{"metadata":{"kernelspec":{"language":"python","display_name":"Python 3","name":"python3"},"language_info":{"name":"python","version":"3.11.13","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"},"kaggle":{"accelerator":"gpu","dataSources":[],"dockerImageVersionId":31193,"isInternetEnabled":true,"language":"python","sourceType":"notebook","isGpuEnabled":true}},"nbformat_minor":4,"nbformat":4,"cells":[{"cell_type":"code","source":"!pip install -q monai pytorch-lightning albumentations imagecodecs ultralytics nnunetv2 nibabel tifffile \"opencv-python<4.11\" \"numpy==1.26.4\" \"scipy==1.15.3\"","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2025-12-30T20:20:09.087214Z","iopub.execute_input":"2025-12-30T20:20:09.087701Z","iopub.status.idle":"2025-12-30T20:21:44.110249Z","shell.execute_reply.started":"2025-12-30T20:20:09.087679Z","shell.execute_reply":"2025-12-30T20:21:44.109495Z"},"_kg_hide-output":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"!pip freeze > env.txt\n!grep -E \"torch|monai|albumentations|imagecodecs|ultralytics|nnunet|nibabel|tifffile\" env.txt > req.txt\n!cat req.txt","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2025-12-30T20:21:44.111625Z","iopub.execute_input":"2025-12-30T20:21:44.111891Z","iopub.status.idle":"2025-12-30T20:21:46.095390Z","shell.execute_reply.started":"2025-12-30T20:21:44.111854Z","shell.execute_reply":"2025-12-30T20:21:46.094502Z"},"_kg_hide-output":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"!pip wheel -r req.txt","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2025-12-30T20:21:46.096492Z","iopub.execute_input":"2025-12-30T20:21:46.096818Z","iopub.status.idle":"2025-12-30T20:23:33.423897Z","shell.execute_reply.started":"2025-12-30T20:21:46.096784Z","shell.execute_reply":"2025-12-30T20:23:33.423202Z"},"_kg_hide-output":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"!pip download -r req.txt","metadata":{"_uuid":"8f2839f25d086af736a60e9eeb907d3b93b6e0e5","_cell_guid":"b1076dfc-b9ad-4769-8c92-a6c4dae69d19","trusted":true,"execution":{"iopub.status.busy":"2025-12-30T20:23:33.425510Z","iopub.execute_input":"2025-12-30T20:23:33.425743Z","iopub.status.idle":"2025-12-30T20:24:38.331522Z","shell.execute_reply.started":"2025-12-30T20:23:33.425703Z","shell.execute_reply":"2025-12-30T20:24:38.330858Z"},"_kg_hide-output":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"!pip install -q https://github.com/MIC-DKFZ/Skeleton-Recall/archive/refs/heads/master.zip\n\n!pip freeze > env.txt\n!grep -E \"torch|monai|albumentations|imagecodecs|ultralytics|nnunet|nibabel|tifffile\" env.txt > req.txt\n!cat req.txt\n\n!pip wheel -r req.txt\n!pip download -r req.txt","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2025-12-30T20:24:38.332444Z","iopub.execute_input":"2025-12-30T20:24:38.332734Z","iopub.status.idle":"2025-12-30T20:26:39.564136Z","shell.execute_reply.started":"2025-12-30T20:24:38.332693Z","shell.execute_reply":"2025-12-30T20:26:39.563415Z"},"_kg_hide-input":true,"_kg_hide-output":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"!git clone https://github.com/MIC-DKFZ/Skeleton-Recall.git\n!python -m build Skeleton-Recall --outdir .\n!rm -rf Skeleton-Recall","metadata":{"trusted":true,"_kg_hide-input":true,"_kg_hide-output":true,"execution":{"iopub.status.busy":"2025-12-30T20:26:39.565079Z","iopub.execute_input":"2025-12-30T20:26:39.565344Z","iopub.status.idle":"2025-12-30T20:26:45.300831Z","shell.execute_reply.started":"2025-12-30T20:26:39.565305Z","shell.execute_reply":"2025-12-30T20:26:45.300020Z"}},"outputs":[],"execution_count":null},{"cell_type":"code","source":"!pip install -q \"nnunetv2==2.5\" -f . --no-index","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2025-12-30T20:26:45.301790Z","iopub.execute_input":"2025-12-30T20:26:45.302045Z","iopub.status.idle":"2025-12-30T20:26:48.893058Z","shell.execute_reply.started":"2025-12-30T20:26:45.302020Z","shell.execute_reply":"2025-12-30T20:26:48.892066Z"},"_kg_hide-input":true,"_kg_hide-output":true},"outputs":[],"execution_count":null}]}