This repository contains the code for the paper "A high-performance deep-learning-based pipeline for whole-brain vasculature segmentation at the capillary resolution"

HP-VSP is a high-performance deep-learning-based pipeline for whole-brain vascular segmentation. The pipeline contains a lightweight neural network model for multi-scale vessel features extraction and segmentation, which can achieve more accurate segmentation results with only 1% of the parameters of similar methods. The pipeline uses parallel computing to improve the efficiency of segmentation and the scalability of various computing platforms.

segmentation network

The source code of proposed segmentation network is in this folder. Users can use this network to train and segment their own vascular datasets.

• Training the network

dataset: path of the training dataset, the dataset should be structured like

data
   |-- datasets
   |-- image
       |-- img001.tif
       |-- img002.tif
       |-- ...
   |-- label
       |-- img001.tif
       |-- img002.tif
       |-- ...
   |--predataset.py

then, run predataset.py to generate the training, validation, and test set in dataset/datasets.

run data2list.py to the data path of the training, validation, and test set.

train_new.py is used to train the network.

vascular segmentation pipeline

The source code of proposed HP-VSP is in this folder. The pipeline consists of three parts: overlapping blocking, block segmentation, and blocks fusion. Users can use this pipeline to segment large-scacle or whole-brain 3D vascular datasets.

• Resample the dataset run mpi_resample.py. Two parameters need to be set before running

    #original 2D slices path
    src = '/lustre/ExternalData/liyuxin/dataset/hip/193882/left_merge/'
    #resampled 2D slices path
    dst = '/lustre/ExternalData/liyuxin/dataset/hip/193882/left_merge2x2x2/'

then, run mpiexec -n num_proc -f nodefile python mpi_resample.py. num_proc is the total number of parallels, nodefile is a list of the names of the specified compute nodes.

• To chunk the two-dimensional sequence dataset, run mpi_overlap_blocking.py. Four parameters need to be set before running

    #2D slices path
    src = '/lustre/ExternalData/liyuxin/dataset/193882/2x2x2/'
    #overlapped 3D blocks save path
    dst = '/lustre/ExternalData/liyuxin/dataset/193882/block_2x2x2/'
    #size of blocks
    block_size = 192
    #size of  overlap area
    overlap = 32

then, run mpiexec -n num_proc -f nodefile python mpi_overlap_blocking.py.

• Segment the overlaping cubes, run parallel_segmentation.py. Five parameters need to be set before running

    #avg pixel value of dataset
    all_mean1 = np.array([40], dtype=np.float32)
    # set the uesed GPUs
    os.environ["CUDA_VISIBLE_DEVICES"] = '0,1,2,3,4,5,6,7'
    #overlapped 3D blocks path
    tiff_path = '/lustre/ExternalData/liyuxin/dataset/hip/193882/right_block/'
    #segmented blocks save path
    dst = '/lustre/ExternalData/liyuxin/dataset/hip/193882/right_seg/'
    ......
    #load pertrained network parameters
    temp = torch.load("model_pretrained.pth")

then, run python parallel_segmentation.py

• Merge the segmented blocks to generate the segmented 2D sequence data, run mpi_block_fusion.py. Two parameters need to be set

    # segmented 3D blocks path
    src = '/lustre/ExternalData/liyuxin/dataset/hip/193882/right_seg/'
    # 2D slices save path
    dst = '/lustre/ExternalData/liyuxin/dataset/hip/193882/right_merge/'

then, run mpiexec -n num_proc -f nodefile python mpi_block_fusion.py.

Citation

Li Yuxin, Liu Xuhua, Jia Xueyan, Jiang Tao, Wu Jianghao, Zhang Qianlong, Li Junhuai, Li Xiangning, Li Anan. A high-performance deep-learning-based pipeline for whole-brain vasculature segmentation at the capillary resolution. Bioinformatics, 2023, 39(4): btad145.