├── CeLEry_package ├── CeLEry │ ├── ClusterVAE.py │ ├── DNN.py │ ├── TrainerExe.py │ ├── __init__.py │ ├── __pycache__ │ │ ├── ClusterVAE.cpython-36.pyc │ │ ├── ClusterVAE.cpython-38.pyc │ │ ├── DNN.cpython-36.pyc │ │ ├── DNN.cpython-38.pyc │ │ ├── SpaCluster.cpython-36.pyc │ │ ├── TrainerExe.cpython-38.pyc │ │ ├── VanillaVAE.cpython-36.pyc │ │ ├── __init__.cpython-36.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── autoencoder.cpython-36.pyc │ │ ├── data_augmentation.cpython-38.pyc │ │ ├── datasetgenemap.cpython-36.pyc │ │ ├── datasetgenemap.cpython-38.pyc │ │ ├── fit_functions.cpython-38.pyc │ │ ├── type_.cpython-36.pyc │ │ ├── types_.cpython-36.pyc │ │ ├── types_.cpython-38.pyc │ │ ├── util.cpython-36.pyc │ │ ├── util.cpython-38.pyc │ │ ├── util_Mouse.cpython-36.pyc │ │ └── util_Mouse.cpython-38.pyc │ ├── data_augmentation.py │ ├── datasetgenemap.py │ ├── fit_functions.py │ ├── layers.py │ ├── types_.py │ ├── util.py │ └── util_Mouse.py ├── CeLEryPy.egg-info │ ├── PKG-INFO │ ├── SOURCES.txt │ ├── dependency_links.txt │ ├── requires.txt │ └── top_level.txt ├── LICENSE ├── README.md ├── dist │ ├── CeLEryPy-1.2.1-py3-none-any.whl │ └── CeLEryPy-1.2.1.tar.gz ├── pyproject.toml └── setup.py ├── LICENSE ├── README.md ├── code_paper ├── 1_LIBD │ ├── CeLEry_train_Scenario1and2.py │ ├── CeLEry_train_Scenario3and4.py │ ├── LIBDVisual.R │ ├── LIBDacc.R │ ├── README.md │ ├── prediction.py │ └── preprocess.py ├── 2_Alzheimer │ ├── CeLEry_train.py │ ├── README.md │ ├── preprocess.py │ └── test.py ├── 3_Mouse_10x_Visium │ ├── Mouse_CeLEry.ipynb │ ├── Mouse_Tangram.ipynb │ ├── Mouse_novosparc.ipynb │ └── Mouse_spotOTsc.ipynb ├── 4_Mouse_brain_MERFISH │ ├── CeLEry_brain.ipynb │ ├── CeLEry_figure 6_scenario 2.ipynb │ ├── CeLEry_figure 6_scenario 3.ipynb │ ├── README.md │ ├── SpaOTsc_brain.ipynb │ ├── Tangram_brain.ipynb │ ├── brain_result.ipynb │ └── novoSpaRc_brain.ipynb ├── 5_liver_MERFISH │ ├── CeLEry_liver.ipynb │ ├── README.md │ ├── SpaOTsc_liver.ipynb │ ├── Tangram_liver.ipynb │ ├── liver_result.ipynb │ └── novoSpaRc_liver.ipynb ├── 6_breast_cancer_10x_Xenium │ ├── 2D_locationRecovery │ │ ├── Xenium_BreastCancer_CELERY_Rep1_Scheme4_2DRecovery.ipynb │ │ ├── Xenium_BreastCancer_Tangram_Rep1_Scheme4_2DRecovery.ipynb │ │ ├── Xenium_BreastCancer_novosparc_Rep1_Scheme4_2DRecovery.ipynb │ │ └── Xenium_BreastCancer_spaOTsc_Rep1_Scheme4_2DRecovery.ipynb │ └── Domain_prediction │ │ ├── Xenium_BreastCancer_CELEREY_Scheme2_domainPred.ipynb │ │ ├── Xenium_BreastCancer_novosparc_Rep1_Scheme2_domainPred.ipynb │ │ ├── Xenium_BreastCancer_spaOTsc_Rep1_Scheme2_domainPred.ipynb │ │ └── Xenium_BreastCancer_tangram_Scheme2_domainPred.ipynb ├── 7_data_augmentation │ └── CeLEry-data-agumentation.ipynb └── 8_mouse_single_cell_prediction │ ├── Mouse_sc_analysis.py │ ├── Mouse_sc_analysis_spaOTsc_novosparc.ipynb │ ├── analysis-results.py │ └── preprocessing.py ├── docs └── asserts │ └── images │ └── workflow.png ├── pretrainmodel └── Biogen │ ├── 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