118 research outputs found
A Comprehensive Overview of Computational Nuclei Segmentation Methods in Digital Pathology
In the cancer diagnosis pipeline, digital pathology plays an instrumental
role in the identification, staging, and grading of malignant areas on biopsy
tissue specimens. High resolution histology images are subject to high variance
in appearance, sourcing either from the acquisition devices or the H\&E
staining process. Nuclei segmentation is an important task, as it detects the
nuclei cells over background tissue and gives rise to the topology, size, and
count of nuclei which are determinant factors for cancer detection. Yet, it is
a fairly time consuming task for pathologists, with reportedly high
subjectivity. Computer Aided Diagnosis (CAD) tools empowered by modern
Artificial Intelligence (AI) models enable the automation of nuclei
segmentation. This can reduce the subjectivity in analysis and reading time.
This paper provides an extensive review, beginning from earlier works use
traditional image processing techniques and reaching up to modern approaches
following the Deep Learning (DL) paradigm. Our review also focuses on the weak
supervision aspect of the problem, motivated by the fact that annotated data is
scarce. At the end, the advantages of different models and types of supervision
are thoroughly discussed. Furthermore, we try to extrapolate and envision how
future research lines will potentially be, so as to minimize the need for
labeled data while maintaining high performance. Future methods should
emphasize efficient and explainable models with a transparent underlying
process so that physicians can trust their output.Comment: 47 pages, 27 figures, 9 table
Deep Learning in Breast Cancer Imaging: A Decade of Progress and Future Directions
Breast cancer has reached the highest incidence rate worldwide among all
malignancies since 2020. Breast imaging plays a significant role in early
diagnosis and intervention to improve the outcome of breast cancer patients. In
the past decade, deep learning has shown remarkable progress in breast cancer
imaging analysis, holding great promise in interpreting the rich information
and complex context of breast imaging modalities. Considering the rapid
improvement in the deep learning technology and the increasing severity of
breast cancer, it is critical to summarize past progress and identify future
challenges to be addressed. In this paper, we provide an extensive survey of
deep learning-based breast cancer imaging research, covering studies on
mammogram, ultrasound, magnetic resonance imaging, and digital pathology images
over the past decade. The major deep learning methods, publicly available
datasets, and applications on imaging-based screening, diagnosis, treatment
response prediction, and prognosis are described in detail. Drawn from the
findings of this survey, we present a comprehensive discussion of the
challenges and potential avenues for future research in deep learning-based
breast cancer imaging.Comment: Survey, 41 page
Nuclei & Glands Instance Segmentation in Histology Images: A Narrative Review
Instance segmentation of nuclei and glands in the histology images is an
important step in computational pathology workflow for cancer diagnosis,
treatment planning and survival analysis. With the advent of modern hardware,
the recent availability of large-scale quality public datasets and the
community organized grand challenges have seen a surge in automated methods
focusing on domain specific challenges, which is pivotal for technology
advancements and clinical translation. In this survey, 126 papers illustrating
the AI based methods for nuclei and glands instance segmentation published in
the last five years (2017-2022) are deeply analyzed, the limitations of current
approaches and the open challenges are discussed. Moreover, the potential
future research direction is presented and the contribution of state-of-the-art
methods is summarized. Further, a generalized summary of publicly available
datasets and a detailed insights on the grand challenges illustrating the top
performing methods specific to each challenge is also provided. Besides, we
intended to give the reader current state of existing research and pointers to
the future directions in developing methods that can be used in clinical
practice enabling improved diagnosis, grading, prognosis, and treatment
planning of cancer. To the best of our knowledge, no previous work has reviewed
the instance segmentation in histology images focusing towards this direction.Comment: 60 pages, 14 figure
Semi-supervised Pathological Image Segmentation via Cross Distillation of Multiple Attentions
Segmentation of pathological images is a crucial step for accurate cancer
diagnosis. However, acquiring dense annotations of such images for training is
labor-intensive and time-consuming. To address this issue, Semi-Supervised
Learning (SSL) has the potential for reducing the annotation cost, but it is
challenged by a large number of unlabeled training images. In this paper, we
propose a novel SSL method based on Cross Distillation of Multiple Attentions
(CDMA) to effectively leverage unlabeled images. Firstly, we propose a
Multi-attention Tri-branch Network (MTNet) that consists of an encoder and a
three-branch decoder, with each branch using a different attention mechanism
that calibrates features in different aspects to generate diverse outputs.
Secondly, we introduce Cross Decoder Knowledge Distillation (CDKD) between the
three decoder branches, allowing them to learn from each other's soft labels to
mitigate the negative impact of incorrect pseudo labels in training.
Additionally, uncertainty minimization is applied to the average prediction of
the three branches, which further regularizes predictions on unlabeled images
and encourages inter-branch consistency. Our proposed CDMA was compared with
eight state-of-the-art SSL methods on the public DigestPath dataset, and the
experimental results showed that our method outperforms the other approaches
under different annotation ratios. The code is available at
\href{https://github.com/HiLab-git/CDMA}{https://github.com/HiLab-git/CDMA.}Comment: Provisional Accepted by MICCAI 202
Domain Generalization in Computational Pathology: Survey and Guidelines
Deep learning models have exhibited exceptional effectiveness in
Computational Pathology (CPath) by tackling intricate tasks across an array of
histology image analysis applications. Nevertheless, the presence of
out-of-distribution data (stemming from a multitude of sources such as
disparate imaging devices and diverse tissue preparation methods) can cause
\emph{domain shift} (DS). DS decreases the generalization of trained models to
unseen datasets with slightly different data distributions, prompting the need
for innovative \emph{domain generalization} (DG) solutions. Recognizing the
potential of DG methods to significantly influence diagnostic and prognostic
models in cancer studies and clinical practice, we present this survey along
with guidelines on achieving DG in CPath. We rigorously define various DS
types, systematically review and categorize existing DG approaches and
resources in CPath, and provide insights into their advantages, limitations,
and applicability. We also conduct thorough benchmarking experiments with 28
cutting-edge DG algorithms to address a complex DG problem. Our findings
suggest that careful experiment design and CPath-specific Stain Augmentation
technique can be very effective. However, there is no one-size-fits-all
solution for DG in CPath. Therefore, we establish clear guidelines for
detecting and managing DS depending on different scenarios. While most of the
concepts, guidelines, and recommendations are given for applications in CPath,
we believe that they are applicable to most medical image analysis tasks as
well.Comment: Extended Versio
Improved Breast Cancer Diagnosis through Transfer Learning on Hematoxylin and Eosin Stained Histology Images
Breast cancer is one of the leading causes of death for women worldwide.
Early screening is essential for early identification, but the chance of
survival declines as the cancer progresses into advanced stages. For this
study, the most recent BRACS dataset of histological (H\&E) stained images was
used to classify breast cancer tumours, which contains both the whole-slide
images (WSI) and region-of-interest (ROI) images, however, for our study we
have considered ROI images. We have experimented using different pre-trained
deep learning models, such as Xception, EfficientNet, ResNet50, and
InceptionResNet, pre-trained on the ImageNet weights. We pre-processed the
BRACS ROI along with image augmentation, upsampling, and dataset split
strategies. For the default dataset split, the best results were obtained by
ResNet50 achieving 66\% f1-score. For the custom dataset split, the best
results were obtained by performing upsampling and image augmentation which
results in 96.2\% f1-score. Our second approach also reduced the number of
false positive and false negative classifications to less than 3\% for each
class. We believe that our study significantly impacts the early diagnosis and
identification of breast cancer tumors and their subtypes, especially atypical
and malignant tumors, thus improving patient outcomes and reducing patient
mortality rates. Overall, this study has primarily focused on identifying seven
(7) breast cancer tumor subtypes, and we believe that the experimental models
can be fine-tuned further to generalize over previous breast cancer histology
datasets as well.Comment: 11 pages, 4 figure
A Survey on Deep Learning in Medical Image Analysis
Deep learning algorithms, in particular convolutional networks, have rapidly
become a methodology of choice for analyzing medical images. This paper reviews
the major deep learning concepts pertinent to medical image analysis and
summarizes over 300 contributions to the field, most of which appeared in the
last year. We survey the use of deep learning for image classification, object
detection, segmentation, registration, and other tasks and provide concise
overviews of studies per application area. Open challenges and directions for
future research are discussed.Comment: Revised survey includes expanded discussion section and reworked
introductory section on common deep architectures. Added missed papers from
before Feb 1st 201
- …