bioengineering

Article
RGSB-UNet: Hybrid Deep Learning Framework for Tumour
Segmentation in Digital Pathology Images
Tengfei Zhao 1 , Chong Fu 1,2,3, * , Ming Tie 4 , Chiu-Wing Sham 5 and Hongfeng Ma 6

1 School of Computer Science and Engineering, Northeastern University, Shenyang 110819, China
2 Engineering Research Center of Security Technology of Complex Network System, Ministry of Education,
Shenyang 110819, China
3 Key Laboratory of Intelligent Computing in Medical Image, Ministry of Education, Northeastern University,
Shenyang 110819, China
4 Science and Technology on Space Physics Laboratory, Beijing 100076, China
5 School of Computer Science, The University of Auckland, Auckland 1142, New Zealand
6 Dopamine Group Ltd., Auckland 1542, New Zealand
* Correspondence: fuchong@mail.neu.edu.cn

Abstract: Colorectal cancer (CRC) is a prevalent gastrointestinal tumour with high incidence and
mortality rates. Early screening for CRC can improve cure rates and reduce mortality. Recently, deep
convolution neural network (CNN)-based pathological image diagnosis has been intensively studied
to meet the challenge of time-consuming and labour-intense manual analysis of high-resolution
whole slide images (WSIs). Despite the achievements made, deep CNN-based methods still suffer
from some limitations, and the fundamental problem is that they cannot capture global features. To
address this issue, we propose a hybrid deep learning framework (RGSB-UNet) for automatic tumour
segmentation in WSIs. The framework adopts a UNet architecture that consists of the newly-designed
residual ghost block with switchable normalization (RGS) and the bottleneck transformer (BoT) for
downsampling to extract refined features, and the transposed convolution and 1 × 1 convolution with
ReLU for upsampling to restore the feature map resolution to that of the original image. The proposed
framework combines the advantages of the spatial-local correlation of CNNs and the long-distance
feature dependencies of BoT, ensuring its capacity of extracting more refined features and robustness
Citation: Zhao, T.; Fu, C.; Tie, M.;
to varying batch sizes. Additionally, we consider a class-wise dice loss (CDL) function to train the
Sham, C.-W.; Ma, H. RGSB-UNet:
segmentation network. The proposed network achieves state-of-the-art segmentation performance
Hybrid Deep Learning Framework
under small batch sizes. Experimental results on DigestPath2019 and GlaS datasets demonstrate that
for Tumour Segmentation in Digital
Pathology Images. Bioengineering
our proposed model produces superior evaluation scores and state-of-the-art segmentation results.
2023, 10, 957. https://doi.org/
10.3390/bioengineering10080957 Keywords: hybrid deep learning framework; tumour segmentation; whole slide image; Residual-
Ghost-SN; bottleneck transformer
Academic Editors: Yan Pei
and Jijiang Yang

Received: 31 May 2023

Revised: 6 August 2023 1. Introduction
Accepted: 9 August 2023 Colorectal cancer (CRC) is a gastrointestinal tumour that has a higher incidence and
Published: 12 August 2023 mortality rate than common tumours [1,2]. However, early screening with colonoscopy
followed by pathological biopsy can significantly reduce the mortality rate [3]. Pathology
is considered the gold standard for distinguishing between benign and malignant CRCs.
During a diagnosis, physicians analyse the tumour’s condition by observing the H&E-
Copyright: © 2023 by the authors.
stained pathological section, drawing on their clinical expertise [4].
Licensee MDPI, Basel, Switzerland.
The use of high-resolution, large-scale whole slide images (WSIs) has become a routine
This article is an open access article
distributed under the terms and
diagnostic method with the rapid development of image scanning techniques [5]. WSI
conditions of the Creative Commons
technology has great potential for developing and using algorithms for pathological di-
Attribution (CC BY) license (https:// agnosis [6]. WSIs are widely used for digital pathology analysis, particularly in clinical
creativecommons.org/licenses/by/ practice [7]. However, the large size of WSIs can make manual analysis by pathologists
4.0/). time-consuming, and the unavoidable cognitive biases can lead to varying diagnoses.

Bioengineering 2023, 10, 957. https://doi.org/10.3390/bioengineering10080957 https://www.mdpi.com/journal/bioengineering

Bioengineering 2023, 10, 957 2 of 16

CRC segmentation in whole slide images presents a unique set of implementation

challenges due to the high-resolution and large size of these images, including gigapixel-
scale data, computational resources, data handling and preprocessing, and integration with
clinical workflow. Addressing these challenges often involves a combination of advanced
image processing techniques, deep learning architectures tailored for large images, efficient
data handling methods, and collaboration between medical experts and computer scientists.
Overcoming these challenges is critical to harness the full potential of whole slide image
segmentation in improving the accuracy and efficiency of colon cancer diagnosis and
treatment planning.
In recent years, deep learning-based approaches [8] have been widely applied to
histopathology image analysis, achieving remarkable results. In [9], Xu et al., proposed a
deep learning method based on convolutional neural networks (CNNs) to automatically
segment and classify epithelial and stromal regions in histopathology images. In [10],
Liu et al., proposed a framework for the automatic detection and localization of breast
tumours. In [11], Wang et al. proposed a deep CNN method to automatically identify
the tumour in lung cancer images, using the shape feature to predict survival outcomes.
In [12], Johnson et al. used Mask-RCNN to segment the nuclei in pathology images. In [13],
Fan et al. proposed an improved deep learning method based on a classification pipeline to
detect cancer metastases in WSI. In [14], Cho et al. proposed a deep neural network with
scribbles for interactive pathology image segmentation. In [15], Zhai et al. proposed deep
neural network guided by an attention mechanism for segmentation of liver pathology
images. In [16], Deng et al. proposed a interpretable multi-modal image registration
network based on disentangled convolutional sparse coding to solve the problem of lack
of interpretability. In [17], Jin et al. proposed a two-stage deep learning system named
iERM to provide accurate automatic grading of epiretinal membranes for clinical practice.
In [18], Xiong et al. proposed DCGNN, a novel single-stage 3D object detection network
based on density clustering and graph neural networks. DCGNN utlized density clustering
ball query to partition the point cloud space and exploits local and global relationships by
graph neural networks.
While histopathological image analysis has shown remarkable results, few studies
have investigated deep learning-based methods for CRC tissue segmentation, particularly
in WSIs. In [19], Qaiser et al. introduced two versions of our tumour segmentation
method: one aimed at achieving faster processing while maintaining accuracy, and the other
focused on achieving higher accuracy. The faster version relied on selecting representative
image patches from a convolutional neural network (CNN) and classifying the patches by
quantifying the difference between the exemplars’ persistent homology profiles (PHPs) and
the input image patch. In contrast, the more accurate version combined the PHPs with high-
level CNN features and utilized a multi-stage ensemble strategy to label image patches.
In [20], Zhu et al. proposed an adversarial context-aware and appearance consistency
UNet (CAC-UNet) for segmentation and classification tasks, and achieved first place
in the DigestPath2019 challenge. In [21], Feng et al. employed a UNet with a VGG
backbone for WSI-based colorectal tumour segmentation, and achieved second place in the
DigestPath2019 challenge.
Despite the remarkable results achieved by the methods mentioned above, several
challenges still persist, including fewer public CRC datasets with expert annotations and
difficulty accurately segmenting the refined boundary of the tumour, impeding further
research on CRC tissue segmentation. Additionally, most existing deep learning frame-
works rely on convolutional stacking, which reduces local redundancy but fails to capture
global dependencies owing to the limited receptive field [22]. By contrast, transformers
can capture long-distance dependencies through self-attention. However, excessive visual-
semantic alignment may lead to redundancy in token representation, making it necessary
to balance global dependency and local specificity when designing deep learning models.
This study proposes a hybrid deep learning framework for segmenting the CRC tu-
mour in WSIs with a focus on refining the boundary segmentation and addressing network
Bioengineering 2023, 10, 957 3 of 16

stability under small batch sizes. The proposed encoder–decoder architecture utilizes a
newly designed encoder that includes residual ghost blocks with switchable normalization
(RGS) and a bottleneck transformer block (BoT) for downsampling, while the decoder em-
ploys transpose convolution for upsampling [23–27]. By leveraging the benefits of CNNs
and the transformer, the proposed encoder uses RGS and BoT as downsampling operations
to extract more refined features from input images. The operation extracts local informa-
tion, and the multi-head self-attention (MHSA) in the BoT models global dependency [27].
Experimental results demonstrate that the proposed model can accurately segment the
tumour and produce a more refined boundary, leading to improved segmentation accuracy
under small batch sizes. The primary contributions of our study are outlined below:
• We propose a deep hybrid network that combines a transformer and CNN for auto-
matic tumour region segmentation in pathology images of the colon.
• A newly-designed feature extraction block RGS is presented. The block can adaptively
determine the optimal combination of normalizers for each layer, making our model
robust to varying batch sizes.
• Our novel hybrid backbone encoder, which includes RGS and BoT blocks, can extract
more refined features.
• Experimental results demonstrate that the proposed RGSB-UNet achieves higher
evaluation scores and produces finer segmentation results than state-of-the-art seg-
mentation methods under small batch sizes.
The remainder of this paper is structured as follows. In Section 2, we present the
proposed network architecture. Section 3 describes the datasets and evaluation criteria used
in our experiments, while Section 4 presents our experimental results. Finally, in Section 5,
we summarize the study results and suggest potential avenues for future research.

2. Proposed Method
2.1. Network Architecture
Our proposed deep learning framework for colon pathology WSI analysis is illustrated
in Figure 1. As shown in Figure 2, to extract relevant features from original images, we start
with 512 × 512 × 3 image patches using dense cropping methods. The encoder includes a
novel downsampling operation that combines RGS and BoT blocks as the feature extraction
backbone. The details of the design of the encoder and decoder, GBS, RGS, and BoT will be
discussed below.

Figure 1. An overview of RGSB-UNet. The TRCCR denotes transposed convolution, ReLU, concate-
nate, convolution, and ReLU.
Bioengineering 2023, 10, 957 4 of 16

3×3 conv s=1 p=1 1×1 conv s=1 p=1

BN
ReLU
ReLU
3×3 conv s=1 p=1
3×3 conv s=1 p=1
concatenate
BN
ReLU
ReLU
3×3 Tconv s=2 p=1

3×3 MP s=2 p=1 ReLU

RGS s=1 p=1 3×3 conv s=1 p=1
concatenate
ReLU

RGS s=2 p=1 3×3 Tconv s=2 p=1

RGS s=1 p=1
ReLU
3×3 conv s=1 p=1
RGS s=2 p=1 concatenate
RGS s=1 p=1 ReLU
RGS s=1 p=1 3×3 Tconv s=2 p=1

ReLU
BoT
3×3 conv s=1 p=1
2×2 AP s=2 p=0
concatenate
ReLU
3×3 Tconv s=2 p=1

Figure 2. Schematic diagram of RGSB-UNet. RGS denotes the proposed residual ghost block with
switchable normalization, and BoT denotes the bottleneck transformer. MP and AP denote the max
and average pooling, respectively. Tconv denotes the transposed convolution used for upsampling.

2.1.1. Encoder and Decoder

In order to extract an efficient set of features, we use two 3 × 3 convolutions with
batch normalization and ReLU, following a max pooling for downsampling, and devise
a new residual ghost network, embedding a BoT at the end of the encoder as part of the
encoder in our network architecture. The network employs four downsampling modules,
each utilizing a different number of residual ghost blocks. As shown in Figure 2, the first
downsampling module uses a 3 × 3 max pooling (MP) and a residual ghost block; the
second and third downsampling modules use two and three stacked residual ghost blocks,
respectively. By leveraging the ghost convolution technique, our network can generate rich
feature maps using significantly fewer input features than traditional convolution methods,
which improves the computational efficiency of our encoder. Additionally, the stability
of our network is enhanced by the ability to select optimal combinations of different
normalizers for each normalization layer, resulting in an accuracy that is not impacted
by batch size. The fourth downsampling module incorporates a BoT block and a 2 × 2
average pooling (AP), which significantly boosts the extraction of refined features. Each
downsampling module reduces the input spatial resolution by a factor of two.
Bioengineering 2023, 10, 957 5 of 16

The decoder is composed of four upsampling modules that utilize a transposed

convolution and a 1 × 1 convolution with ReLU [28], increasing the input spatial resolution
by a factor of two. The concatenate block concatenates the skip and output features of
Tconv-ReLU; this operation attaches more local information extracted from different layers
of the encoder directly into their corresponding decoder layers at the same level, which
adds detailed information to the general area of the target of judgment. Further elaboration
on the RGS and BoT components will be provided in subsequent subsections.

2.1.2. Ghost Block with Switchable Normalization

Our proposed Ghost-Block-SN architecture is presented in Figure 3, which utilizes
the Ghost-Block to generate more representative features at a lower computational cost.
The Ghost-Block firstly employs traditional convolution to generate intrinsic feature maps
and then utilizes cost-effective linear operations to expand the features and channels. The
computational cost of linear operations on feature maps is much lower than traditional
convolution, making the block more efficient than other existing efficient methods. The
size of the primary convolution kernel in Ghost-Block is customizable, and we used a 1 × 1
point-wise convolution in our study. A BN layer is introduced after each Ghost-Block in
Residual-Ghost-Block, which provides stability and speeds up the training process.

1×1 conv s=1 p=1

SN

ReLU

3×3 conv s=1 p=1

g=Cout/2

SN

ReLU

Concatenate

Figure 3. Schematic diagram of Ghost block with switchable normalization. The dash box denotes
the cheap operation that uses a 3 × 3 group convolution in the ghost block.

However, the performance of Ghost-Block-BN is restricted by the batch size as BN

uses a single normalizer throughout the network, which can be unstable and degrade
accuracy under small batch sizes. To overcome this issue, we incorporated switchable
normalization (SN) [29], a technique that is robust to a wide range of batch sizes. SN
measures channel-wise, layer-wise, and minibatch-wise statistics using BN [30], instance
normalization (IN) [31], and layer normalization (LN) [32], respectively, and learns their
important weights to find their optimal combination, ensuring network stability and
accuracy in the case of small batch sizes.
Bioengineering 2023, 10, 957 6 of 16

2.1.3. Residual Ghost Block with Switchable Normalization

As shown in Figure 4a, our RGS is constructed by incorporating the above presented
GBS with a residual bottleneck, which is the fundamental building block of a ResNet [23],
due to its exceptional performance. The core concept behind a residual block is to refor-
mulate the layers as learning residual functions with respect to the layer inputs, rather
than learning unreferenced functions. Compared to ResNet-50, our encoder employs fewer
building units, boosting the computational efficiency. Moreover, the proposed RGS is
highly robust and can handle a wide range of batch sizes.

GBS GBS

SN SN

3×3 conv s=1 p=1 MHSA

SN SN

GSB GBS

SN SN

Add Add

(a) (b)

Figure 4. Schematic diagram of the proposed bottleneck. (a) RGS Bottleneck. (b) Bottleneck trans-
former. GBS and SN denote the ghost block with switchable normalization and switchable normaliza-
tion, respectively. MHSA denotes multi-head self-attention.

2.1.4. Bottleneck Transformer

Figure 4b shows the bottleneck transformer (BoT), an important block in the proposed
hybrid network, which uses multi-head self-attention (MHSA) to replace the 3 × 3 convolu-
tion compared with RGS. The BoT is embedded in the last layer of the encoder. As is known,
the self-attention (Figure 5a) can process and aggregate the information in the feature maps
to complement the CNN handle long-distance dependencies. Particularly, the self-attention
in MHSA can help the network better understand the relationships between different
regions and improve the accuracy of segmentation when working with highly detailed
images. In addition, as shown in Figure 5b, the MHSA with sufficient heads is at least as
expressive as any convolutional layer [27]. The MHSA produces multiple attention maps
and embedding features from an image to encode rich information, enhancing the deep
model’s robustness towards representation learning. Benefiting from the MHSA, the BoT
block can help the network to boost the segmentation performance.
Bioengineering 2023, 10, 957 7 of 16

z
H×W×d
Self-Attention Layer H*W×H*W H*W×d Multi-headed Self-attention

softmax
b4
b3 Concatenate
2
b
H* W×H*W H*W×H*W b1
qrT qkT Self-Attention Layer
content-content
content-position Self-Attention Layer head=4
H×W×d Self-Attention Layer Linear
Self-Attention Layer
q k v
a1
H×1×d a1
1×W×d
H×W×d H×W×d H×W×d a1
a1
WQ:1×1 WK:1×1 WV:1×1 b1

Rh Rw

H×W×d
(a) x (b)

Figure 5. Schematic diagram of (a) self-attention [26] and (b) multi-head self-attention.

2.2. Loss Function

Dice loss is leveraged as a standard loss function in image segmentation tasks and
indicates the difference between the predicted and ground-truth mask [33]. However, there
are still some limitations when employing this function. For instance, there is no segmenting
target, and the dice loss is 0. Clearly, the dice loss function receives no punishment when
predicting a false positive.
To address this issue, the improved class-wise dice loss function is leveraged to
compute the background and lesion segmentation dice similarity coefficients (DSCs) for
benign and malignant images, respectively [21]. The improved loss function can effectively
reduce false positives, including its practicality for clinical applications. The improved
class-wise dice loss (CDL) function is described by

N (1 − y p )(1 − yi )(1 − ŷi ) + e

yi ŷi
LCDL = 1 − ∑(y p + ), (1)
i
yi + ŷi (1 − yi ) + (1 − ŷi ) + e

where yi is the binary label of pixel i, ŷi is the predicted probability, and N is the total
number of pixels in a patch. e is a small number to avoid the denominator becoming 0.
The presence of a lesion area determines the patch label (y p ). The CDL function can
alleviate pixel-level class imbalance, resulting in an all-zero mask when training nega-
tive samples.

3. Evaluation and Datasets

3.1. Evaluation
We use the DSC, Jaccard Index (JI), and relative volume difference (RVD) to measure
the segmentation performance of our proposed model [34]. The DSC measures the similarity
between the network segmentation results when using the proposed method and the gold
standard mask in image segmentation. DSC, JI, and RVD are defined as

2|YA ∩ YP |
DSC = , (2)
|YA | + |YP |

|YA ∩ YP |
JI = , (3)
|YA | + |YP | − |YA ∩ YP |
and
|YP | − |YA |
RVD = , (4)
|YA |
where YA is the set of lesion pixels in the annotation, and YP is the corresponding set of
lesion pixels in the segmentation result.
Bioengineering 2023, 10, 957 8 of 16

We use pixel accuracy (PA) and area under the curve (AUC) to measure the classi-
fication performance of our proposed model. AUC is defined as the area of the receiver
operating characteristic (ROC) curve, determined by the true positive rate (TPR) and false
positive rate (FPR). TPR, FPR, and Precision are defined as follows:

TP
TPR = , (5)
TP + FN

FP
FPR = , (6)
FP + TN
and
TP
Precision = , (7)
TP + FP
where TP, FP, TN, and FN are true positives, false positives, true negatives, and false
negatives, respectively.
AUC and PA are defined as
Z 1
AUC = TPR( FPR−1 ( x ))dx = P( X1 > X0 ) (8)
x =0

and
TP + TN
PA = , (9)
TP + TN + FP + FN
where X0 and X1 are the scores for the negative and positive instances, respectively.

3.2. Datasets and Implementation

We trained the proposed network on the DigestPath2019 [35] gland segmentation
(GlaS) [36] datasets. In these datasets, numerous expert-level annotations on digestive
system pathological images are available, which will substantially advance research on
automatic segmentation and classification of pathological tissues.
The DigestPath2019 dataset contains positive and negative samples of 872 tissue
slices from 476 patients. The average size of a tissue slice is 3000 × 3000. The training
set comprises 660 images from 324 patients, from which 250 images from 93 patients are
annotated by pathologists. The positive training samples contain 250 tissue images from
93 WSIs, with pixel-level annotation, where 0 indicates the background and 255 indicates the
foreground (malignant lesion). Some samples cropped from WSI are shown in Figure 6. The
negative training samples contain 410 tissue images from 231 WSIs. These negative images
have no annotation because they have no malignant lesions. The entry to DigestPath2019
competition has closed and the official test set is not publicly accessible. To address this
issue, we remake a balanced test set by randomly selecting 108 samples with a 54:54 positive
to negative ratio from the original training set. We retrained all the compared models on
the DigestPath2019 dataset using their original code, and the test set images are not used in
training. Defining an objective criteria for distinguishing between benign (negative) and
malignant (positive) lesions is difficult. To make it easier for academic research, according
to the WHO classification of digestive system tumours, we regarded the following lesions as
malignant: high-grade intraepithelial neoplasia and adenocarcinoma, including papillary
adenocarcinoma, mucinous adenocarcinoma, poorly cohesive carcinoma, and signet ring
cell carcinoma. Low-grade intraepithelial neoplasia and severe inflammation are not
included in the dataset because they are generally difficult for pathologists to detect.
The GlaS dataset consists of 165 tissue slices containing both positive and negative
samples. The GlaS dataset contains a training set of 85 samples from which we selected
17 samples as the validation data. The dataset offers two different test sets, testA and
testB, consisting of 60 and 20 samples, respectively. We used the validation set to select the
optimal model and all the performance evaluations are carried out on the joining of testA
and testB. Glands are vital histological structures found in various organ systems, serving
Bioengineering 2023, 10, 957 9 of 16

as the primary mechanism for protein and carbohydrate secretion. Adenocarcinomas,

which are malignant tumors originating from glandular epithelium, have been identified
as the most prevalent form of cancer. Pathologists routinely rely on gland morphology
to assess the malignancy level of several adenocarcinomas, such as those affecting the
prostate, breast, lung, and colon. Accurately segmenting glands is often a crucial step in
obtaining reliable morphological statistics. However, this task is inherently challenging
due to the significant variation in glandular morphology across different histologic grades.
Most studies to date have primarily focused on gland segmentation in healthy or benign
samples, with limited attention given to intermediate or high-grade cancer. Additionally,
these studies often optimize their methods for specific datasets.

Figure 6. Samples cropped from WSI.

The simulations were run on a station equipped with an NVIDIA GeForce RTX 3090
GPU and Intel(R) Xeon(R) CPU E5-2680v4×2. We augmented the training data during
training. Table 1 lists the detailed hyperparameters of the proposed framework. We
embarked on an iterative journey of manual tuning, wherein we systematically explored
and fine-tuned various hyperparameters within our framework. By meticulously adjusting
parameters such as learning rates, batch sizes, and model architecture, we meticulously
tracked the impact of each modification on the overall performance metrics. This exhaustive
process allowed us to discover the optimal combination of hyperparameters, leading to a
highly refined and efficient version of our framework that exhibits superior accuracy and
generalization on diverse datasets.

Table 1. Hyperparameters of our framework.

Hyperparameters Value
Crop Method Dense Crop
Crop Stride 512
Crop Patch Size 512 × 512 × 3
Batch Size 2
MHSA Head 4
Optimizer SGD
Learning Rate 1.0 × e−2
Weight Deacy 1.0 × e−4
Momentum 0.9
Epoch Number 500
Bioengineering 2023, 10, 957 10 of 16

4. Experimental Results
Table 2 shows the results of the ablation study, which demonstrate the performance
gains when integrating different blocks into UNet, including residual block (RSB), residual
ghost block (RGB), RGS, and BoT. Especially, our proposed RGSB-UNet achieves the
highest DSC score of 0.8336. We further analyze the performance of different batch sizes
and MHSA head numbers based on RGSB-UNet. As is shown in Table 3, the proposed
network maintains high performance even with small batch sizes. We tried different small
batch sizes in our experiments. We prove that batch size is no longer a strict limitation for
the proposed network. In addition, the head numbers of MHSA impact the performance
of the proposed network. We have tried different numbers of heads for the MHSA in
the proposed network to search for the best results, and our network achieved optimal
performance when the heads are four. When integrating RGS and BoT together to the UNet,
the segmentation model produces the best performance, which indicates that these blocks
can improve the performance of pathology image segmentation.

Table 2. Performance gains by integrating different blocks into UNet on the DigestPath2019 dataset.
RSB and RGB denote the residual block and residual ghost block with batch normalization, respectively.

UNet RSB RGB RGS BoT DSC

0.8150
0.8197
0.8201
0.8203
0.8261
0.8263
0.8336

Table 3. Effect of batch size and MHSA head on model performance. The best results are marked
in bold.

Batch Size 1 2
MHSA Head 1 2 4 1 2 4
DSC 0.8126 0.8241 0.8220 0.8331 0.8263 0.8294 0.8250 0.8336

Table 4 compares the performance of the proposed and other popular models in terms
of six metrics on the DigestPath2019 dataset; the numbers in bold indicate the best results for
each metric. As can be seen from this table, under a small batch of two, our proposed model
achieves the highest DSC, PA, JI, and Precision; it also achieves the second best RVD and
AUC. Furthermore, although DeepLab with Xception backbone outperforms other models
in terms of RVD, and the CAC-UNet (first place) achieves the highest AUC, our model
performs significantly better in the other three metrics. In Figure 7, we illustrate the results
of tumour segmentation on the sample images and compare them with that of [20,21,37–46].
As shown in this figure, the mask predicted by the proposed network is extremely close
to the ground truth. Compared with other leading networks, our proposed network can
successfully segment tumour regions with nearly overlapping margins, indicated in the
red boxes. Overall, our proposed model can capture more refined features and achieve
state-of-the-art accuracy in tumour segmentation tasks.
Bioengineering 2023, 10, 957 11 of 16

Figure 7. Segmentation results of different networks on the DigestPath2019 dataset. In the superim-
posed images, the areas marked in green represent the ground truth.
Bioengineering 2023, 10, 957 12 of 16

Table 4. Comparative results for tumour segmentation on the DigestPath2019 dataset. The best
results are marked in bold.

Methods DSC AUC PA JI RVD Precision

CAC-UNet [20] 0.8292 1.0000 0.8935 0.7082 0.3219 0.9072

UNet (Baseline) [37] 0.8150 0.9060 0.8611 0.6914 0.2852 0.6511
UNet (Backbone: Vgg11) [38] 0.8258 0.9187 0.8796 0.7081 0.2964 0.6829
UNet (Backbone: Vgg16) [39] 0.8323 0.9562 0.9351 0.7177 0.2445 0.8000
UNet (Backbone: Vgg19) [21] 0.7417 0.5875 0.3889 0.5990 0.4803 0.2987
UNet (Backbone: ResNet50) [40] 0.8197 0.9312 0.8981 0.7019 0.3652 0.7179
UNet (Backbone: DenseNet121) [41] 0.2183 0.5758 0.5092 0.1441 0.4825 0.3076
NestedUNet [42] 0.7609 0.7625 0.6481 0.6254 0.5561 0.4242
Unet3+ [43] 0.7467 0.6250 0.4450 0.6127 0.3977 0.3181
DeepLab (Backbone: Xception) [44] 0.6999 0.9500 0.9259 0.5517 0.1925 0.7778
DeepLab (Backbone: ResNet50) [44] 0.7964 0.6375 0.4629 0.6684 0.3829 0.3255
DeepLab (Backbone: Drn) [44] 0.7917 0.7125 0.5740 0.6605 0.3214 0.3783
DeepLab (Backbone: MobileNet) [44] 0.7943 0.8250 0.7407 0.6658 0.4206 0.5000
DCAN [45] 0.8322 0.9562 0.9351 0.7169 0.2291 0.8000
GCN [46] 0.6372 0.6625 0.5000 0.4903 0.5051 0.3414
SegNet [47] 0.7564 0.7937 0.6944 0.6174 0.5845 0.4590
Proposed 0.8336 0.9813 0.9722 0.7190 0.2122 0.9032

To demonstrate our proposed method’s generalizability and its performance in dif-

ferent contexts, we use the GlaS dataset to verify the network. As shown in Table 5, our
proposed model achieves the highest scores in state-of-the-art accuracy in gland segmenta-
tion tasks. Figure 8 shows the results of gland segmentation on the test set and compares
them with [21,37–46]. As shown from this figure, compared with other leading works, our
proposed network can significantly segment gland boundaries, as indicated in the red box.
Our idea can be directly applied to a computer-aided pathological diagnosis system to
reduce the workload of pathologists.

Table 5. Comparative results for gland segmentation on the GlaS dataset. The best results are marked
in bold.

Methods DSC AUC PA JI RVD Precision

UNet (Baseline) [37] 0.5132 0.4339 0.8125 0.3745 0.4959 0.9285

UNet (Backbone: Vgg11) [38] 0.7486 0.5068 0.9480 0.6195 0.6165 0.9313
UNet (Backbone: Vgg16) [39] 0.7324 0.6328 0.8265 0.6038 0.7378 0.8375
UNet (Backbone: Vgg19) [21] 0.7289 0.5979 0.8975 0.5999 0.7595 0.7928
UNet (Backbone: ResNet50) [40] 0.6511 0.5000 0.9375 0.5065 0.9228 0.9375
UNet (Backbone: DenseNet121) [41] 0.6491 0.5998 0.9263 0.5037 0.9046 0.9261
NestedUNet [42] 0.6003 0.4533 0.8500 0.4651 0.8031 0.9315
Unet3+ [43] 0.6650 0.6725 0.9450 0.5170 0.8459 0.9428
DeepLab (Backbone: Xception) [44] 0.6867 0.4735 0.8875 0.5564 0.4423 0.9342
DeepLab (Backbone: ResNet50) [44] 0.6887 0.4866 0.9125 0.5503 0.5648 0.9358
DeepLab (Backbone: Drn) [44] 0.7367 0.5306 0.9375 0.6039 0.6299 0.9375
DeepLab (Backbone: MobileNet) [44] 0.6839 0.4933 0.9250 0.5410 0.6062 0.9367
DCAN [45] 0.6415 0.6107 0.9177 0.4896 0.9459 0.9370
GCN [46] 0.5696 0.5079 0.6983 0.4220 0.9918 0.7863
SegNet [47] 0.5206 0.5533 0.8625 0.3799 0.3995 0.9445
Proposed 0.8865 0.8920 0.9823 0.7953 0.2128 0.9475
Bioengineering 2023, 10, 957 13 of 16

Figure 8. Segmentation results of different networks on the GlaS dataset. In the superimposed images,
the areas marked in green represent the ground truth.
Bioengineering 2023, 10, 957 14 of 16

5. Conclusions
In this paper, we propose a hybrid deep learning framework for segmenting tumours
in WSIs. Our model employs an encoder–decoder architecture, with a newly designed RGS
block and a BoT block in the decoder part. These blocks are implemented to capture more
refined features and improve network stability, particularly when working with small batch
sizes. To evaluate the performance of our approach, we conducted extensive experiments
on the DigestPath2019 and GlaS datasets, and the results indicate that our model achieved
state-of-the-art segmentation accuracy.
Our proposed framework is generic and can be easily applied to other histopathology
image analysis tasks. In addition, the decoder architecture proposed in this study is flexible
and can be incorporated into other deep CNNs for histopathology image analysis. However,
we are yet to conduct experiments using natural images; therefore the superiority of our
approach in this context cannot be guaranteed. We consider this an open problem and plan
to conduct further research to provide a theoretical analysis with complete proof.

Author Contributions: Conceptualization, T.Z. and C.F.; methodology, T.Z. and C.F.; validation,
T.Z.; formal analysis, T.Z., M.T. and C.-W.S.; investigation, T.Z. and C.F.; resources, T.Z.; data curation,
T.Z., H.M. and C.F.; writing—original draft preparation, T.Z.; writing—review and editing, T.Z., C.F.
and C.-W.S.; visualization, T.Z.; supervision, T.Z.; project administration, T.Z.; funding acquisition,
C.F. All authors have read and agreed to the published version of the manuscript.
Funding: This research is supported by the National Natural Science Foundation of China (No.
62032013), and the Fundamental Research Funds for the Central Universities (No. N2224001-7).
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement: The data that support the findings of this study are available from the
corresponding author upon reasonable request.
Conflicts of Interest: The authors declare no conflict of interest.

References
1. Siegel, R.L.; Miller, K.D.; Goding Sauer, A.; Fedewa, S.A.; Butterly, L.F.; Anderson, J.C.; Cercek, A.; Smith, R.A.; Jemal, A.
Colorectal cancer statistics, 2020. CA Cancer J. Clin. 2020, 70, 145–164. [CrossRef] [PubMed]
2. Xia, C.; Dong, X.; Li, H.; Cao, M.; Sun, D.; He, S.; Yang, F.; Yan, X.; Zhang, S.; Li, N.; et al. Cancer statistics in China and United
States, 2022: Profiles, trends, and determinants. Chin. Med. J. 2022, 135, 584–590. [CrossRef]
3. Vega, P.; Valentín, F.; Cubiella, J. Colorectal cancer diagnosis: Pitfalls and opportunities. World J. Gastrointest. Oncol. 2015, 7, 422.
[CrossRef] [PubMed]
4. Song, W.; Fu, C.; Zheng, Y.; Cao, L.; Tie, M. A practical medical image cryptosystem with parallel acceleration. J. Ambient. Intell.
Humaniz. Comput. 2022, 14, 9853–9867. [CrossRef]
5. Wang, S.; Yang, D.M.; Rong, R.; Zhan, X.; Xiao, G. Pathology image analysis using segmentation deep learning algorithms. Am. J.
Pathol. 2019, 189, 1686–1698. [CrossRef]
6. Kumar, N.; Gupta, R.; Gupta, S. Whole slide imaging (WSI) in pathology: Current perspectives and future directions. J. Digit.
Imaging 2020, 33, 1034–1040. [CrossRef]
7. Wright, A.M.; Smith, D.; Dhurandhar, B.; Fairley, T.; Scheiber-Pacht, M.; Chakraborty, S.; Gorman, B.K.; Mody, D.; Coffey, D.M.
Digital slide imaging in cervicovaginal cytology: A pilot study. Arch. Pathol. Lab. Med. 2013, 137, 618–624. [CrossRef]
8. Zhang, W.; Fu, C.; Chang, X.; Zhao, T.; Li, X.; Sham, C.W. A more compact object detector head network with feature enhancement
and relational reasoning. Neurocomputing 2022, 499, 23–34. [CrossRef]
9. Xu, J.; Luo, X.; Wang, G.; Gilmore, H.; Madabhushi, A. A deep convolutional neural network for segmenting and classifying
epithelial and stromal regions in histopathological images. Neurocomputing 2016, 191, 214–223. [CrossRef]
10. Liu, Y.; Gadepalli, K.; Norouzi, M.; Dahl, G.E.; Kohlberger, T.; Boyko, A.; Venugopalan, S.; Timofeev, A.; Nelson, P.Q.; Corrado,
G.S.; et al. Detecting Cancer Metastases on Gigapixel Pathology Images. arXiv 2017, arXiv:1703.02442.
11. Wang, S.; Chen, A.; Yang, L.; Cai, L.; Xie, Y.; Fujimoto, J.; Gazdar, A.; Xiao, G. Comprehensive analysis of lung cancer pathology
images to discover tumor shape and boundary features that predict survival outcome. Sci. Rep. 2018, 8, 10393. [CrossRef]
[PubMed]
12. Johnson, J.W. Adapting mask-rcnn for automatic nucleus segmentation. arXiv 2018, arXiv:1805.00500.
13. Fan, K.; Wen, S.; Deng, Z. Deep learning for detecting breast cancer metastases on WSI. In Innovation in Medicine and Healthcare
Systems, and Multimedia; Springer: Berlin/Heidelberg, Germany, 2019; pp. 137–145.
Bioengineering 2023, 10, 957 15 of 16

14. Cho, S.; Jang, H.; Tan, J.W.; Jeong, W.K. DeepScribble: Interactive Pathology Image Segmentation Using Deep Neural Networks
with Scribbles. In Proceedings of the 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), Nice, France, 13–16
April 2021; pp. 761–765.
15. Zhai, Z.; Wang, C.; Sun, Z.; Cheng, S.; Wang, K. Deep Neural Network Guided by Attention Mechanism for Segmentation of
Liver Pathology Image. In Proceedings of the 2021 Chinese Intelligent Systems Conference, Fuzhou, China, 16–17 October 2021;
Springer: Berlin/Heidelberg, Germany, 2022; pp. 425–435.
16. Deng, X.; Liu, E.; Li, S.; Duan, Y.; Xu, M. Interpretable Multi-Modal Image Registration Network Based on Disentangled
Convolutional Sparse Coding. IEEE Trans. Image Process. 2023, 32, 1078–1091. [CrossRef] [PubMed]
17. Jin, K.; Yan, Y.; Wang, S.; Yang, C.; Chen, M.; Liu, X.; Terasaki, H.; Yeo, T.H.; Singh, N.G.; Wang, Y.; et al. iERM: An Interpretable
Deep Learning System to Classify Epiretinal Membrane for Different Optical Coherence Tomography Devices: A Multi-Center
Analysis. J. Clin. Med. 2023, 12, 400. [CrossRef] [PubMed]
18. Xiong, S.; Li, B.; Zhu, S. DCGNN: A single-stage 3D object detection network based on density clustering and graph neural
network. Complex Intell. Syst. 2022, 9, 3399–3408. [CrossRef]
19. Qaiser, T.; Tsang, Y.W.; Taniyama, D.; Sakamoto, N.; Nakane, K.; Epstein, D.; Rajpoot, N. Fast and accurate tumor segmentation of
histology images using persistent homology and deep convolutional features. Med. Image Anal. 2019, 55, 1–14. [CrossRef]
20. Zhu, C.; Mei, K.; Peng, T.; Luo, Y.; Liu, J.; Wang, Y.; Jin, M. Multi-level colonoscopy malignant tissue detection with adversarial
CAC-UNet. Neurocomputing 2021, 438, 165–183. [CrossRef]
21. Feng, R.; Liu, X.; Chen, J.; Chen, D.Z.; Gao, H.; Wu, J. A deep learning approach for colonoscopy pathology WSI analysis:
Accurate segmentation and classification. IEEE J. Biomed. Health Inform. 2020, 25, 3700–3708. [CrossRef]
22. Song, W.; Fu, C.; Zheng, Y.; Cao, L.; Tie, M.; Sham, C.W. Protection of image ROI using chaos-based encryption and DCNN-based
object detection. Neural Comput. Appl. 2022, 34, 5743–5756. [CrossRef]
23. He, K.; Zhang, X.; Ren, S.; Sun, J. Deep residual learning for image recognition. In Proceedings of the IEEE Conference on
Computer Vision and Pattern Recognition, Las Vegas, NV, USA, 27–30 June 2016; pp. 770–778.
24. Han, K.; Wang, Y.; Tian, Q.; Guo, J.; Xu, C. GhostNet: More Features From Cheap Operations. In Proceedings of the 2020
IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), Seattle, WA, USA, 13–19 June 2020.
25. Luo, P.; Ren, J.; Peng, Z.; Zhang, R.; Li, J. Differentiable Learning-to-Normalize via Switchable Normalization. In Proceedings of
the 7th International Conference on Learning Representations, ICLR, New Orleans, LA, USA, 6–9 May 2019.
26. Srinivas, A.; Lin, T.Y.; Parmar, N.; Shlens, J.; Abbeel, P.; Vaswani, A. Bottleneck transformers for visual recognition. In Proceedings
of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Nashville, TN, USA, 20–25 June 2021; pp. 16514–16524.
27. Cordonnier, J.B.; Loukas, A.; Jaggi, M. On the Relationship between Self-Attention and Convolutional Layers. In Proceedings of
the 8th International Conference on Learning Representations, ICLR, Addis Ababa, Ethiopia, 26–30 April 2020.
28. Dumoulin, V.; Visin, F. A guide to convolution arithmetic for deep learning. Stat 2018, 1050, 11. [CrossRef]
29. Luo, P.; Zhang, R.; Ren, J.; Peng, Z.; Li, J. Switchable Normalization for Learning-to-Normalize Deep Representation. IEEE Trans.
Pattern Anal. Mach. Intell. 2021, 43, 712–728. [CrossRef] [PubMed]
30. Ioffe, S.; Szegedy, C. Batch normalization: Accelerating deep network training by reducing internal covariate shift. PMLR 2015,
37, 448–456.
31. Huang, X.; Belongie, S. Arbitrary style transfer in real-time with adaptive instance normalization. In Proceedings of the IEEE
International Conference on Computer Vision, Venice, Italy, 22–29 October 2017; pp. 1510–1519.
32. Ba, J.L.; Kiros, J.R.; Hinton, G.E. Layer normalization. arXiv 2016, arXiv:1607.06450.
33. Milletari, F.; Navab, N.; Ahmadi, S.A. V-net: Fully convolutional neural networks for volumetric medical image segmentation. In
Proceedings of the 2016 Fourth International Conference on 3D Vision (3DV), Stanford, CA, USA, 25–28 October 2016; pp. 565–571.
34. Qadri, S.F.; Lin, H.; Shen, L.; Ahmad, M.; Qadri, S.; Khan, S.; Khan, M.; Zareen, S.S.; Akbar, M.A.; Bin Heyat, M.B.; et al. CT-Based
Automatic Spine Segmentation Using Patch-Based Deep Learning. Int. J. Intell. Syst. 2023, 2023, 2345835. [CrossRef]
35. Da, Q.; Huang, X.; Li, Z.; Zuo, Y.; Zhang, C.; Liu, J.; Chen, W.; Li, J.; Xu, D.; Hu, Z.; et al. DigestPath: A benchmark dataset
with challenge review for the pathological detection and segmentation of digestive-system. Med. Image Anal. 2022, 80, 102485.
[CrossRef]
36. Sirinukunwattana, K.; Pluim, J.P.; Chen, H.; Qi, X.; Heng, P.A.; Guo, Y.B.; Wang, L.Y.; Matuszewski, B.J.; Bruni, E.; Sanchez, U.;
et al. Gland segmentation in colon histology images: The glas challenge contest. Med. Image Anal. 2017, 35, 489–502. [CrossRef]
37. Ronneberger, O.; Fischer, P.; Brox, T. U-net: Convolutional networks for biomedical image segmentation. In Proceedings of the
International Conference on Medical Image Computing and Computer-Assisted Intervention, Munich, Germany, 5–9 October
2015; Springer: Berlin/Heidelberg, Germany, 2015; pp. 234–241.
38. Sri, S.V.; Kavya, S. Lung Segmentation Using Deep Learning. Asian J. Appl. Sci. Technol. AJAST 2021, 5, 10–19. [CrossRef]
39. Pravitasari, A.A.; Iriawan, N.; Almuhayar, M.; Azmi, T.; Irhamah, I.; Fithriasari, K.; Purnami, S.W.; Ferriastuti, W. UNet-VGG16
with transfer learning for MRI-based brain tumor segmentation. TELKOMNIKA Telecommun. Comput. Electron. Control. 2020,
18, 1310–1318. [CrossRef]
40. Diakogiannis, F.I.; Waldner, F.; Caccetta, P.; Wu, C. ResUNet-a: A deep learning framework for semantic segmentation of remotely
sensed data. ISPRS J. Photogramm. Remote Sens. 2020, 162, 94–114. [CrossRef]
41. Li, X.; Chen, H.; Qi, X.; Dou, Q.; Fu, C.W.; Heng, P.A. H-DenseUNet: Hybrid densely connected UNet for liver and tumor
segmentation from CT volumes. IEEE Trans. Med. Imaging 2018, 37, 2663–2674. [CrossRef]
Bioengineering 2023, 10, 957 16 of 16

42. Zhou, Z.; Rahman Siddiquee, M.M.; Tajbakhsh, N.; Liang, J. UNet++: A Nested U-Net Architecture for Medical Image
Segmentation. In Proceedings of the Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision
Support, Granada, Spain, 20 September 2018; Stoyanov, D., Taylor, Z., Carneiro, G., Syeda-Mahmood, T., Martel, A., Maier-Hein,
L., Tavares, J.M.R., Bradley, A., Papa, J.P., Belagiannis, V., et al., Eds.; Springer International Publishing: Cham, Switzerland, 2018;
pp. 3–11.
43. Huang, H.; Lin, L.; Tong, R.; Hu, H.; Zhang, Q.; Iwamoto, Y.; Han, X.; Chen, Y.W.; Wu, J. UNet 3+: A Full-Scale Connected UNet
for Medical Image Segmentation. In Proceedings of the ICASSP 2020—2020 IEEE International Conference on Acoustics, Speech
and Signal Processing (ICASSP), Barcelona, Spain, 4–8 May 2020; pp. 1055–1059. [CrossRef]
44. Chen, L.C.; Papandreou, G.; Kokkinos, I.; Murphy, K.; Yuille, A.L. Deeplab: Semantic image segmentation with deep convolutional
nets, atrous convolution, and fully connected crfs. IEEE Trans. Pattern Anal. Mach. Intell. 2017, 40, 834–848. [CrossRef] [PubMed]
45. Chen, H.; Qi, X.; Yu, L.; Heng, P.A. DCAN: Deep contour-aware networks for accurate gland segmentation. In Proceedings of the
IEEE Conference on Computer Vision and Pattern Recognition, Las Vegas, NV, USA, 26 June–1 July 2016; pp. 2487–2496.
46. Wang, X.; Yao, L.; Wang, X.; Paik, H.Y.; Wang, S. Global Convolutional Neural Processes. In Proceedings of the 2021 IEEE
International Conference on Data Mining (ICDM), Auckland, New Zealand, 7–10 December 2021; pp. 699–708.
47. Badrinarayanan, V.; Kendall, A.; Cipolla, R. SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation.
IEEE Trans. Pattern Anal. Mach. Intell. 2017, 39, 2481–2495. [CrossRef] [PubMed]

Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual
author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to
people or property resulting from any ideas, methods, instructions or products referred to in the content.