a) Raw EM data can be found in  /ccdbprod/ccdbprod23/home/CCDB_DATA_USER.portal/CCDB_DATA_USER/acquisition/project_20271/microscopy_5391395/segmentation/testAppOut/em

b) Membrane Prediction folder can be found in /ccdbprod/ccdbprod23/home/CCDB_DATA_USER.portal/CCDB_DATA_USER/acquisition/project_20271/microscopy_5391395/segmentation/testAppOut/predictions-003

c) Myelin Prediction folder can be found in /ccdbprod/ccdbprod23/home/CCDB_DATA_USER.portal/CCDB_DATA_USER/acquisition/project_20271/microscopy_5391395/segmentation/testAppOut/predictions-007

Step 1

Find the closest membrane model in the existing models. In this case, we want to use membranes_Aug05_40k, which can be downloaded at https://doi.org/10.7295/W9CDEEP3M50772

Step 1.1 Create the retrain data:

Go to membrane prediction data (a). Create the binary version of the prediction data by using the ImageMagick command:

convert $input.png -threshold 50% $output.png

Step 1.2 Create the augmented data using CDeep3M

PreprocessTrainingData.py /images /labels /mem_augmented

Step 1.3 Feed the retrain data to the model (membranes_Aug05_40k) that I picked

runtraining.sh --additerations 5000 --retrain ~/W9CDEEP3M50772 ~/mem_augmented ~/mem_retrain_out

Step 2

Step 2.1 Convert the Myelin prediction result (c) to the binary format:

convert $input.png -threshold 50% $output.png

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:

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