{"id":66395,"date":"2026-11-11T09:35:46","date_gmt":"2026-11-11T01:35:46","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=66395"},"modified":"2026-11-11T09:35:46","modified_gmt":"2026-11-11T01:35:46","slug":"spalp-million-cell-spatial-omics-gpu-memory","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/spalp-million-cell-spatial-omics-gpu-memory\/","title":{"rendered":"212\u4e07\u7ec6\u80de\u53ea\u8dd162\u79d2\uff1fSpaLP\u544a\u8bc9\u4f60\uff1a\u7a7a\u95f4\u7ec4\u5b66\u663e\u5b58\u4e0d\u80fd\u53ea\u6309\u7ec6\u80de\u6570\u4f30"},"content":{"rendered":"
\n

Xenium\u3001CosMx\u3001Stereo-seq\u548cCODEX\u628a\u7a7a\u95f4\u7ec4\u5b66\u63a8\u5230\u767e\u4e07\u7ec6\u80de\u540e\uff0c\u8bb8\u591a\u8bfe\u9898\u7ec4\u9047\u5230\u7684\u7b2c\u4e00\u4e2a\u95ee\u9898\u5df2\u4e0d\u662f\u201c\u80fd\u4e0d\u80fd\u753b\u56fe\u201d\uff0c\u800c\u662f\u90bb\u5c45\u56fe\u6784\u5efa\u3001\u7279\u5f81\u77e9\u9635\u548c\u5d4c\u5165\u8bad\u7ec3\u80fd\u5426\u5728\u6709\u9650\u663e\u5b58\u4e2d\u7a33\u5b9a\u5b8c\u6210\u3002\u66f4\u5bb9\u6613\u8e29\u5751\u7684\u662f\uff1a\u770b\u5230\u67d0\u4e2a\u767e\u4e07\u7ec6\u80de\u6848\u4f8b\u53ea\u7528\u4e86\u5341\u51e0GB\u663e\u5b58\uff0c\u5c31\u6309\u7ec6\u80de\u6570\u7ebf\u6027\u5916\u63a8\u81ea\u5df1\u7684\u9879\u76ee\uff0c\u7ed3\u679c\u7ec6\u80de\u66f4\u5c11\u5374\u5148\u7206\u663e\u5b58\u3002<\/p>\n

2026\u5e74\u9884\u5370\u672c\u65b9\u6cd5SpaLP\uff08Spatial Local Pooling\uff09\u9488\u5bf9\u8d85\u5927\u89c4\u6a21\u7a7a\u95f4\u7ec4\u5b66\u5d4c\u5165\uff0c\u652f\u6301\u7a7a\u95f4\u56fe\u8c31\u6784\u5efa\u3001niche\u8bc6\u522b\u3001\u8868\u8fbe\u91cd\u5efa\u3001\u591a\u5207\u7247\u6574\u5408\u3001\u8de8\u5e73\u53f0\u53ca\u591a\u7ec4\u5b66\u6574\u5408\u3002\u5b98\u65b9\u4ed3\u5e93\u516c\u5e03\u4e86\u9010\u6570\u636e\u96c6\u8d44\u6e90\u8868\uff1a212.8\u4e07\u7ec6\u80de\u3001329\u4e2a\u7279\u5f81\u7684\u8de8\u5e73\u53f0\u4efb\u52a1\uff0c\u5728NVIDIA A800 80GB\u4e0a\u5cf0\u503c\u663e\u5b5821.96GB\u3001CPU\u5185\u5b5836GB\u3001\u8fd0\u884c\u7ea662\u79d2\uff1b\u800c123.6\u4e07\u7ec6\u80de\u30011000\u4e2a\u57fa\u56e0\u7684CosMx\u4efb\u52a1\u53cd\u800c\u4f7f\u752830.15GB\u663e\u5b58\u3002\u8fd9\u6b63\u8bf4\u660e\u8d44\u6e90\u7531\u201c\u7ec6\u80de\u6570\u00d7\u7279\u5f81\u6570\u00d7\u90bb\u5c45\u56fe\u201d\u5171\u540c\u51b3\u5b9a\u3002<\/p>\n

\"SpaLP\u767e\u4e07\u7ea7\u7a7a\u95f4\u7ec4\u5b66\u8d44\u6e90\u89c4\u5212\u6d77\u62a5\"
SpaLP\u8d44\u6e90\u5224\u65ad\uff1a\u7ec6\u80de\u6570\u3001\u7279\u5f81\u6570\u4e0e\u90bb\u5c45\u56fe\u5fc5\u987b\u4e00\u8d77\u6d4b\u91cf\u3002<\/figcaption><\/figure>\n

\u5b98\u65b9\u8d44\u6e90\u8868\u91cc\u6700\u503c\u5f97\u770b\u7684\u56db\u7ec4\u6570\u5b57<\/h2>\n
\n\n\n\n\n\n\n\n\n
\u6570\u636e\u573a\u666f<\/th>\n\u7ec6\u80de\/\u70b9\u4f4d<\/th>\n\u8f93\u5165\u7279\u5f81<\/th>\n\u5cf0\u503c\u663e\u5b58<\/th>\n\u8fd0\u884c\u65f6\u95f4<\/th>\n<\/tr>\n<\/thead>\n
\u8de8\u5e73\u53f0\u6574\u5408<\/td>\n2,127,707<\/td>\n329\u57fa\u56e0<\/td>\n21.96GB<\/td>\n1\u520602\u79d2<\/td>\n<\/tr>\n
CosMx<\/td>\n1,236,281<\/td>\n1,000\u57fa\u56e0<\/td>\n30.15GB<\/td>\n1\u520603\u79d2<\/td>\n<\/tr>\n
Xenium<\/td>\n1,355,849<\/td>\n379\u57fa\u56e0<\/td>\n15.89GB<\/td>\n47\u79d2<\/td>\n<\/tr>\n
CODEX<\/td>\n1,395,992<\/td>\n43\u86cb\u767d<\/td>\n5.29GB<\/td>\n25\u79d2<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u8fd9\u4e9b\u7ed3\u679c\u6765\u81eaA800-SXM4-80GB\u548c32\u6838Xeon Platinum 8462Y+\uff0c\u5e76\u975e\u6240\u6709GPU\u7684\u56fa\u5b9a\u8868\u73b0\u3002\u76f8\u540c\u7ec6\u80de\u89c4\u6a21\u4e0b\uff0c\u8f93\u5165\u7279\u5f81\u4ece43\u4e2a\u86cb\u767d\u589e\u52a0\u5230\u6570\u767e\u6216\u4e0a\u5343\u57fa\u56e0\uff0c\u7279\u5f81\u77e9\u9635\u3001\u68af\u5ea6\u4e0e\u4e2d\u95f4\u5f20\u91cf\u90fd\u4f1a\u653e\u5927\uff1bKNN\u53c2\u6570\u548c\u5207\u7247\u6570\u91cf\u4e5f\u4f1a\u5f71\u54cd\u7a7a\u95f4\u90bb\u63a5\u53ca\u6279\u6b21\u6574\u5408\u6210\u672c\u3002\u4e0d\u80fd\u53ea\u95ee\u201c\u6709\u591a\u5c11\u7ec6\u80de\u201d\uff0c\u8fd8\u8981\u540c\u65f6\u95ee\u201c\u6bcf\u4e2a\u7ec6\u80de\u4fdd\u7559\u591a\u5c11\u7279\u5f81\u3001\u5efa\u591a\u5c11\u90bb\u5c45\u3001\u6574\u5408\u591a\u5c11\u6279\u6b21\u201d\u3002<\/p>\n

\u5148\u628a\u8f93\u5165\u5bf9\u8c61\u505a\u5bf9\uff0c\u518d\u8c08GPU<\/h2>\n

SpaLP\u63a5\u6536AnnData\u5bf9\u8c61\uff0c\u4e8c\u7ef4\u5750\u6807\u5fc5\u987b\u653e\u5728adata.obsm['spatial']<\/code>\uff0c\u9884\u5904\u7406\u540e\u7684\u7279\u5f81\u77e9\u9635\u653e\u5728adata.obsm['feat']<\/code>\u3002\u539f\u59cbcount\u5efa\u8bae\u5148\u603b\u91cf\u5f52\u4e00\u5316\u3001log1p<\/code>\u548cscale\uff1b\u5df2\u7ecf\u5bf9\u6570\u8f6c\u6362\u7684\u8868\u8fbe\u6216\u86cb\u767d\u6570\u636e\u53ea\u9700\u6309\u6559\u7a0b\u8fdb\u884cscale\u3002\u5bf9\u4e8e\u8d85\u8fc73000\u57fa\u56e0\u7684\u5e73\u53f0\uff0c\u5b98\u65b9\u5efa\u8bae\u9009\u62e9\u524d2000\u62163000\u4e2a\u9ad8\u53d8\u57fa\u56e0\uff1b\u5c0f\u4e8e2000\u57fa\u56e0\u7684\u9776\u5411\u9762\u677f\u5219\u53ef\u4fdd\u7559\u5168\u90e8\u57fa\u56e0\u3002<\/p>\n

import scanpy as sc\r\nimport SpaLP\r\n\r\nadata = sc.read_h5ad("sample.h5ad")\r\nassert "spatial" in adata.obsm\r\n\r\nsc.pp.highly_variable_genes(adata, n_top_genes=2000, flavor="seurat_v3")\r\nadata = adata[:, adata.var.highly_variable].copy()\r\nsc.pp.normalize_total(adata, inplace=True)\r\nsc.pp.log1p(adata)\r\nsc.pp.scale(adata)\r\nadata.obsm["feat"] = adata.X\r\n\r\nprint(adata.n_obs, adata.n_vars, adata.obsm["spatial"].shape)\r\n<\/code><\/pre>\n
\u771f\u6b63\u8fd0\u884c\u524d\u8fd8\u5e94\u68c0\u67e5\u5750\u6807\u662f\u5426\u542b\u7f3a\u5931\u503c\u3001\u7ec6\u80deID\u662f\u5426\u552f\u4e00\u3001\u4e0d\u540c\u5207\u7247\u7684\u5750\u6807\u5355\u4f4d\u662f\u5426\u4e00\u81f4\u3001\u7a00\u758f\u77e9\u9635\u6709\u6ca1\u6709\u88ab\u65e0\u610f\u8f6c\u6210dense\u3002\u767e\u4e07\u7ec6\u80de\u00d72000\u57fa\u56e0\u82e5\u4ee5float32\u7a20\u5bc6\u5b58\u50a8\uff0c\u5355\u4e2a\u77e9\u9635\u7406\u8bba\u4e0a\u5c31\u63a5\u8fd18GB\uff0c\u590d\u5236\u3001\u6807\u51c6\u5316\u548c\u5199\u56deobsm<\/code>\u4f1a\u4ea7\u751f\u989d\u5916\u5cf0\u503c\uff1b\u8fd9\u4e5f\u662f\u201c\u6a21\u578b\u663e\u5b58\u591f\u4e86\uff0cPython\u8fdb\u7a0b\u5374\u88ab\u7cfb\u7edf\u6740\u6389\u201d\u7684\u5e38\u89c1\u539f\u56e0\u3002<\/p>\n
\u4e00\u5957\u53ef\u6267\u884c\u7684\u8d44\u6e90\u753b\u50cf\u65b9\u6cd5<\/h2>\n
\u4e0d\u8981\u76f4\u63a5\u628a\u5168\u91cf\u6570\u636e\u9001\u4e0aGPU\u3002\u5148\u4ece10\u4e07\u300150\u4e07\u548c100\u4e07\u7ec6\u80de\u505a\u4e09\u7ea7\u62bd\u6837\uff0c\u4fdd\u6301\u771f\u5b9e\u5e73\u53f0\u6bd4\u4f8b\u548c\u7ec4\u7ec7\u533a\u57df\uff0c\u5206\u522b\u8bb0\u5f55\u9884\u5904\u7406\u5cf0\u503c\u5185\u5b58\u3001KNN\u65f6\u95f4\u3001GPU\u5cf0\u503c\u3001\u8bad\u7ec3\u65f6\u95f4\u548c\u8f93\u51fa\u5927\u5c0f\u3002\u968f\u540e\u56fa\u5b9a\u7ec6\u80de\u6570\uff0c\u628a\u7279\u5f81\u6570\u4ece500\u63d0\u9ad8\u52301000\u30012000\uff0c\u89c2\u5bdf\u663e\u5b58\u589e\u957f\uff1b\u6700\u540e\u518d\u6539\u53d8KNN\u7684k\u503c\u3002\u53ea\u6709\u628a\u4e09\u4e2a\u7ef4\u5ea6\u62c6\u5f00\uff0c\u624d\u80fd\u77e5\u9053\u74f6\u9888\u6765\u81ea\u7ec6\u80de\u3001\u7279\u5f81\u8fd8\u662f\u56fe\u7ed3\u6784\u3002<\/p>\n
\u5efa\u8bae\u7528\/usr\/bin\/time -v<\/code>\u8bb0\u5f55CPU\u5185\u5b58\uff0c\u7528nvidia-smi --query-compute-apps=used_memory<\/code>\u5b9a\u65f6\u91c7\u6837\u663e\u5b58\uff0c\u5e76\u4fdd\u5b58\u8f6f\u4ef6\u7248\u672c\u3001\u968f\u673a\u79cd\u5b50\u3001\u8f93\u5165h5ad\u6821\u9a8c\u503c\u548c\u6700\u7ec8\u53c2\u6570\u3002\u82e5\u663e\u5b58\u4e0d\u8db3\uff0c\u53ef\u4ee5\u51cf\u5c11\u9ad8\u53d8\u57fa\u56e0\u6570\u91cf\u3001\u964d\u4f4e\u5355\u6b21\u6574\u5408\u89c4\u6a21\u6216\u8f6cCPU\u9a8c\u8bc1\u6d41\u7a0b\uff1b\u4f46\u964d\u7ef4\u548c\u62c6\u6279\u4f1a\u5f71\u54cd\u751f\u7269\u5b66\u5206\u8fa8\u7387\u4e0e\u8de8\u5207\u7247\u5173\u7cfb\uff0c\u4e0d\u80fd\u53ea\u4e3a\u201c\u8dd1\u901a\u201d\u800c\u4e0d\u505a\u7ed3\u679c\u5bf9\u7167\u3002<\/p>\n
\u4e0d\u80fd\u5ffd\u89c6h5ad\u4e4b\u5916\u7684\u4e34\u65f6\u7a7a\u95f4<\/h2>\n
\u7a7a\u95f4\u6570\u636e\u4ece\u539f\u59cb\u77e9\u9635\u5230\u6a21\u578b\u8f93\u5165\u901a\u5e38\u4f1a\u7ecf\u5386\u8fc7\u6ee4\u3001\u5f52\u4e00\u5316\u3001\u9ad8\u53d8\u57fa\u56e0\u9009\u62e9\u3001scale\u548c\u90bb\u5c45\u641c\u7d22\u3002\u6bcf\u4e00\u6b65\u90fd\u53ef\u80fd\u4ea7\u751f\u526f\u672c\uff0c\u5c24\u5176\u662f\u628a\u7a00\u758f\u77e9\u9635\u5199\u5165obsm['feat']<\/code>\u6216\u8c03\u7528\u4f1a\u8fd4\u56dedense\u7ed3\u679c\u7684\u51fd\u6570\u65f6\u3002\u670d\u52a1\u5668\u78c1\u76d8\u89c4\u5212\u5e94\u540c\u65f6\u8003\u8651\u539f\u59cbh5ad\u3001\u5904\u7406\u540eh5ad\u3001\u4e34\u65f6\u77e9\u9635\u3001\u6a21\u578b\u8f93\u51fa\u4e0e\u65e5\u5fd7\uff0c\u4e0d\u80fd\u6309\u6700\u7ec8\u6587\u4ef6\u5927\u5c0f\u4e00\u6bd4\u4e00\u5206\u914d\u3002\u5efa\u8bae\u628a\u53ea\u8bfb\u539f\u59cb\u6570\u636e\u653e\u5728\u5bb9\u91cf\u76d8\uff0c\u628a\u53ef\u91cd\u5efa\u7f13\u5b58\u548c\u4e34\u65f6\u5bf9\u8c61\u653e\u5728\u672c\u5730NVMe\uff0c\u5e76\u7ed9\u6bcf\u4e2a\u4efb\u52a1\u72ec\u7acb\u76ee\u5f55\u3002<\/p>\n
\u591a\u5207\u7247\u6574\u5408\u8fd8\u8981\u9632\u6b62\u6837\u672c\u4e0d\u5747\u8861\u3002\u4e00\u5f20\u5207\u7247\u6709100\u4e07\u7ec6\u80de\uff0c\u53e6\u5916\u51e0\u5f20\u53ea\u6709\u6570\u4e07\u7ec6\u80de\u65f6\uff0c\u7b80\u5355\u968f\u673a\u62bd\u6837\u4f1a\u8ba9\u5927\u5207\u7247\u4e3b\u5bfc\u8d44\u6e90\u6d4b\u8bd5\u548c\u5d4c\u5165\u7ed3\u6784\u3002\u4e09\u7ea7\u8bd5\u8dd1\u5e94\u6309\u5207\u7247\u3001\u533a\u57df\u4e0e\u7ec6\u80de\u7c7b\u578b\u5206\u5c42\u62bd\u6837\uff0c\u540c\u65f6\u8bb0\u5f55\u6bcf\u7247\u7ec6\u80de\u6570\u548c\u5750\u6807\u8303\u56f4\u3002\u6b63\u5f0f\u6574\u5408\u524d\uff0c\u5148\u5728\u5355\u5207\u7247\u4e0a\u9a8c\u8bc1\u8f93\u5165\u548c\u7a7a\u95f4\u90bb\u5c45\uff0c\u518d\u589e\u52a0\u8de8\u5207\u7247\u5173\u7cfb\uff1b\u8fd9\u6837\u51fa\u73b0\u5f02\u5e38\u65f6\uff0c\u624d\u80fd\u533a\u5206\u6570\u636e\u95ee\u9898\u3001\u56fe\u6784\u5efa\u95ee\u9898\u548c\u663e\u5b58\u95ee\u9898\u3002<\/p>\n
\u5982\u679c\u9700\u8981\u56e2\u961f\u591a\u4eba\u91cd\u590d\u5206\u6790\uff0c\u6700\u597d\u628a\u73af\u5883\u5199\u6210\u56fa\u5b9a\u7684Conda\u9501\u5b9a\u6587\u4ef6\u6216\u5bb9\u5668\uff0c\u8f93\u51fa\u4e2d\u4fdd\u7559pip freeze<\/code>\u3001\u4ee3\u7801\u63d0\u4ea4\u53f7\u4e0e\u53c2\u6570JSON\u3002Jupyter\u9002\u5408\u63a2\u7d22\uff0c\u4f46\u767e\u4e07\u7ec6\u80de\u6b63\u5f0f\u4efb\u52a1\u5e94\u7531\u811a\u672c\u6216\u8c03\u5ea6\u5668\u542f\u52a8\uff0c\u8bbe\u7f6e\u9000\u51fa\u7801\u3001\u65e5\u5fd7\u3001\u8d44\u6e90\u4e0a\u9650\u548c\u5b8c\u6210\u6807\u8bb0\uff0c\u907f\u514d\u6d4f\u89c8\u5668\u65ad\u5f00\u540e\u65e0\u6cd5\u5224\u65ad\u4efb\u52a1\u72b6\u6001\u3002<\/p>\n
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