├── 1 - Data Preparation.ipynb ├── 2A - Discrete Shape Analysis.ipynb ├── 2B - Continuous Shape Analysis.ipynb ├── 3 - Shape Embeddings.ipynb ├── LICENSE ├── README.md ├── data ├── C. elegans │ ├── 1649_1109_0003_Amp5-1_B_20070424_A23_w1_081248D4-0AB4-4063-8157-8EC25863447E.tif │ ├── 1649_1109_0003_Amp5-1_B_20070424_A23_w2_71C5704E-F745-4D29-B3B2-51216C02A45D.tif │ ├── 1649_1109_0003_Amp5-1_B_20070424_B07_w1_3474AF91-8AE9-4340-AEA0-BC54ECA6A43E.tif │ ├── 1649_1109_0003_Amp5-1_B_20070424_B07_w2_F3BB43AA-D215-44C1-B2FD-A89741699E5F.tif │ ├── B07_06_ground_truth.png │ ├── labels.npy │ ├── point_models.npy │ └── spline_models.npy └── MEF_LMNA │ ├── lmna_deficient │ └── raw_images │ │ ├── xy001c1.tif │ │ └── xy001c2.tif │ ├── mef_data.npy │ ├── wildtype │ └── raw_images │ │ ├── xy001c1.tif │ │ └── xy001c2.tif │ └── xy001c1_instances.h5 ├── env_wo_gpu.yml ├── shape_embeddings ├── criterion.py ├── data_handling.py ├── main.py ├── model.py └── utils.py ├── shapeanalysis101_env.yml ├── solutions ├── [Solution] 1 - Data Preparation .ipynb ├── [Solution] 2A - Discrete Shape Analysis.ipynb ├── [Solution] 2B - Continuous Shape Analysis.ipynb └── [Solution] 3 - Shape Embeddings.ipynb └── spline_models ├── .DS_Store ├── spline_curve_model.py └── spline_shape_space.py /1 - Data Preparation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uhlmanngroup/shapeanalysis101/HEAD/1 - Data Preparation.ipynb -------------------------------------------------------------------------------- /2A - Discrete Shape Analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uhlmanngroup/shapeanalysis101/HEAD/2A - Discrete Shape Analysis.ipynb -------------------------------------------------------------------------------- /2B - Continuous Shape Analysis.ipynb: -------------------------------------------------------------------------------- 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