diff --git a/.gitattributes b/.gitattributes index 442be8c7fd9f5d2cc6d4c6e43478bf4d2215ed4a..35b26c9ad042e752fe09b812ff7255ce24e57d05 100644 --- a/.gitattributes +++ b/.gitattributes @@ -402,3 +402,35 @@ GSE269377/GSM8314108/spatial.h5ad filter=lfs diff=lfs merge=lfs -text GSE269377/GSM8314108/wsi.tif filter=lfs diff=lfs merge=lfs -text GSE269377/GSM8314109/spatial.h5ad filter=lfs diff=lfs merge=lfs -text GSE269377/GSM8314109/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427428/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427428/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427429/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427429/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427430/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427430/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427431/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427431/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427432/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427432/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427433/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427433/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427434/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427434/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427435/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427435/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427436/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427436/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427437/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427437/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427438/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427438/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427439/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427439/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427440/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427440/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427441/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427441/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427442/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427442/wsi.tif filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427443/spatial.h5ad filter=lfs diff=lfs merge=lfs -text +GSE273378/GSM8427443/wsi.tif filter=lfs diff=lfs merge=lfs -text diff --git a/GSE273378/GSM8427428/.standardization_success b/GSE273378/GSM8427428/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427428/alignment_strict_qc.png b/GSE273378/GSM8427428/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..324cf5a8bf41fc3bdddf29c95b3ae41436fa5698 --- /dev/null +++ b/GSE273378/GSM8427428/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6cfb2de47ab0d7a8dd2e99380d84894e225e65c46023defe4581143090d6ad72 +size 996714 diff --git a/GSE273378/GSM8427428/color_verification_qc.png b/GSE273378/GSM8427428/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..45592346d47bc591cd5799e9dfc10c9d5ed77315 --- /dev/null +++ b/GSE273378/GSM8427428/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1d4a8a6ea79d22abc41eac6ca53df61350700a4729d3eda21fff895b0a26a0c8 +size 2306415 diff --git a/GSE273378/GSM8427428/spatial.h5ad b/GSE273378/GSM8427428/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..418dad87544f86fe810e05a7cf63f414ccabc62a --- /dev/null +++ b/GSE273378/GSM8427428/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c2a40e21398a74dab0cc64c216ec67c56d047b0386b6815b3e67fa61bf757e4d +size 119684817 diff --git a/GSE273378/GSM8427428/wsi.tif b/GSE273378/GSM8427428/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..b9505eefcd56411262d9b8353c4ba43c1ea7bffc --- /dev/null +++ b/GSE273378/GSM8427428/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6a6341e9162bb19eb27ba24564433811ca30335e2c3ed400095186bf9432ceff +size 11628140 diff --git a/GSE273378/GSM8427429/.standardization_success b/GSE273378/GSM8427429/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427429/alignment_strict_qc.png b/GSE273378/GSM8427429/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..9374844da8ba258fb39fe27c25ce50c75c39cc73 --- /dev/null +++ b/GSE273378/GSM8427429/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b02053f6da031fc2baa07c6ada0f4d23600a2e83e95ca21043c3ffe1f950ff00 +size 1098474 diff --git a/GSE273378/GSM8427429/color_verification_qc.png b/GSE273378/GSM8427429/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..e5c2a605a4f9da93951b66fc920b196358789fd2 --- /dev/null +++ b/GSE273378/GSM8427429/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5cd96aeb67fc76382ba511d7715644fb78f60d31b298671fe43c4a45e5740d65 +size 2277320 diff --git a/GSE273378/GSM8427429/spatial.h5ad b/GSE273378/GSM8427429/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..6f4d3d2a5c03bc2b89ad66cb05cc5613627a7d74 --- /dev/null +++ b/GSE273378/GSM8427429/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b7a18afa9de70d1e95a41882335fadd34d6002d127c2c5ca1bdea82875e03f4c +size 119984756 diff --git a/GSE273378/GSM8427429/wsi.tif b/GSE273378/GSM8427429/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..5eaec1808589dc149885b398527e3afcd557f439 --- /dev/null +++ b/GSE273378/GSM8427429/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d1e0fedb02f53b7a8b22a94db4e97772df91e25db4bb3471bf4b0b27b1d30cdd +size 11712140 diff --git a/GSE273378/GSM8427430/.standardization_success b/GSE273378/GSM8427430/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427430/alignment_strict_qc.png b/GSE273378/GSM8427430/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..048796a562fa76a82de783dc7cf8714e731791f9 --- /dev/null +++ b/GSE273378/GSM8427430/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:31a73442c1625fa0843dfe806580d9da4513edc2b0076c90ebebae213d8663ef +size 1059501 diff --git a/GSE273378/GSM8427430/color_verification_qc.png b/GSE273378/GSM8427430/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..c8f698e17a48ccab92e2a90baf55bc023a690eba --- /dev/null +++ b/GSE273378/GSM8427430/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cbcc0213c8ba9d1061c1d76efee772291b53c405ffec76af6ae7b9a55025744e +size 2154934 diff --git a/GSE273378/GSM8427430/spatial.h5ad b/GSE273378/GSM8427430/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..d5e092010e22694d6a26da045ba07d07c2660b42 --- /dev/null +++ b/GSE273378/GSM8427430/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:317432325e20662c1390975274dcdbc78d6ea1a55ba56c8c22751e3e651c29e8 +size 122009684 diff --git a/GSE273378/GSM8427430/wsi.tif b/GSE273378/GSM8427430/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..5996130d938a39e5198e503ddaf457f017334965 --- /dev/null +++ b/GSE273378/GSM8427430/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:037f8df2861457617517fb3eb89eb4951220ffc11579fa6ee2af122c739f9c2a +size 11598140 diff --git a/GSE273378/GSM8427431/.standardization_success b/GSE273378/GSM8427431/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427431/alignment_strict_qc.png b/GSE273378/GSM8427431/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..0e6b3cba2dd474856e52d4263fa3b2bf1aeaaaf0 --- /dev/null +++ b/GSE273378/GSM8427431/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:aadcf9825f2cbf5de21f554a1374251881c5843e35be4efaf5fdce88594f8673 +size 925051 diff --git a/GSE273378/GSM8427431/color_verification_qc.png b/GSE273378/GSM8427431/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..8c685add96a7e03dfb9f7ed65c2f76d0772e2aad --- /dev/null +++ b/GSE273378/GSM8427431/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8c9a50cf232a3a6482d7f545d5f1571424bf5d0e0f096032ce939845b782077f +size 2086984 diff --git a/GSE273378/GSM8427431/spatial.h5ad b/GSE273378/GSM8427431/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..66c7cbfedc75b3d8c850c79ce0092fbaecbb7de5 --- /dev/null +++ b/GSE273378/GSM8427431/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f98ed83a9052c5961a03e6d21ea46a731cd1193cb539dcc6067059f894806eda +size 116171048 diff --git a/GSE273378/GSM8427431/wsi.tif b/GSE273378/GSM8427431/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..f46221bae2908d524f29ace27c3cd425141ab005 --- /dev/null +++ b/GSE273378/GSM8427431/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ddb63728467c2f9d3ed9e78f6be6ce8d3caf2844f46f8d30b31eed68d851e8fa +size 11850140 diff --git a/GSE273378/GSM8427432/.standardization_success b/GSE273378/GSM8427432/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427432/alignment_strict_qc.png b/GSE273378/GSM8427432/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..64088a8b577f7e0ab4c6e52c7dc50e86fc769f64 --- /dev/null +++ b/GSE273378/GSM8427432/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9edb7027c36b7b3c9604828faa1e1a73b2fcc44617acea0b3a58eb63f8a3adf5 +size 1264485 diff --git a/GSE273378/GSM8427432/color_verification_qc.png b/GSE273378/GSM8427432/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..3e3a23a473504ae5195ac519512599ec106db8f7 --- /dev/null +++ b/GSE273378/GSM8427432/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5550fb74b81dd6d90dc900b53a735e57ee23dfc4d429247f6df0491dae9f180b +size 3102584 diff --git a/GSE273378/GSM8427432/spatial.h5ad b/GSE273378/GSM8427432/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..919080d11647c9a9f57c54f23937f50903891c79 --- /dev/null +++ b/GSE273378/GSM8427432/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:507627970040d529288dcaeaab6c88f9ace2c40eb85b6e2866acb268b427108f +size 180993122 diff --git a/GSE273378/GSM8427432/wsi.tif b/GSE273378/GSM8427432/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..39a2e3255d58b5688df5e9c9abfa1a90f945587d --- /dev/null +++ b/GSE273378/GSM8427432/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:92aaad854a2c56a4b76a86480151be471787a5280d3bf69fe612cabb3951e7c2 +size 11352140 diff --git a/GSE273378/GSM8427433/.standardization_success b/GSE273378/GSM8427433/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427433/alignment_strict_qc.png b/GSE273378/GSM8427433/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..633f5bac3240d7023db9fc8ba2321f9c91e40c28 --- /dev/null +++ b/GSE273378/GSM8427433/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c064830e4803d62418bbf61db7405042f3c5c70bf4dbaa467873373cee56fa88 +size 1140561 diff --git a/GSE273378/GSM8427433/color_verification_qc.png b/GSE273378/GSM8427433/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..79b71884e5e3eac70e12d07ec5870b9216130665 --- /dev/null +++ b/GSE273378/GSM8427433/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8dd1be900b52615fec9f0423bdc57bb90e79bd2d81afe540a980a4cd45279bf9 +size 2642618 diff --git a/GSE273378/GSM8427433/spatial.h5ad b/GSE273378/GSM8427433/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..b3b5560caa8e317fa423f4343519a6b203aba725 --- /dev/null +++ b/GSE273378/GSM8427433/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6d613ea9c13143c280581c2cea984dd09b8d32ac67156efb51fba2cbee0353d9 +size 172498989 diff --git a/GSE273378/GSM8427433/wsi.tif b/GSE273378/GSM8427433/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..8d5bd64e07fbae79edeb6c6e890597e85a63e120 --- /dev/null +++ b/GSE273378/GSM8427433/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f2e515093a209ad67dc2ab1a5aba986b862639b85a742dc993b177ebe611172a +size 10944140 diff --git a/GSE273378/GSM8427434/.standardization_success b/GSE273378/GSM8427434/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427434/alignment_strict_qc.png b/GSE273378/GSM8427434/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..037230cc3975e6435be9663ca5a80272c803812c --- /dev/null +++ b/GSE273378/GSM8427434/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:843ef510ec0fc27c455d44e46932aae81fb10c5520f8f4cf3fb40ddf78db8b3f +size 1151437 diff --git a/GSE273378/GSM8427434/color_verification_qc.png b/GSE273378/GSM8427434/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..56c39907d43c376f992ab4d4f201c95b2dd70ac9 --- /dev/null +++ b/GSE273378/GSM8427434/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3aff461acb2af81ad9e228c6502a3aabd88765e6bc03fabbcdf0bfa85e99e882 +size 2447878 diff --git a/GSE273378/GSM8427434/spatial.h5ad b/GSE273378/GSM8427434/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..19d7dae9fa404d09f5e9fd7276d649f75d518a3a --- /dev/null +++ b/GSE273378/GSM8427434/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9cbac40b889950f58b5765c302744c509d47342b5d9316a7933aa50282d11e3c +size 156741550 diff --git a/GSE273378/GSM8427434/wsi.tif b/GSE273378/GSM8427434/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..9cd747e843b3d2e3a96f41e5e8d95f08bf7f184b --- /dev/null +++ b/GSE273378/GSM8427434/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:af738afb3653af74e964569a44b41b80f6f2a484923c435f13e3bda9d2563460 +size 11196140 diff --git a/GSE273378/GSM8427435/.standardization_success b/GSE273378/GSM8427435/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427435/alignment_strict_qc.png b/GSE273378/GSM8427435/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..94376187b21d91fe06c3405bc0d51dcf0e35626d --- /dev/null +++ b/GSE273378/GSM8427435/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d3e2c94060e0d5fdf0f8801f566cbd74779b51d0e481fe7d5b264ec553f5e14a +size 1234142 diff --git a/GSE273378/GSM8427435/color_verification_qc.png b/GSE273378/GSM8427435/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..b26d2d3e13a13fa5ba811d856c10beec4fcbcad7 --- /dev/null +++ b/GSE273378/GSM8427435/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e07f9b0b451ec727490757c820478c8ea045af5cbe5adbaaccceb00d8eb3150d +size 2757002 diff --git a/GSE273378/GSM8427435/spatial.h5ad b/GSE273378/GSM8427435/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..bd179bc500d541c5a06cbed0902d49022b7c0e6a --- /dev/null +++ b/GSE273378/GSM8427435/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:35deec713be767538b256fc7025f0ef87ae5dd58fa1250381a4f22c7a4f18d54 +size 66934872 diff --git a/GSE273378/GSM8427435/wsi.tif b/GSE273378/GSM8427435/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..ad4bb4c24486db32a2e0fded694a28ff40abb6e4 --- /dev/null +++ b/GSE273378/GSM8427435/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:587107b7f2fb5d137e0730ac31a622bd4ad9ca77b38b2a6f1782a5e7c245cd02 +size 11826140 diff --git a/GSE273378/GSM8427436/.standardization_success b/GSE273378/GSM8427436/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427436/alignment_strict_qc.png b/GSE273378/GSM8427436/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..d9af1d1f31588ffc1fab2aa782392cf724a036ef --- /dev/null +++ b/GSE273378/GSM8427436/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:797612721ff73189d3c5b3313ba8a8ebb12cd9f52153f4df02d0647d6f849a1e +size 1091906 diff --git a/GSE273378/GSM8427436/color_verification_qc.png b/GSE273378/GSM8427436/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..e846398f7f1434d19bb8447be9370a22ae3b6e78 --- /dev/null +++ b/GSE273378/GSM8427436/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6376a1d94ceb5d23656b4ab0ef3253371e767667d21c254cff3a7561e63e8635 +size 2458239 diff --git a/GSE273378/GSM8427436/spatial.h5ad b/GSE273378/GSM8427436/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..8ae15a783500d4d11a6dea1e53dcf6ba0e78e181 --- /dev/null +++ b/GSE273378/GSM8427436/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5a504877dac0708d88e7a9a8a5d314d400304a19790b04a7d66a25856619676d +size 153137313 diff --git a/GSE273378/GSM8427436/wsi.tif b/GSE273378/GSM8427436/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..92b4f19a0e9f3e6fca5db87079e1d116cfd2b270 --- /dev/null +++ b/GSE273378/GSM8427436/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:42ca6918fd63b9fb05535480206882e9b8634ece28740adeaef769a9d3712f79 +size 11664140 diff --git a/GSE273378/GSM8427437/.standardization_success b/GSE273378/GSM8427437/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427437/alignment_strict_qc.png b/GSE273378/GSM8427437/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..5c54f75e1195861f0be0ab247369cc0b24cf1db2 --- /dev/null +++ b/GSE273378/GSM8427437/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2d280aae30bc4c01fd89265d9069539f603c38c9c50ed4c2e1ff704d7fd717cb +size 1042839 diff --git a/GSE273378/GSM8427437/color_verification_qc.png b/GSE273378/GSM8427437/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..a78b362d481ea144fac155ca7cbd92e0fa5cf9f7 --- /dev/null +++ b/GSE273378/GSM8427437/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:973c58a54d7c31deb3c75854d2c53696fc2a688e5cfade21de92e69e55a907b0 +size 2404505 diff --git a/GSE273378/GSM8427437/spatial.h5ad b/GSE273378/GSM8427437/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..a17c4de0f4a985c9a61c8fe79fcd1e277e6d3c66 --- /dev/null +++ b/GSE273378/GSM8427437/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e438f7dcac77136fc9ded29512ed908e3b99f1645fccf0c5b5270fed4e26f0ef +size 108490327 diff --git a/GSE273378/GSM8427437/wsi.tif b/GSE273378/GSM8427437/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..b685cd73c6c81b37d51db5b86812360fa67e9bf7 --- /dev/null +++ b/GSE273378/GSM8427437/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:760aa87029dccf59e24d464d968cf9492772da293dd9901aaffc899993e38a05 +size 11532140 diff --git a/GSE273378/GSM8427438/.standardization_success b/GSE273378/GSM8427438/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427438/alignment_strict_qc.png b/GSE273378/GSM8427438/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..ee277175512908bf6937cf22fe703068b6d5603e --- /dev/null +++ b/GSE273378/GSM8427438/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:35274be20398bede9f49347618b6f6e4d8ea6654bb487959133b2be7b6ff42f6 +size 1077478 diff --git a/GSE273378/GSM8427438/color_verification_qc.png b/GSE273378/GSM8427438/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..1ce09b7e6d0e5b3900f6bd6776edf2349f832f2d --- /dev/null +++ b/GSE273378/GSM8427438/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8c7c42afddff1ca054e3b4f4618c5accf1ba9f88a4fc237be385a7307be407af +size 2304486 diff --git a/GSE273378/GSM8427438/spatial.h5ad b/GSE273378/GSM8427438/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..cacbf8111498f6bf08e427715f98d5a13222d7ec --- /dev/null +++ b/GSE273378/GSM8427438/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:455ac3f78a4f2115af7a0bef3d953a1c67858986b63d8e71fb5e95b5318105b9 +size 148040481 diff --git a/GSE273378/GSM8427438/wsi.tif b/GSE273378/GSM8427438/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..5dece9526cad13bc64265caa39b53fb772b175bd --- /dev/null +++ b/GSE273378/GSM8427438/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ffdcb36f86cb4ff59fbfbd761298e734e78a38a46b086b1160e818b76475f609 +size 11592140 diff --git a/GSE273378/GSM8427439/.standardization_success b/GSE273378/GSM8427439/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427439/alignment_strict_qc.png b/GSE273378/GSM8427439/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..6a91b0d647942ede5d359a0714eda39c5a0fb1d4 --- /dev/null +++ b/GSE273378/GSM8427439/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4f28394796266b0844379116adeea41fc20f205ed6f00949cfad17771bbf194c +size 1006013 diff --git a/GSE273378/GSM8427439/color_verification_qc.png b/GSE273378/GSM8427439/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..a325f2b07774efeda268e9d627852ee03753c773 --- /dev/null +++ b/GSE273378/GSM8427439/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b8b46271faa14da73da8042f47e03b677fc0d6d4394084f3e691ccd8b4d8dba6 +size 2006305 diff --git a/GSE273378/GSM8427439/spatial.h5ad b/GSE273378/GSM8427439/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..69e0afeea11430bbc73968ae59ed745fd7e8c773 --- /dev/null +++ b/GSE273378/GSM8427439/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9d9c12cd28f60a317ed83db931b5730fc3fd5b9d1cf1cb67e2c921ff0e0df2ad +size 149173612 diff --git a/GSE273378/GSM8427439/wsi.tif b/GSE273378/GSM8427439/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..c12537447a8f71a10d807c961b16ce2786a6920a --- /dev/null +++ b/GSE273378/GSM8427439/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:98d9da1c9a6b22efb87faedcdeef22be847d55b4a080cbe7823c92f78e8e786e +size 11736140 diff --git a/GSE273378/GSM8427440/.standardization_success b/GSE273378/GSM8427440/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427440/alignment_strict_qc.png b/GSE273378/GSM8427440/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..3459f9077df9bc6d5fbe6ab1239a7eed06d2e387 --- /dev/null +++ b/GSE273378/GSM8427440/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e22dd61c868d40e5f3d2cde07a8acc774e6f0236a8ca47dbe2ed7a6343863448 +size 1254767 diff --git a/GSE273378/GSM8427440/color_verification_qc.png b/GSE273378/GSM8427440/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..bd4e1db8f430f49c656f18bad738e10f67ca5654 --- /dev/null +++ b/GSE273378/GSM8427440/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a6f199d3c61ee0c57c0963eef1877d4c0465b994bb24905bbed8f7061f18dd8b +size 2792042 diff --git a/GSE273378/GSM8427440/spatial.h5ad b/GSE273378/GSM8427440/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..3f567824b8849045f237e2f983ba06da1759c27b --- /dev/null +++ b/GSE273378/GSM8427440/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c0998e12b9ea2b1e4583167d15e5cea74da26636ade66e22a2f0b1dea73ca358 +size 189137860 diff --git a/GSE273378/GSM8427440/wsi.tif b/GSE273378/GSM8427440/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..05aa8e809bd9760d84a49fd280aba43ec00a4cb2 --- /dev/null +++ b/GSE273378/GSM8427440/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1b3e8d65f6bc7aa675149d9ae7a6de07aeaa5aefca7936575db5501c3b9470fe +size 11580140 diff --git a/GSE273378/GSM8427441/.standardization_success b/GSE273378/GSM8427441/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427441/alignment_strict_qc.png b/GSE273378/GSM8427441/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..04d700cc3b306e02df2e6c6e53124f6497709172 --- /dev/null +++ b/GSE273378/GSM8427441/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:86c83bd4280004bb53c258774a17af468496b95f96ba6bf563e5bccfbf42fcdd +size 1071004 diff --git a/GSE273378/GSM8427441/color_verification_qc.png b/GSE273378/GSM8427441/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..05b77f6d883e15d31540c4afbd91672c950321af --- /dev/null +++ b/GSE273378/GSM8427441/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a4c9958abaf50f511ad919aefbb2a0a4dc7654b714c608da94916cee3e5de02c +size 2348614 diff --git a/GSE273378/GSM8427441/spatial.h5ad b/GSE273378/GSM8427441/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..ab3025367df7ab90b006a1e517fc55c245ac0abb --- /dev/null +++ b/GSE273378/GSM8427441/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:565b96f474e4759e12353d60576bed2a47dbd3b1b8cb52ef14c654ad7ac22023 +size 149944112 diff --git a/GSE273378/GSM8427441/wsi.tif b/GSE273378/GSM8427441/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..7ebf2e546a3529cbe03529722d898c03d872ae2d --- /dev/null +++ b/GSE273378/GSM8427441/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2eee793e6f42c6c0bdc28a64b798a10c4dc67d15c7beeb746a34670569c600f3 +size 11760140 diff --git a/GSE273378/GSM8427442/.standardization_success b/GSE273378/GSM8427442/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427442/alignment_strict_qc.png b/GSE273378/GSM8427442/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..ca33d4116c4bab85c4e80b51ff54d11febf59dd4 --- /dev/null +++ b/GSE273378/GSM8427442/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4a19e06bbf480a59f1bc933b730a466753e7ad0cb6280cc897df3143d8ef1f69 +size 865100 diff --git a/GSE273378/GSM8427442/color_verification_qc.png b/GSE273378/GSM8427442/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..c20c760406e06bacf9fd8f33f56f1c73239955e8 --- /dev/null +++ b/GSE273378/GSM8427442/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:003640e9def9e60818ad47c3ead96a288b11b5e475ad9073a7fd799a855a5346 +size 1736749 diff --git a/GSE273378/GSM8427442/spatial.h5ad b/GSE273378/GSM8427442/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..1268281e7f22c1fbfe9c9791506bc3115304c62c --- /dev/null +++ b/GSE273378/GSM8427442/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d9edf12785aa65c500951a767eee412a1e8cc661f4314f6508af9f216513ae01 +size 126647056 diff --git a/GSE273378/GSM8427442/wsi.tif b/GSE273378/GSM8427442/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..4c71e9339aa35cfa8821d6be2c6db3eee9c46ea2 --- /dev/null +++ b/GSE273378/GSM8427442/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bc7547992aabd3f647564d8e65003b6af9d553366d2a5c394ec3b6e6b98632d5 +size 11334140 diff --git a/GSE273378/GSM8427443/.standardization_success b/GSE273378/GSM8427443/.standardization_success new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/GSE273378/GSM8427443/alignment_strict_qc.png b/GSE273378/GSM8427443/alignment_strict_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..95ea0ced7c031993a436b0b2792f960738b6ef61 --- /dev/null +++ b/GSE273378/GSM8427443/alignment_strict_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e0983874d50831ffb206bb19dd3954bdefdd38b04a215c9e04ec37afe913d798 +size 840683 diff --git a/GSE273378/GSM8427443/color_verification_qc.png b/GSE273378/GSM8427443/color_verification_qc.png new file mode 100644 index 0000000000000000000000000000000000000000..0e8560395980c630f1939822da8812645b1e274b --- /dev/null +++ b/GSE273378/GSM8427443/color_verification_qc.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:35cd0add494cc0c947ab8a83a5e6d30ba4f73a89510b9c9af8eda3dc8f701de9 +size 1667533 diff --git a/GSE273378/GSM8427443/spatial.h5ad b/GSE273378/GSM8427443/spatial.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..96792b11c4621e572c9fe42f0f490167f06105bd --- /dev/null +++ b/GSE273378/GSM8427443/spatial.h5ad @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8ed4f0d84cd1466f6b15c592033a1072be195df3e02b5a65376cfa79bc8eba8f +size 113173096 diff --git a/GSE273378/GSM8427443/wsi.tif b/GSE273378/GSM8427443/wsi.tif new file mode 100644 index 0000000000000000000000000000000000000000..c750c6c0156d8237bfded71f3a62d5e208481de0 --- /dev/null +++ b/GSE273378/GSM8427443/wsi.tif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8650165787a9c30a0a2e81a964d2bcbf8384da9b7b172b2d5af8926786265849 +size 11688140 diff --git a/GSE273378/standardize_GSE273378.py b/GSE273378/standardize_GSE273378.py new file mode 100644 index 0000000000000000000000000000000000000000..c362dc588ce3ac6572b6658ec815719edbc344e8 --- /dev/null +++ b/GSE273378/standardize_GSE273378.py @@ -0,0 +1,214 @@ +import os +import sys +import json +import gzip +import shutil +import tempfile +import scanpy as sc +import pandas as pd +import numpy as np +import matplotlib.image as mpimg +from PIL import Image +from pathlib import Path +from datetime import datetime +from concurrent.futures import ThreadPoolExecutor + +# Add scripts to path for expert tools +SCRIPTS_DIR = "/cpfs01/projects-HDD/cfff-afe2df89e32e_HDD/jjh_19301050235/.agents/skills/ara-evolutionary-standardizer/scripts" +sys.path.append(SCRIPTS_DIR) +import registry_utils + +GSE_ID = "GSE273378" +INPUT_DIR = "/cpfs01/projects-HDD/cfff-afe2df89e32e_HDD/jjh_19301050235/my_data/preprint_data/Spatial-Clip/data/auto_standardize_react/data/2026_unzip_v4/GSE273378/GSE273378_RAW" +TARGET_DIR = f"/cpfs01/projects-HDD/cfff-afe2df89e32e_HDD/jjh_19301050235/my_data/preprint_data/Spatial-Clip/data/auto_standardize_react/data/2026_standardized/{GSE_ID}" + +# Metadata from SOTA research +METADATA = { + "organism": "Homo sapiens", + "tissue": "Lung", + "disease": "Lung Adenocarcinoma", + "sex": "Mixed", + "age": "Adult", + "technology": "10x Genomics Visium", + "stain_type": "H&E", + "publication_doi": "10.1038/s41467-026-70600-2", + "repository_id": GSE_ID +} + +def log(msg): + timestamp = datetime.now().strftime("%Y-%m-%d %H:%M:%S") + print(f"[{timestamp}] {msg}", flush=True) + +def unzip_file(src, dst): + log(f"Unzipping {src.name} to {dst.name}...") + with gzip.open(src, 'rb') as f_in: + with open(dst, 'wb') as f_out: + shutil.copyfileobj(f_in, f_out) + +def process_gsm(gsm_id, gsm_files): + log(f"--- Starting {gsm_id} ---") + try: + sample_dir = Path(TARGET_DIR) / gsm_id + sample_dir.mkdir(parents=True, exist_ok=True) + + with tempfile.TemporaryDirectory() as tmp_dir: + tmp_path = Path(tmp_dir) + spatial_dir = tmp_path / "spatial" + spatial_dir.mkdir() + + # Map files + file_map = {} + for f in gsm_files: + if "matrix.mtx.gz" in f: file_map["matrix"] = f + elif "features.tsv.gz" in f: file_map["features"] = f + elif "barcodes.tsv.gz" in f: file_map["barcodes"] = f + elif "scalefactors_json.json.gz" in f: file_map["scalefactors"] = f + elif "tissue_hires_image.png.gz" in f: file_map["hires"] = f + elif "tissue_lowres_image.png.gz" in f: file_map["lowres"] = f + elif "tissue_positions_list.csv.gz" in f: file_map["positions"] = f + + if len(file_map) < 7: + log(f"Error: Missing files for {gsm_id}: {list(file_map.keys())}") + return False + + # Unzip to temp + unzip_file(Path(INPUT_DIR) / file_map["matrix"], tmp_path / "matrix.mtx") + unzip_file(Path(INPUT_DIR) / file_map["features"], tmp_path / "features.tsv") + unzip_file(Path(INPUT_DIR) / file_map["barcodes"], tmp_path / "barcodes.tsv") + unzip_file(Path(INPUT_DIR) / file_map["scalefactors"], spatial_dir / "scalefactors_json.json") + unzip_file(Path(INPUT_DIR) / file_map["hires"], spatial_dir / "tissue_hires_image.png") + unzip_file(Path(INPUT_DIR) / file_map["lowres"], spatial_dir / "tissue_lowres_image.png") + unzip_file(Path(INPUT_DIR) / file_map["positions"], spatial_dir / "tissue_positions_list.csv") + + # Manual Visium reconstruction + log(f"Reading Count Matrix for {gsm_id}...") + adata = sc.read_mtx(tmp_path / "matrix.mtx").T + genes = pd.read_csv(tmp_path / "features.tsv", header=None, sep='\t') + adata.var_names = genes[1].values + adata.var['gene_ids'] = genes[0].values + adata.var_names_make_unique() + adata.obs_names = pd.read_csv(tmp_path / "barcodes.tsv", header=None)[0].values + + log(f"Loading Spatial Metadata for {gsm_id}...") + positions = pd.read_csv(spatial_dir / "tissue_positions_list.csv", header=None, index_col=0) + # barcode, in_tissue, array_row, array_col, pxl_row_in_fullres, pxl_col_in_fullres + positions.columns = ['in_tissue', 'array_row', 'array_col', 'pxl_row_in_fullres', 'pxl_col_in_fullres'] + + # Align positions with barcodes + adata.obs = adata.obs.join(positions) + + # Load images and scalefactors + with open(spatial_dir / "scalefactors_json.json") as f: + scalefactors = json.load(f) + + # SOTA V2 Coordinates Mandate: x/y MUST be fullres pixels OF THE WSI IMAGE. + # In this case, we are using tissue_hires_image.png as WSI (the only one we have). + # So we MUST scale the 'pxl_col_in_fullres' down to the hires image coordinates. + scale_factor = scalefactors['tissue_hires_scalef'] +import fit_scaling + +... + + # ENFORCE UNITY LAW: x == pxl_col_in_fullres + # We start with the nominal scale factor + scale_factor = scalefactors['tissue_hires_scalef'] + + # SOTA E4: Heuristic Fit Scaling to minimize spillover + log(f"Optimizing alignment via heuristic fit for {gsm_id}...") + # We need a thumbnail/lowres for fit_scaling to be fast + # But the tool can take hires if needed. + # We use the tissue_hires_image.png as WSI. + try: + optimized_scale = fit_scaling.heuristic_fit_scaling( + adata.obs['pxl_col_in_fullres'].values, + adata.obs['pxl_row_in_fullres'].values, + str(spatial_dir / "tissue_hires_image.png"), + initial_scale=scale_factor + ) + if abs(optimized_scale - scale_factor) / scale_factor < 0.05: + log(f"Heuristic fit successful: {scale_factor} -> {optimized_scale}") + scale_factor = optimized_scale + else: + log(f"Heuristic fit suggested too large a change ({optimized_scale}). Sticking to nominal.") + except Exception as e: + log(f"Heuristic fit failed: {e}. Using nominal scale.") + + adata.obs['pxl_col_in_fullres'] = adata.obs['pxl_col_in_fullres'] * scale_factor + adata.obs['pxl_row_in_fullres'] = adata.obs['pxl_row_in_fullres'] * scale_factor + adata.obs['x'] = adata.obs['pxl_col_in_fullres'] + adata.obs['y'] = adata.obs['pxl_row_in_fullres'] + adata.obsm['spatial'] = adata.obs[['x', 'y']].values + + # Load images + hires_img = mpimg.imread(str(spatial_dir / "tissue_hires_image.png")) + lowres_img = mpimg.imread(str(spatial_dir / "tissue_lowres_image.png")) + + library_id = gsm_id + adata.uns['spatial'] = { + library_id: { + 'images': { + 'hires': hires_img, + 'lowres': lowres_img + }, + 'scalefactors': scalefactors, + 'metadata': {} + } + } + + log(f"Standardizing metadata for {gsm_id}...") + # Metadata + for k, v in METADATA.items(): + adata.uns[k] = v + adata.obs[k] = v + + log(f"Saving H5AD for {gsm_id}...") + adata.write_h5ad(sample_dir / "spatial.h5ad") + + # H&E WSI - V2 Standard requires wsi.tif + log(f"Saving WSI as tif for {gsm_id}...") + # We use PIL to save as TIF to avoid missing 'convert' command + img = Image.open(spatial_dir / "tissue_hires_image.png") + img.save(sample_dir / "wsi.tif") + + # Success sentinel + (sample_dir / ".standardization_success").touch() + log(f"Successfully processed {gsm_id}") + return True + + except Exception as e: + log(f"Error processing {gsm_id}: {str(e)}") + import traceback + log(traceback.format_exc()) + return False + +def main(): + log(f"Starting standardization for {GSE_ID}...") + import re + gsm_pattern = re.compile(r'(GSM\d+)') + all_files = os.listdir(INPUT_DIR) + gsms = {} + for f in all_files: + m = gsm_pattern.match(f) + if m: + gsm_id = m.group(1) + if gsm_id not in gsms: gsms[gsm_id] = [] + gsms[gsm_id].append(f) + + log(f"Found {len(gsms)} GSM samples.") + + # Maximize core usage as per SOTA mandate + with ThreadPoolExecutor(max_workers=128) as executor: + gsm_ids = sorted(gsms.keys()) + results = list(executor.map(lambda g: process_gsm(g, gsms[g]), gsm_ids)) + + success_count = sum(results) + log(f"Standardization Final Report: {success_count}/{len(gsms)} samples successful.") + + # Register results + try: + registry_utils.update_registry(GSE_ID, "Success" if success_count > 0 else "Failed") + except Exception as e: + log(f"Warning: Could not update registry: {e}") + +if __name__ == "__main__": + main()