...

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:

runtraining.sh --numiterations 50000 /myelin_augmented  /myelin_trainednet

Step3 

Step 3.1 Run the CDeep3M on the membrane using the training model in step 1:

runprediction.sh --augspeed 10 --models 1fm  ~/mem_retrain_out ~/em ~/membrane_predictions

Prediction:

Image Added

Note that the prediction result contains the myelin layer.

Step 3.2 Run the CDeep3M on the Myelin data:

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