AnoushkaJain3
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Update README.md
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README.md
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@@ -31,26 +31,30 @@ There are two tutorial notebooks:
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2. load your sorting depending on the spike sorter you used to create the 'sorting' object
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3. Then you can create a Sorting_Analyzer object and you compute quality metrics.
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auto_label_units is the main in this notebook.
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(https://spikeinterface--2918.org.readthedocs.build/en/2918/api.html#spikeinterface.curation.auto_label_units)
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from spikeinterface.curation import auto_label_units
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labels = auto_label_units(
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sorting_analyzer = sorting_analyzer,
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model_folder = “SpikeInterface/a_folder_for_a_model”,
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trusted = [‘numpy.dtype’])
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If you have your own manually curated data (e.g., from other species), this notebook allows you to train a new model using your specific data.
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from spikeinterface.curation.train_manual_curation import train_model
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trainer = train_model(mode = "analyzers",
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output_folder = str(output_folder),
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imputation_strategies = None,
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scaling_techniques = None,
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classifiers = None
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# "LogisticRegression", "MLPClassifier", "XGBoost", "LightGBM", "CatBoost"]
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Acknowledgments:
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2. load your sorting depending on the spike sorter you used to create the 'sorting' object
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3. Then you can create a Sorting_Analyzer object and you compute quality metrics.
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auto_label_units is the main in this notebook. API link to know the parameters:
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(https://spikeinterface--2918.org.readthedocs.build/en/2918/api.html#spikeinterface.curation.auto_label_units)
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from spikeinterface.curation import auto_label_units
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labels = auto_label_units(
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sorting_analyzer = sorting_analyzer,
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model_folder = “SpikeInterface/a_folder_for_a_model”,
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trusted = [‘numpy.dtype’])
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2. Train_new_model.ipynb
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If you have your own manually curated data (e.g., from other species), this notebook allows you to train a new model using your specific data.
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Here you need to follow the three steps mentioned before but you need to provide your manually curated labels.
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train_model is the main function to do train your model. API Link:
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https://spikeinterface--2918.org.readthedocs.build/en/2918/api.html#spikeinterface.curation.train_model
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from spikeinterface.curation.train_manual_curation import train_model
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trainer = train_model(mode = "analyzers",
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output_folder = str(output_folder),
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imputation_strategies = None,
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scaling_techniques = None,
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classifiers = None) # Default to Random Forest only. Other classifiers you can try [ "AdaBoostClassifier", "GradientBoostingClassifier",
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# "LogisticRegression", "MLPClassifier", "XGBoost", "LightGBM", "CatBoost"]
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Acknowledgments:
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