143 research outputs found
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
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
Automate Nuclei Detection Using Neural Networks
Nuclei identification is a pivotal first step in many areas of biomedical research. Pathologists often observe images containing microscopic nuclei as part of their day to day jobs. During research, pathologists must identify nuclei characteristics from microscopic images such as: volume of nuclei, size, density and individual position within image. The pathology field can benefit from image detection enhancements done through the use of computer image segmentation techniques. This research presents methods that can be used to identify all the cell nuclei contained in images. Multiple techniques were experimented with such as edge detection and Convolutional Neural Networks with U-Net architecture. The data for training these models was sourced from the 2018 Data Science Bowl sponsored by Kaggle and Booz, Allen, Hamilton. As a result, there were various methods identified to assist the pathology industry for automating nuclei detection by using computer image detection methods. These computer methods rapidly process images for research purposes, with a reasonably high accuracy which has the potential to greatly accelerate the pace of research
A review and comparison of breast tumor cell nuclei segmentation performances using deep convolutional neural networks
Abstract: Breast cancer is currently the second most common cause of cancer-related death in women. Presently, the clinical benchmark in cancer diagnosis is tissue biopsy examination. However, the manual process of histopathological analysis is laborious, time-consuming, and limited by the quality of the specimen and the experience of the pathologist. This study's objective was to determine if deep convolutional neural networks can be trained, with transfer learning, on a set of histopathological images independent of breast tissue to segment tumor nuclei of the breast. Various deep convolutional neural networks were evaluated for the study, including U-Net, Mask R-CNN, and a novel network (GB U-Net). The networks were trained on a set of Hematoxylin and Eosin (H&E)-stained images of eight diverse types of tissues. GB U-Net demonstrated superior performance in segmenting sites of invasive diseases (AJI = 0.53, mAP = 0.39 & AJI = 0.54, mAP = 0.38), validated on two hold-out datasets exclusively containing breast tissue images of approximately 7,582 annotated cells. The results of the networks, trained on images independent of breast tissue, demonstrated that tumor nuclei of the breast could be accurately segmented
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
GenSelfDiff-HIS: Generative Self-Supervision Using Diffusion for Histopathological Image Segmentation
Histopathological image segmentation is a laborious and time-intensive task,
often requiring analysis from experienced pathologists for accurate
examinations. To reduce this burden, supervised machine-learning approaches
have been adopted using large-scale annotated datasets for histopathological
image analysis. However, in several scenarios, the availability of large-scale
annotated data is a bottleneck while training such models. Self-supervised
learning (SSL) is an alternative paradigm that provides some respite by
constructing models utilizing only the unannotated data which is often
abundant. The basic idea of SSL is to train a network to perform one or many
pseudo or pretext tasks on unannotated data and use it subsequently as the
basis for a variety of downstream tasks. It is seen that the success of SSL
depends critically on the considered pretext task. While there have been many
efforts in designing pretext tasks for classification problems, there haven't
been many attempts on SSL for histopathological segmentation. Motivated by
this, we propose an SSL approach for segmenting histopathological images via
generative diffusion models in this paper. Our method is based on the
observation that diffusion models effectively solve an image-to-image
translation task akin to a segmentation task. Hence, we propose generative
diffusion as the pretext task for histopathological image segmentation. We also
propose a multi-loss function-based fine-tuning for the downstream task. We
validate our method using several metrics on two publically available datasets
along with a newly proposed head and neck (HN) cancer dataset containing
hematoxylin and eosin (H\&E) stained images along with annotations. Codes will
be made public at
https://github.com/PurmaVishnuVardhanReddy/GenSelfDiff-HIS.git
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