...
Step 2.2 Create the augmented data using CDeep3M:https://github.com/slash-segmentation/Membrane_Myelin_Subtract/blob/main/getMembraneOnly.php
PreprocessTrainingData.py /myelin_images /myelin_labels /myelin_augmented
Con
Step 2.3 Create the training model:
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runprediction.sh --augspeed 10 --models 1fm ~/mem_retrain_out ~/em ~/membrane_predictions
Prediction:
Note that the prediction result contains the myelin layer.
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runprediction.sh --augspeed 10 --models 1fm ~/myelin_trainednet ~/em ~/myelin_predictions
Step 4 Subtract the myelin layer from the membrane prediction
Convert the membrane result to the binary format:
https://github.com/slash-segmentation/Membrane_Myelin_Subtract/blob/main/convert2Bin.php
Convert the myelin result to the binary format:
https://github.com/slash-segmentation/Membrane_Myelin_Subtract/blob/main/myelin2Bin.php
Invert the myelin binary result:
https://github.com/slash-segmentation/Membrane_Myelin_Subtract/blob/main/invertMyelin.php
Extract the membrane result without myelin:
https://github.com/slash-segmentation/Membrane_Myelin_Subtract/blob/main/getMembraneOnly.php
Create the membrane only overlay:
https://github.com/slash-segmentation/Membrane_Myelin_Subtract/blob/main/runOverlay.php