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EM_mask

EM_mask is a Python library for large scale tissue mask predictions on serial EM data inspired by and compatible with FFN standard (https://github.com/google/ffn). It can be used to run UNets on h5 volumes or an arbiturarily large precomputed volume chunkwise with MPI parallelization. It is built-in with tensorflow implementations of classic 2D/3D UNets, and Distance Transformed UNets.

Installation

pip install -e .

Usage

  1. Prepare training data into an h5 file with grayscale image and binary mask label(soma, vessicle cloud, synaptic junctions) in z,y,x shape

  2. Prepare training coordinates with the same technique in (https://github.com/google/ffn) by evenly sample coordinates depending on coverage percentage of mask.

  3. Training

Assuming a dual-gpu setup:

horovodrun -n 2 -H localhost:2 \
    python ${INSTALL_DIR}/train.py \
    --data_volumes=${INPUT_NAME}:${INPUT_PATH}:image \
    --label_volumes=${INPUT_NAME}:${INPUT_PATH}:label \
    --tf_coords=${TF_COORD_FILES} \
    --train_dir=${CHECKPOINT_DIR} \
    --model_name='models.unets.unet_dtu_2_pad_concat' \
    --model_args="{\"fov_size\": [128, 128, 12], \"num_classes\": 1, \"label_size\": [128, 128, 12]}" \
    --learning_rate=0.001 \
    --batch_size=2 \
    --image_mean=120 \
    --image_stddev=46 \
    --rotation \
    --max_steps 100000 \
  1. Inference

Inference can be performed on either h5 data or precomputed, refer to Neuroglancer, CloudVolume h5:

mpirun -n 2 \
  python ${INSTALL_DIR}/predict_h5.py \
    --input_volume=${INPUT_PATH}:image \
    --input_offset='0,0,0' \
    --input_size='512,512,128' \
    --output_volume=${OUTPUT_PATH} \
    --model_name='models.unets.unet_dtu_2_pad_concat' \
    --model_args="{\"fov_size\": [218, 218, 23], \"num_classes\": 1}" \
    --model_checkpoint=${CHECKPOINT} \
    --overlap='32,32,16' \
    --batch_size=2 \
    --image_mean=120 \
    --image_stddev=46 \
    --var_threshold=10 \
    --use_gpu=0,1 \
    --alsologtostderr

the output will be an h5 file with two datasets "class_prediction" and "logits"

Precomputed:

mpirun -n 2 \
  python ${INSTALL_DIR}/predict_precomputed.py \
    --input_volume=$INPUT_PRECOMPUTED_DIR \
    --input_offset='0,0,0' \
    --input_size='512,512,128' \
    --input_mip=1 \
    --output_volume=$OUTPUT_PRECOMPUTED_DIR \
    --model_name='models.unets.unet_dtu_2_pad_concat' \
    --model_args="{\"fov_size\": [218, 218, 23], \"num_classes\": 1}" \
    --model_checkpoint=$CHECKPOINT \
    --overlap='32,32,16' \
    --batch_size=2 \
    --image_mean=120 \
    --image_stddev=46 \
    --var_threshold=10 \
    --use_gpu=0,1 \
    --alsologtostderr

The output will be two precomputed volumes "class_label" and "logits"

License

MIT