├── ISS_Anduril_Pipeline_Example.scala ├── LICENSE ├── README.md ├── decoding_pipelines ├── 1442_OB.scala ├── 1442_hippo.scala ├── 161230_161220_hippo_3_1.scala └── 170315_161220_hippo_4_1.scala ├── notebooks ├── 40xvs20x_analysis.ipynb ├── AllenBrainAtlas_analysis.ipynb ├── DE_analysis.R ├── GraphISS_pipeline.ipynb ├── Morphological_Analysis.ipynb ├── NMF_analysis.ipynb ├── SpatialDE_analysis.ipynb ├── queryAllenBrainAtlas.ipynb └── spatial_analysis.ipynb ├── pgm_pipeline ├── README.md ├── basecalling │ ├── __init__.py │ ├── pgm │ │ ├── __init__.py │ │ └── max_flow_min_cost.py │ └── pgm_basecalling.py └── main.py ├── prePro_pipeline ├── README.md ├── functions │ ├── candidates_extraction.py │ ├── execute_correspondences_create_inputs.py │ ├── find_correspondences_create_inputs.py │ ├── parameters_map.py │ └── registration.py ├── main.py ├── mainReg.py ├── network │ ├── get_proba_DNN.py │ ├── model_FT3.json │ └── model_FT3_weights └── norm.py ├── prePro_pipeline_3D ├── functions │ ├── candidates_extraction.py │ ├── execute_correspondences_create_inputs.py │ ├── find_correspondences_create_inputs.py │ ├── parameters_map.py │ └── registration.py ├── main.py ├── mainReg.py ├── network │ ├── get_proba_DNN.py │ ├── model_FT3.json │ └── model_FT3_weights └── norm.py └── wiki └── Build-and-install-SimpleElastix.md /ISS_Anduril_Pipeline_Example.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wahlby-lab/graph-iss/HEAD/ISS_Anduril_Pipeline_Example.scala -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wahlby-lab/graph-iss/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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