049e7c4379" }, { "path": "rankridge_tutorial_packs/human__breast/reference_rank_features.npz", "bytes": 1433846, "sha256": "51b98fc47f01df626618d400ec0adc880a713f281447982eca6281685ccb6693" }, { "path": "rankridge_tutorial_packs/human__breast/reference_rows.csv", "bytes": 871751, "sha256": "2162a15d989209a489ddce29f2049be73d38c15893b359a8a86d089029022884" }, { "path": "rankridge_tutorial_packs/human__breast/ridge_coefficients.npy", "bytes": 6128, "sha256": "6c12751fbe73d2483b47664fdf3ba600a777b609faa0efa3047691bc823cab12" }, { "path": "rankridge_tutorial_packs/human__breast/target_genes.txt", "bytes": 7, "sha256": "77acb2999ee146ba1005aadc6a304dde76836abdf579e5b811f2b21711df9d7a" }, { "path": "rankridge_tutorial_packs/human__kidney/feature_genes.txt", "bytes": 11316, "sha256": "efb764341c52cbec025fb1bddbdad120e1e325476079eab839134d59a463c0a9" }, { "path": "rankridge_tutorial_packs/human__kidney/pack_manifest.json", "bytes": 630, "sha256": "8a203fcd9cd77a8252f8c31b724d45fcc6b7dd306838cfb4b4bba2c2cf106500" }, { "path": "rankridge_tutorial_packs/human__kidney/query_expression.npy", "bytes": 102720, "sha256": "830b93a2f9bb21d4fe11491a1a2b2830ce65a375175e8f1560a13d0a142fee36" }, { "path": "rankridge_tutorial_packs/human__kidney/query_genes.txt", "bytes": 44, "sha256": "d2ed0184dd1b8ef113c09039156c500de8a889d31997282f4bb2ded1252c4732" }, { "path": "rankridge_tutorial_packs/human__kidney/query_rank_features.npz", "bytes": 237983, "sha256": "b7091b04ced6d00f78e57979224fea24bcb8ccab6559f0828a1d9ee5d596e646" }, { "path": "rankridge_tutorial_packs/human__kidney/query_rows.csv", "bytes": 143178, "sha256": "59d0c6dd78196d4a973dbb9f5d9ae8c21ad8055fc68bdc85eb0b3efacc081f74" }, { "path": "rankridge_tutorial_packs/human__kidney/reference_expression_targets.npz", "bytes": 153590, "sha256": "d30a945d4708348b108d79f4f38a6258a0bb408456a2abc6d9a9d5289e0d1000" }, { "path": "rankridge_tutorial_packs/human__kidney/reference_rank_features.npz", "bytes": 1456936, "sha256": "80ab11cf1374e3a23f81ec83b4a17cf65aeb4adbf055495831873858b90914bc" }, { "path": "rankridge_tutorial_packs/human__kidney/reference_rows.csv", "bytes": 468796, "sha256": "6b5e5ab60531ad444dcb545ac5ef3ff61db48067e18467d37157db1866ec911b" }, { "path": "rankridge_tutorial_packs/human__kidney/ridge_coefficients.npy", "bytes": 48128, "sha256": "8250fa21e9d251b903d6f91e78724c12cfc5eaf7768aaac9dc0e458f80a3025a" }, { "path": "rankridge_tutorial_packs/human__kidney/target_genes.txt", "bytes": 44, "sha256": "d2ed0184dd1b8ef113c09039156c500de8a889d31997282f4bb2ded1252c4732" }, { "path": "rankridge_tutorial_packs/human__stomach/feature_genes.txt", "bytes": 9421, "sha256": "1582f390c8df429990148ead17e72d683947b71cbe610471b1cf5d60caced50b" }, { "path": "rankridge_tutorial_packs/human__stomach/pack_manifest.json", "bytes": 2862, "sha256": "7c953b672cd92a02a8fc7564d625711d4efec75c5f7e7f3bf71681c2fb40bfeb" }, { "path": "rankridge_tutorial_packs/human__stomach/query_expression.npy", "bytes": 9832, "sha256": "08486c2f6b85550812ba8605d44430c7181689908f1a30c221507b83ab0fb172" }, { "path": "rankridge_tutorial_packs/human__stomach/query_genes.txt", "bytes": 5, "sha256": "179e7f9c42e394feb61be22cff8abd9644ab8ef14a229e85a91dddbf3d9301b9" }, { "path": "rankridge_tutorial_packs/human__stomach/query_rank_features.npz", "bytes": 191869, "sha256": "7e1f7aadecccf9c923c28f280f15ebc1c3657ada96615e70691d5f6c04585337" }, { "path": "rankridge_tutorial_packs/human__stomach/query_rows.csv", "bytes": 108078, "sha256": "b61ea98a04d9ea07a849b6def22bf0cfdac0fdd6bd8f30f0d9b934d9ebf98829" }, { "path": "rankridge_tutorial_packs/human__stomach/reference_expression_targets.npz", "bytes": 50601, "sha256": "fe3394e8c1685520f7d3cf54c7dac60d583c74496d6fb086859d1709a3eedd26" }, { "path": "rankridge_tutorial_packs/human__stomach/reference_rank_features.npz", "bytes": 1573611, "sha256": "e5df1e33bb9893fe53d7a15cc66703b4ccf73f1bd890bd3f7a8d4524679ab640" }, { "path": "rankridge_tutorial_packs/human__stomach/reference_rows.csv", "bytes": 574081, "sha256": "353e33d8c673a082410d9b692fa08bbcf66fc050c3f8e054872661351ae66b0e" }, { "path": "rankridge_tutorial_packs/human__stomach/ridge_coefficients.npy", "bytes": 6128, "sha256": "f90e093d832c9dad40826b9a3457675312c3cb27d9c2b2ff867266d0adac095a" }, { "path": "rankridge_tutorial_packs/human__stomach/target_genes.txt", "bytes": 5, "sha256": "179e7f9c42e394feb61be22cff8abd9644ab8ef14a229e85a91dddbf3d9301b9" }, { "path": "rankridge_tutorial_packs/mouse__lung/feature_genes.txt", "bytes": 10031, "sha256": "cd73a4ed06b27dc514d9aa21c58f840d2c602d822e42a5a2cdeb88e2abad3ef9" }, { "path": "rankridge_tutorial_packs/mouse__lung/pack_manifest.json", "bytes": 2674, "sha256": "b7d236be4bc3ff66fbb22b76057e4162462260c8b966d4b533a10c66ae5dbb25" }, { "path": "rankridge_tutorial_packs/mouse__lung/query_expression.npy", "bytes": 11516, "sha256": "ad09760c2013a0e242f7026d68364d4f36a15720dda66e23c772033fc97ada0e" }, { "path": "rankridge_tutorial_packs/mouse__lung/query_genes.txt", "bytes": 6, "sha256": "6537216280d377d7ec9b522d89f72c74d8cd8601df2b27f02cffbac2816105b3" }, { "path": "rankridge_tutorial_packs/mouse__lung/query_rank_features.npz", "bytes": 209964, "sha256": "4b2d7deb933c5111608859e1d7da474867c683d3d07a14a79668e0af562dfb47" }, { "path": "rankridge_tutorial_packs/mouse__lung/query_rows.csv", "bytes": 127023, "sha256": "8b44af7ec856b67fb6da58166d29331a5f716a5ea62c378fe97203f2a0358514" }, { "path": "rankridge_tutorial_packs/mouse__lung/reference_expression_targets.npz", "bytes": 3227, "sha256": "010d9d09a207572c20be1d13680b4efab8222f94595862813d754f865f5c797f" }, { "path": "rankridge_tutorial_packs/mouse__lung/reference_rank_features.npz", "bytes": 1543810, "sha256": "5ee20fd6da74d588000932efbb1bc09c66c0963a9ba8c30e450a250b3d5f3213" }, { "path": "rankridge_tutorial_packs/mouse__lung/reference_rows.csv", "bytes": 535472, "sha256": "458f5584bb47be8ab3ae07b13ad059e0a8698282225e90da869877144dbfd4f4" }, { "path": "rankridge_tutorial_packs/mouse__lung/ridge_coefficients.npy", "bytes": 6128, "sha256": "8b77decc604a3c1f888d383d71bd6ac0d5d1dd0105b04e61196f4fdd7538014b" }, { "path": "rankridge_tutorial_packs/mouse__lung/target_genes.txt", "bytes": 6, "sha256": "6537216280d377d7ec9b522d89f72c74d8cd8601df2b27f02cffbac2816105b3" }, { "path": "rankridge_tutorial_packs/mouse__spleen/feature_genes.txt", "bytes": 9974, "sha256": "1a52a89861b07bc858f15687bd16e7e9dabb209175dcd16b285686408803eade" }, { "path": "rankridge_tutorial_packs/mouse__spleen/pack_manifest.json", "bytes": 2676, "sha256": "1282a00ee61ef2590b28c5eae29268ca0ab20c0711fc610ccf4296543a92a760" }, { "path": "rankridge_tutorial_packs/mouse__spleen/query_expression.npy", "bytes": 10340, "sha256": "a86a3a2910f0a9936713d97cb10eb24e54dd33099322c6b0b59cc60c0cdf2efc" }, { "path": "rankridge_tutorial_packs/mouse__spleen/query_genes.txt", "bytes": 5, "sha256": "ebf861d6db865edab7f8eaff2a60e4624456a269084fe136654668903fa3d6d6" }, { "path": "rankridge_tutorial_packs/mouse__spleen/query_rank_features.npz", "bytes": 170175, "sha256": "edfec65ff59deca57401a2bc792a529245e8f8398a9f39880e5eec8bc9a483ae" }, { "path": "rankridge_tutorial_packs/mouse__spleen/query_rows.csv", "bytes": 113793, "sha256": "c07f43efd4cf6b1c4826324ed853a5e3f6df8b151cb8f42a4cf91282475b8164" }, { "path": "rankridge_tutorial_packs/mouse__spleen/reference_expression_targets.npz", "bytes": 54810, "sha256": "1e511d7c81e2b77771aab947db24052cb966d6710615c3184ef7146c4953d90f" }, { "path": "rankridge_tutorial_packs/mouse__spleen/reference_rank_features.npz", "bytes": 1534693, "sha256": "4a008aaa204e523c9225c9349836395a8fa09e44a9be868a1a104982db165be4" }, { "path": "rankridge_tutorial_packs/mouse__spleen/reference_rows.csv", "bytes": 535472, "sha256": "458f5584bb47be8ab3ae07b13ad059e0a8698282225e90da869877144dbfd4f4" }, { "path": "rankridge_tutorial_packs/mouse__spleen/ridge_coefficients.npy", "bytes": 6128, "sha256": "6644493c94d5007092bddbc64a0d5d14cbc84769d689bf242f8d957c5b59a790" }, { "path": "rankridge_tutorial_packs/mouse__spleen/target_genes.txt", "bytes": 5, "sha256": "ebf861d6db865edab7f8eaff2a60e4624456a269084fe136654668903fa3d6d6" }, { "path": "rankridge_tutorial_packs/rcc__human_kidney/feature_genes.txt", "bytes": 6806, "sha256": "6baac431037e62f4f08b051d8d948e60890b893e8f5fa13f86766c11cb19fcc5" }, { "path": "rankridge_tutorial_packs/rcc__human_kidney/pack_manifest.json", "bytes": 1411, "sha256": "52b1fb08ca99bece4cae750767419defa953c2aba25d2ade1f840356fe47324a" }, { "path": "rankridge_tutorial_packs/rcc__human_kidney/query_expression.npy", "bytes": 102720, "sha256": "a3c9bb5a759f7b13a785b5c237d4838a1c0126863391a6c2443fd64e2f1ee78c" }, { "path": "rankridge_tutorial_packs/rcc__human_kidney/query_genes.txt", "bytes": 44, "sha256": "d2ed0184dd1b8ef113c09039156c500de8a889d31997282f4bb2ded1252c4732" }, { "path": "rankridge_tutorial_packs/rcc__human_kidney/query_rank_features.npz", "bytes": 239273, "sha256": "ab372d4e8226ce02fd4abeb3b8e77c42ce369e027df2cb363537ca0cbd579373" }, { "path": "rankridge_tutorial_packs/rcc__human_kidney/query_rows.csv", "bytes": 143178, "sha256": "59d0c6dd78196d4a973dbb9f5d9ae8c21ad8055fc68bdc85eb0b3efacc081f74" }, { "path": "rankridge_tutorial_packs/rcc__human_kidney/reference_expression_targets.npz", "bytes": 253805, "sha256": "a7561fdf3a4f56dfd50e2e6154768593551ef3bd24cdc06c09adf80f96c1dd32" }, { "path": "rankridge_tutorial_packs/rcc__human_kidney/reference_rank_features.npz", "bytes": 3493967, "sha256": "c01c8661c9d7c21540d090aa333d7a4dfe19e67d096ecde906ec80f01742ed4a" }, { "path": "rankridge_tutorial_packs/rcc__human_kidney/reference_rows.csv", "bytes": 1146961, "sha256": "9ab1535defe38010508290cab775ab9f184d33b40e82cca74f47f7dd52a398ce" }, { "path": "rankridge_tutorial_packs/rcc__human_kidney/ridge_coefficients.npy", "bytes": 32128, "sha256": "fc7a3012386edd0083764b53ae7b29125eca63d55d7d6b8db17c78a9e1f7772c" }, { "path": "rankridge_tutorial_packs/rcc__human_kidney/target_genes.txt", "bytes": 44, "sha256": "d2ed0184dd1b8ef113c09039156c500de8a889d31997282f4bb2ded1252c4732" }, { "path": "rankridge_validation.csv", "bytes": 666, "sha256": "51c9fd51ca74fe42c8b90360c36381028d54d266c3e268b6fa4f9829d374e322" }, { "path": "tutorials/clinical_abmil_stad_seed142_fold00.pt", "bytes": 2115645, "sha256": "9a2d9395d3b5a4af7a516aeb34cfbe5823932a45e2ca729e68b03784e242ddb3" }, { "path": "tutorials/clinical_abmil_stad_seed142_fold01.pt", "bytes": 2115645, "sha256": "19c9833b4e7b91b1f6f041efd779efbac5b3cb39a41fcafe7f7353d839912bc4" }, { "path": "tutorials/clinical_abmil_stad_seed142_fold02.pt", "bytes": 2115645, "sha256": "a659a6e9c4a7cde5d0240fe51e3b3a5fb6fd3da86fdec827bda1b98cf71a59a0" }, { "path": "tutorials/clinical_abmil_stad_seed142_fold03.pt", "bytes": 2115645, "sha256": "a00b9e89efb7977192ccc20c503977fda7fdfdfe141f9cde9120ce79ca76016e" }, { "path": "tutorials/clinical_abmil_stad_seed142_fold04.pt", "bytes": 2115645, "sha256": "42fbb461cc4772aabc44583717094173d3e66292d8895ebcb8df0071b851c26f" }, { "path": "tutorials/clinical_abmil_tcga_e2_a1lh.pt", "bytes": 2112573, "sha256": "1000a387f09e3b62abfb9e052fbc9b6708ae90914daa7ef81cf33caf44e3ea3f" }, { "path": "tutorials/clinical_cases.json", "bytes": 2212, "sha256": "4b08b229cef0cd96a9e8bc1abab152891eae4cf875ec100730f33312e5e82bb3" }, { "path": "tutorials/clinical_embeddings_tcga_br_8486.npz", "bytes": 147742482, "sha256": "a9eb9fe196acf003e93c6dfdc5a25677c650ed7d41ddc7dcda03da89c3942889" }, { "path": "tutorials/clinical_embeddings_tcga_e2_a1lh.npz", "bytes": 142990926, "sha256": "49f6cf21ae652e6adda9b301b8e977c6e4fde1aab7bc01e571a7c07fa7770403" }, { "path": "tutorials/clinical_embeddings_tcga_vq_aa6b.npz", "bytes": 140063435, "sha256": "2169e2d54cb8ad1dc4ba712d1755f3dffdbb11670307061aeae7538ff491d979" }, { "path": "tutorials/fig2b_pcc.json", "bytes": 478, "sha256": "8c06d8ac73dd3d416c6a2e9fed5bcafbcd3d276288ec3b66bedc98a5da542c83" }, { "path": "tutorials/fig2b_spots.json", "bytes": 2693033, "sha256": "bee499c4316e473f980bb6aae3cb2820636b38623759f95b6e565586bb33e3a1" }, { "path": "tutorials/fig2c_metrics.json", "bytes": 510, "sha256": "f7ac5cf2113ce69e8ced6023c94faee287a92a518d523ee7243b938ff8d5cd84" }, { "path": "tutorials/fig2c_spots.json", "bytes": 934433, "sha256": "6beb798a16ce7baa799076cc7c6e5faac78e97b0ce18ee165a471736f5b4263e" }, { "path": "tutorials/fig2e.json", "bytes": 22837, "sha256": "97c7ce4660306128c32b2478652ca7f71ed3814983edcf8b9e72edb40123703c" }, { "path": "tutorials/fig3b.json", "bytes": 70231, "sha256": "477c230875d967b4b2ca5d50f0aa4034d0a1a7bae5b4db98406251f8a471afc9" }, { "path": "tutorials/fig3c.json", "bytes": 106097, "sha256": "8d2e87557448d87fcb580ee869e93e3d2724b9d2e8f1c4035fa51c305ff093e0" }, { "path": "tutorials/fig4d_summary.json", "bytes": 2310, "sha256": "11f136dcebd1eca6f6241408b68f3439b4ae89d0043438e2287ad6ecf4a15558" }, { "path": "tutorials/figure2b_measured_expression.csv", "bytes": 241595, "sha256": "923bb09987f1b351e4e4c6e9f64ff43ecf22e27ab2f536a4572d14c68f203e12" }, { "path": "tutorials/figure3_examples.json", "bytes": 1221, "sha256": "c278dac90dbe7bc7b03c89ec79819548eb4acf00f066687978347c3bca6aaa8c" }, { "path": "tutorials/figure3_examples.npz", "bytes": 283441, "sha256": "54c45d7da787faa5fef2d781a566b81f6ac8a9b62a7dcd4abba69cda19236272" }, { "path": "tutorials/figure3b_rank_metrics_per_section.csv", "bytes": 36227, "sha256": "def172536cb1af10cb763c60a6a8254c19d88360cacf92ea4d52cc42cb54e7c7" }, { "path": "tutorials/figure4_survival_oof.csv", "bytes": 53677, "sha256": "95e1f398a462292c244e648c1a2f7805997d319408c4668e091bfca847819ebf" }, { "path": "tutorials/figure4_wsi/brca_roi.png", "bytes": 3216181, "sha256": "6f4152066d2a46e70a7e4183e710883269ae68479cfba1f46761421610aeb03a" }, { "path": "tutorials/figure4_wsi/brca_roi_annotation.png", "bytes": 32241, "sha256": "42e569cbc99b54cfe30bf6f2367739a12b258b27c5cf9dc3933c4df7316163d4" }, { "path": "tutorials/figure4_wsi/brca_wsi.png", "bytes": 2024529, "sha256": "4897d0ad4fcb3e78cd3691279e2a589954df1bd51c5e8c0ac81135cdf31de6bf" }, { "path": "tutorials/figure4_wsi/stad1_wsi.png", "bytes": 3386448, "sha256": "95babae026d41c9d24572768fd7c3f4880749251e0f02e64d4f81c80faee6fd3" }, { "path": "tutorials/figure4_wsi/stad2_wsi.png", "bytes": 2179914, "sha256": "7184fa1563087fc6a405a49d6280a8af01d3b367f6d9a114e5d93cc8e89b42ea" }, { "path": "tutorials/figure5_embedding_queries.json", "bytes": 2415, "sha256": "70f5db358547a2306a4ff9da0ade404e8656241357e279a7d221c30a8a3e05e0" }, { "path": "tutorials/figure5_embedding_subset.csv", "bytes": 1451864, "sha256": "23e4876bf49f379c0dbb548154902f77d557f02b04b33459625364895f272372" }, { "path": "tutorials/figure5_embedding_subset.npz", "bytes": 416526, "sha256": "1ff266f29c6902a99aa645825469b167c4975a24800a5c60b751d6577ef029f2" }, { "path": "tutorials/figure5_he_query_brain_context.png", "bytes": 182933, "sha256": "ffc91ad6e4cce9e92e7fe4eb6da3d6865806f2319c72ea9e9919403a66bbaefc" }, { "path": "tutorials/figure5_he_query_brain_local.png", "bytes": 102827, "sha256": "15adcc5e1c7f569c8dcadcfdb33af0ab8ab2ffdac0a8e8451d2e9d6aaf165be1" }, { "path": "tutorials/quickstart_expression_maps.json", "bytes": 9656, "sha256": "80488208896400e3df166046fbd9dc65e8c586c6dadf6cbfcb5c56f3208666f0" }, { "path": "tutorials/quickstart_expression_maps.npz", "bytes": 166381, "sha256": "f6e8571b80a3a12615aa01f26e8a03fa236d7643ccd1153d4128223b5bcffb80" }, { "path": "tutorials/tls_worked_example.json", "bytes": 1504, "sha256": "91ff3feff2ae8de8709420c38605627dd5147c04c2a389c70c3b46e933dc133d" } ] }