Add example folder and update readme

brunopalau · Nov 18, 2022 · 347d57e · 347d57e
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diff --git a/example_experiment/cell_classification/CellTypes/cells/example.npz b/example_experiment/cell_classification/CellTypes/cells/example.npz
diff --git a/example_experiment/cell_classification/CellTypes/cells2labels/example.npz b/example_experiment/cell_classification/CellTypes/cells2labels/example.npz
diff --git a/example_experiment/cell_classification/CellTypes/data/images/example.npz b/example_experiment/cell_classification/CellTypes/data/images/example.npz
diff --git a/example_experiment/cell_classification/channels.txt b/example_experiment/cell_classification/channels.txt
@@ -0,0 +1,25 @@
+CD4
+CD8
+CD20
+CD14
+CD68
+CD206
+CD11c
+CD21
+CD3
+CD56
+Granzyme B
+CD163
+Foxp3
+S100A9-Calprotectin
+CD45RA
+CD45RO
+CCR7
+MelanA
+SOX10
+CD45
+CD31
+SMA
+MECA-79
+COL1A1
+DC-SIGN
diff --git a/example_experiment/cell_classification/config.json b/example_experiment/cell_classification/config.json
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+{"crop_input_size": 60, "crop_size": 128, "root_dir": "./example_experiment/cell_classification/", "train_set": ["example"], "val_set": ["example"], "num_classes": 26, "epoch_max": 50, "lr": 0.001, "blacklist": [], "channels_path": "./example_experiment/cell_classification/channels.txt", "weight_to_eval": "", "sample_batch": true, "hierarchy_match": {"0": "B cell", "1": "Myeloid", "2": "Myeloid", "3": "Myeloid", "4": "B cell", "5": "Myeloid", "6": "T cell", "7": "T cell", "8": "Myeloid", "9": "T cell", "10": "other", "11": "other", "12": "Myeloid", "13": "Myeloid", "14": "B cell", "15": "other", "16": "other", "17": "Myeloid", "18": "T cell", "19": "Myeloid", "20": "Myeloid", "21": "Myeloid", "22": "other", "23": "T cell", "24": "other", "25": "tumor"}, "size_data": 10, "aug": true}
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		{"crop_input_size": 60, "crop_size": 128, "root_dir": "./example_experiment/cell_classification/", "train_set": ["example"], "val_set": ["example"], "num_classes": 26, "epoch_max": 50, "lr": 0.001, "blacklist": [], "channels_path": "./example_experiment/cell_classification/channels.txt", "weight_to_eval": "", "sample_batch": true, "hierarchy_match": {"0": "B cell", "1": "Myeloid", "2": "Myeloid", "3": "Myeloid", "4": "B cell", "5": "Myeloid", "6": "T cell", "7": "T cell", "8": "Myeloid", "9": "T cell", "10": "other", "11": "other", "12": "Myeloid", "13": "Myeloid", "14": "B cell", "15": "other", "16": "other", "17": "Myeloid", "18": "T cell", "19": "Myeloid", "20": "Myeloid", "21": "Myeloid", "22": "other", "23": "T cell", "24": "other", "25": "tumor"}, "size_data": 10, "aug": true}