Python library with Neural Networks for Volume (3D) Segmentation based on PyTorch.

This library is based on famous Segmentation Models Pytorch library for images. Most of the documentation can be used directly from there.

• Type 1: pip install segmentation_models_pytorch_3d
• Type 2: Copy segmentation_models_pytorch_3d folder from this repository in your project folder.

Segmentation model is just a PyTorch nn.Module, which can be created as easy as:

import segmentation_models_pytorch_3d as smp
import torch

model = smp.Unet(
    encoder_name="efficientnet-b0", # choose encoder, e.g. resnet34
    in_channels=1,                  # model input channels (1 for gray-scale volumes, 3 for RGB, etc.)
    classes=3,                      # model output channels (number of classes in your dataset)
)

# Shape of input (B, C, H, W, D). B - batch size, C - channels, H - height, W - width, D - depth
res = model(torch.randn(4, 1, 64, 64, 64)) 

• Unet [paper] [docs]
• Unet++ [paper] [docs]
• MAnet [paper] [docs]
• Linknet [paper] [docs]
• FPN [paper] [docs]
• PSPNet [paper] [docs]
• PAN [paper] [docs]
• DeepLabV3 [paper] [docs]

The following is a list of supported encoders in the SMP. Select the appropriate family of encoders and click to expand the table and select a specific encoder and its pre-trained weights (encoder_name and encoder_weights parameters).

Recommended input size for backbones can be calculated as: K = pow(N, 2/3). Where N - is size for input image for the same model in 2D variant.

For example for N = 224, K = 32. For N = 512, K = 64.

Typical strides for 2D case is 2 for H and W. It applied depth times (in almost all cases 5 times). So input image reduced from (224, 224) to (7, 7) on final layers. For 3D case because of very massive input, it's sometimes useful to control strides for every dimension independently. For this you can use input variable strides, which default values is: strides=((2, 2, 2), (2, 2, 2), (2, 2, 2), (2, 2, 2), (2, 2, 2)). Example:

Let's say you have input data of size: (224, 128, 12). You can use strides like that: ((2, 2, 2), (4, 2, 1), (2, 2, 2), (2, 2, 1), (1, 2, 3)). Output shape for these strides will be: (7, 4, 1)

import segmentation_models_pytorch_3d as smp
import torch

model = smp.Unet(
    encoder_name="resnet50",        
    in_channels=1,                  
    strides=((2, 2, 2), (4, 2, 1), (2, 2, 2), (2, 2, 1), (1, 2, 3)),
    classes=3, 
)

res = model(torch.randn(4, 1, 224, 128, 12)) 

Note: Strides currently supported by resnet-family and densenet models with Unet decoder only.

• https://github.com/qubvel/segmentation_models.pytorch - original segmentation 2D repo
• segmentation_models_3D - segmentation models in 3D for keras/tensorflow
• timm_3d - classification models in 3D for pytorch
• volumentations - 3D augmentations

If you find this code useful, please cite it as:

@article{solovyev20223d,
  title={3D convolutional neural networks for stalled brain capillary detection},
  author={Solovyev, Roman and Kalinin, Alexandr A and Gabruseva, Tatiana},
  journal={Computers in Biology and Medicine},
  volume={141},
  pages={105089},
  year={2022},
  publisher={Elsevier},
  doi={10.1016/j.compbiomed.2021.105089}
}

• Support for strides for all encoders
• Add timm_ models