CompSegNet: An enhanced U-shaped architecture for nuclei segmentation in H&E histopathology images

1. Abstract

In histopathology, nuclei within images hold vital diagnostic information. Automated segmentation of nuclei can alleviate pathologists' workload and enhance diagnostic accuracy. Although U-Net-based methods are prevalent, they face challenges like overfitting and limited field-of-view. This paper introduces a new U-shaped architecture (CompSegNet) for nuclei segmentation in H&E histopathology images by developing enhanced convolutional blocks and a Residual Bottleneck Transformer (RBT) block. The proposed convolutional blocks are designed by enhancing the Mobile Convolution (MBConv) block through a receptive fields enlargement strategy, which we referred to as the Zoom-Filter-Rescale (ZFR) strategy and a global context modeling based on the global context (GC) Block; and the proposed RBT block is developed by incorporating the Transformer encoder blocks in a tailored manner to a variant of the Sandglass block. Additionally, a noise-aware stem block and a weighted joint loss function are designed to improve the overall segmentation performance. The proposed CompSegNet outperforms existing methods quantitatively and qualitatively, achieving a competitive AJI score of 0.705 on the MoNuSeg 2018 dataset, 0.72 on the CoNSeP dataset, and 0.779 on the CPM-17 dataset while maintaining a reasonable parameter count.

2. Architecture

2.1 Overall Architecture

2.2 Architecture Specifications

2.3 Building Blocks

CompSeg (CSeg) Block

• Enhances MBConv efficiency through the Zoom-Filter-Rescale (ZFR) strategy.
• Involves:
  • Large stride at the entry expansion layer (Zooming).
  • Large kernel-sized depthwise convolution operation (Zooming and Filtering).
  • Rescaling spatial size using bilinear upsampling to compensate for downsampling (Rescaling).
• Increases receptive fields within MBConv by 8×.
• Decreases inference latency by approximately 30%.

Extended CompSeg (ECSeg) Block

• Extends the CSeg block by incorporating an improved global context (IGC) block for robust global context modeling.
• Increases AJI score of the nuclei segmentation on MoNuSeg 2018 dataset in a lightweight network by approximately 1.9%.
• Achieves improved performance with only a minimal computational cost.

Residual Bottleneck Transformer (RBT) Block

• Incorporates Transformer encoder blocks in a tailored manner to a variant of the Sandglass block.
• Leverages strengths of both convolutional and attention-based mechanisms.
• Effectively captures fine-grained spatial information and comprehensive long-range dependencies.

Noise-aware stem (Block) Block

• Stem block
• Enhances low-level feature extraction while mitigating the impact of noisy features in the model's initial skip connections.

3. Implementation

The proposed architecture is implemented using the Keras API with a TensorFlow 2.12 backend, running on a Google Colab Pro+ instance equipped with an Intel(R) Xeon(R) CPU and an NVIDIA A100-SXM4-40GB GPU.

3.1 Clone the project

For cloning the project run:

   $ git clone https://github.com/mltraore/compsegnet.git
   $ cd compsegnet

3.2 Install requirements

Install requirements using:

   $ chmod +x install_dependencies.sh
   $ pip install -r requirements.txt
   $ sudo ./install_dependencies.sh

3.2 Datasets

The following datasets were used in experiments:

• MoNuSeg 2018
• CoNSeP
• CPM-17

Processed versions of these datasets, along with the original versions, predicted masks, and a checkpoint sample for the MoNuSeg 2018 dataset, can be downloaded here. For automatic download, run:

   $ chmod +x download_resources.sh
   $ ./download_resources.sh

in the project directory.

• Note: The included predicted masks are actual CompSegNet architecture outputs, provided for qualitative comparison and further evaluation by the authors in their research.

To create the datasets yourself, use the prepare_dataset.py script:

# Get script usage info
$ python3 prepare_dataset.py --help

# Example usage
$ python3 prepare_dataset.py --dataset-path datasets/monuseg_2018 \
                             --image-size 1000 \
                             --validation-size 0.10 \
                             --reference-image datasets/monuseg_2018/train/images/1.tif \
                             --prepared-data-path datasets/prepared_datasets/monuseg_2018

3.3 Training

Use the train.py script in the project directory to train the model:

# Get script usage info
$ python3 train.py --help

# Example usage
$ python3 train.py --train-folder datasets/prepared_datasets/monuseg_2018/train \
                   --validation-folder datasets/prepared_datasets/monuseg_2018/validation \
                   --checkpoints-folder checkpoints/ckpts

3.4 Testing

Use the test.py script in the project directory to test the model:

# Get script usage info
$ python3 test.py --help

# Example usage
$ python3 test.py --model-weights-save checkpoints/ckpts \
                  --test-set datasets/prepared_datasets/monuseg_2018/train

This provides Dice Similarity Coefficient (DSC), Aggregated Jaccard Index (AJI), and Hausdorff Distance (HD) scores.

4. Results

4.1 Quantitative Results

  CompSegNet on MoNuSeg 2018 dataset

  CompSegNet on CoNSeP dataset

  CompSegNet on CPM-17 dataset

4.2 Qualitative Results

  CompSegNet on MoNuSeg 2018 dataset

  CompSegNet on CoNSeP dataset

  CompSegNet on CPM-17 dataset

Citation

@article{traore2024compsegnet,
  title={CompSegNet: An enhanced U-shaped architecture for nuclei segmentation in H\&E histopathology images},
  author={Traoré, Mohamed and Hancer, Emrah and Samet, Refik and Yildirim, Zeynep and Nemati, Nooshin},
  journal={Biomedical Signal Processing and Control},
  volume={97},
  pages={106699},
  year={2024},
  publisher={Elsevier}
}

Acknowledgement

This work is supported by TÜBİTAK (Scientific and Technological Research Council of Türkiye) (Project number: 121E379).