96 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
The impact of pre- and post-image processing techniques on deep learning frameworks: A comprehensive review for digital pathology image analysis
Recently, deep learning frameworks have rapidly become the main methodology for analyzing medical images. Due to their powerful learning ability and advantages in dealing with complex patterns, deep learning algorithms are ideal for image analysis challenges, particularly in the field of digital pathology. The variety of image analysis tasks in the context of deep learning includes classification (e.g., healthy vs. cancerous tissue), detection (e.g., lymphocytes and mitosis counting), and segmentation (e.g., nuclei and glands segmentation). The majority of recent machine learning methods in digital pathology have a pre- and/or post-processing stage which is integrated with a deep neural network. These stages, based on traditional image processing methods, are employed to make the subsequent classification, detection, or segmentation problem easier to solve. Several studies have shown how the integration of pre- and post-processing methods within a deep learning pipeline can further increase the model's performance when compared to the network by itself. The aim of this review is to provide an overview on the types of methods that are used within deep learning frameworks either to optimally prepare the input (pre-processing) or to improve the results of the network output (post-processing), focusing on digital pathology image analysis. Many of the techniques presented here, especially the post-processing methods, are not limited to digital pathology but can be extended to almost any image analysis field
The impact of pre- and post-image processing techniques on deep learning frameworks: A comprehensive review for digital pathology image analysis.
Recently, deep learning frameworks have rapidly become the main methodology for analyzing medical images. Due to their powerful learning ability and advantages in dealing with complex patterns, deep learning algorithms are ideal for image analysis challenges, particularly in the field of digital pathology. The variety of image analysis tasks in the context of deep learning includes classification (e.g., healthy vs. cancerous tissue), detection (e.g., lymphocytes and mitosis counting), and segmentation (e.g., nuclei and glands segmentation). The majority of recent machine learning methods in digital pathology have a pre- and/or post-processing stage which is integrated with a deep neural network. These stages, based on traditional image processing methods, are employed to make the subsequent classification, detection, or segmentation problem easier to solve. Several studies have shown how the integration of pre- and post-processing methods within a deep learning pipeline can further increase the model's performance when compared to the network by itself. The aim of this review is to provide an overview on the types of methods that are used within deep learning frameworks either to optimally prepare the input (pre-processing) or to improve the results of the network output (post-processing), focusing on digital pathology image analysis. Many of the techniques presented here, especially the post-processing methods, are not limited to digital pathology but can be extended to almost any image analysis field
An empirical evaluation of nuclei segmentation from H&E images in a real application scenario
Cell nuclei segmentation is a challenging task, especially in real applications, when the target images significantly differ between them. This task is also challenging for methods based on convolutional neural networks (CNNs), which have recently boosted the performance of cell nuclei segmentation systems. However, when training data are scarce or not representative of deployment scenarios, they may suffer from overfitting to a different extent, and may hardly generalise to images that differ from the ones used for training. In this work, we focus on real-world, challenging application scenarios when no annotated images from a given dataset are available, or when few images (even unlabelled) of the same domain are available to perform domain adaptation. To simulate this scenario, we performed extensive cross-dataset experiments on several CNN-based state-of-the-art cell nuclei segmentation methods. Our results show that some of the existing CNN-based approaches are capable of generalising to target images which resemble the ones used for training. In contrast, their effectiveness considerably degrades when target and source significantly differ in colours and scale
Coastal Aquaculture Extraction Using GF-3 Fully Polarimetric SAR Imagery: A Framework Integrating UNet++ with Marker-Controlled Watershed Segmentation
Coastal aquaculture monitoring is vital for sustainable offshore aquaculture management. However, the dense distribution and various sizes of aquacultures make it challenging to accurately extract the boundaries of aquaculture ponds. In this study, we develop a novel combined framework that integrates UNet++ with a marker-controlled watershed segmentation strategy to facilitate aquaculture boundary extraction from fully polarimetric GaoFen-3 SAR imagery. First, four polarimetric decomposition algorithms were applied to extract 13 polarimetric scattering features. Together with the nine other polarisation and texture features, a total of 22 polarimetric features were then extracted, among which four were optimised according to the separability index. Subsequently, to reduce the “adhesion” phenomenon and separate adjacent and even adhering ponds into individual aquaculture units, two UNet++ subnetworks were utilised to construct the marker and foreground functions, the results of which were then used in the marker-controlled watershed algorithm to obtain refined aquaculture results. A multiclass segmentation strategy that divides the intermediate markers into three categories (aquaculture, background and dikes) was applied to the marker function. In addition, a boundary patch refinement postprocessing strategy was applied to the two subnetworks to extract and repair the complex/error-prone boundaries of the aquaculture ponds, followed by a morphological operation that was conducted for label augmentation. An experimental investigation performed to extract individual aquacultures in the Yancheng Coastal Wetlands indicated that the crucial features for aquacultures are Shannon entropy (SE), the intensity component of SE (SE_I) and the corresponding mean texture features (Mean_SE and Mean_SE_I). When the optimal features were introduced, our proposed method performed better than standard UNet++ in aquaculture extraction, achieving improvements of 1.8%, 3.2%, 21.7% and 12.1% in F1, IoU, MR and insF1, respectively. The experimental results indicate that the proposed method can handle the adhesion of both adjacent objects and unclear boundaries effectively and capture clear and refined aquaculture boundaries
CPP-Net: Context-aware Polygon Proposal Network for Nucleus Segmentation
Nucleus segmentation is a challenging task due to the crowded distribution
and blurry boundaries of nuclei. Recent approaches represent nuclei by means of
polygons to differentiate between touching and overlapping nuclei and have
accordingly achieved promising performance. Each polygon is represented by a
set of centroid-to-boundary distances, which are in turn predicted by features
of the centroid pixel for a single nucleus. However, using the centroid pixel
alone does not provide sufficient contextual information for robust prediction.
To handle this problem, we propose a Context-aware Polygon Proposal Network
(CPP-Net) for nucleus segmentation. First, we sample a point set rather than
one single pixel within each cell for distance prediction. This strategy
substantially enhances contextual information and thereby improves the
robustness of the prediction. Second, we propose a Confidence-based Weighting
Module, which adaptively fuses the predictions from the sampled point set.
Third, we introduce a novel Shape-Aware Perceptual (SAP) loss that constrains
the shape of the predicted polygons. Here, the SAP loss is based on an
additional network that is pre-trained by means of mapping the centroid
probability map and the pixel-to-boundary distance maps to a different nucleus
representation. Extensive experiments justify the effectiveness of each
component in the proposed CPP-Net. Finally, CPP-Net is found to achieve
state-of-the-art performance on three publicly available databases, namely
DSB2018, BBBC06, and PanNuke. Code of this paper will be released
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
An Innovative Method for Lung Cancer Identification Using Machine Learning Algorithms
Biological community and the healthcare sector have greatly benefited from technological advancements in biomedical imaging. These advantages include early cancer identification and categorization, prognostication of patients' clinical outcomes following cancer surgery, and prognostication of survival for various cancer types. Medical professionals must spend a lot of time and effort gathering, analyzing, and evaluating enormous amounts of wellness data, such as scan results. Although radiologists spend a lot of time carefully reviewing several scans, tiny nodule diagnosis is incredibly prone to inaccuracy. Low dose computed tomography (LDCT) scans are used to categorize benign (Noncancerous) and malignant (Cancerous) nodules in order to study the issue of lung cancer (LC) diagnosis. Machine learning (ML), Deep learning (DL), and Artificial intelligence (AI) applications aid in the rapid identification of a number of infectious and malignant diseases, including lung cancer, using cutting-edge convolutional neural network (CNN) and Deep CNN architectures, we propose three unique detection models in this study: SEQUENTIAL 1 (Model-1), SEQUENTIAL 2 (Model-2), and transfer learning model Visual Geometry Group, VGG 16 (Model-3). The best accuracy model and methodology that are proposedas an effective and non-invasive diagnostic tool, outperforms other models trained with similar labels using lung CT scans to identify malignant nodules. Using a standard LIDC-IDRI data set that is freely available, the deep learning models are verified. The results of the experiment show a decrease in false positives while an increase in accuracy
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