231 research outputs found
Nucleus segmentation : towards automated solutions
Single nucleus segmentation is a frequent challenge of microscopy image processing, since it is the first step of many quantitative data analysis pipelines. The quality of tracking single cells, extracting features or classifying cellular phenotypes strongly depends on segmentation accuracy. Worldwide competitions have been held, aiming to improve segmentation, and recent years have definitely brought significant improvements: large annotated datasets are now freely available, several 2D segmentation strategies have been extended to 3D, and deep learning approaches have increased accuracy. However, even today, no generally accepted solution and benchmarking platform exist. We review the most recent single-cell segmentation tools, and provide an interactive method browser to select the most appropriate solution.Peer reviewe
Iterative annotation to ease neural network training: Specialized machine learning in medical image analysis
Neural networks promise to bring robust, quantitative analysis to medical
fields, but adoption is limited by the technicalities of training these
networks. To address this translation gap between medical researchers and
neural networks in the field of pathology, we have created an intuitive
interface which utilizes the commonly used whole slide image (WSI) viewer,
Aperio ImageScope (Leica Biosystems Imaging, Inc.), for the annotation and
display of neural network predictions on WSIs. Leveraging this, we propose the
use of a human-in-the-loop strategy to reduce the burden of WSI annotation. We
track network performance improvements as a function of iteration and quantify
the use of this pipeline for the segmentation of renal histologic findings on
WSIs. More specifically, we present network performance when applied to
segmentation of renal micro compartments, and demonstrate multi-class
segmentation in human and mouse renal tissue slides. Finally, to show the
adaptability of this technique to other medical imaging fields, we demonstrate
its ability to iteratively segment human prostate glands from radiology imaging
data.Comment: 15 pages, 7 figures, 2 supplemental figures (on the last page
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning
Understanding the spatial organization of tissues is of critical importance for both basic and translational research. While recent advances in tissue imaging are opening an exciting new window into the biology of human tissues, interpreting the data that they create is a significant computational challenge. Cell segmentation, the task of uniquely identifying each cell in an image, remains a substantial barrier for tissue imaging, as existing approaches are inaccurate or require a substantial amount of manual curation to yield useful results. Here, we addressed the problem of cell segmentation in tissue imaging data through large-scale data annotation and deep learning. We constructed TissueNet, an image dataset containing >1 million paired whole-cell and nuclear annotations for tissue images from nine organs and six imaging platforms. We created Mesmer, a deep learning-enabled segmentation algorithm trained on TissueNet that performs nuclear and whole-cell segmentation in tissue imaging data. We demonstrated that Mesmer has better speed and accuracy than previous methods, generalizes to the full diversity of tissue types and imaging platforms in TissueNet, and achieves human-level performance for whole-cell segmentation. Mesmer enabled the automated extraction of key cellular features, such as subcellular localization of protein signal, which was challenging with previous approaches. We further showed that Mesmer could be adapted to harness cell lineage information present in highly multiplexed datasets. We used this enhanced version to quantify cell morphology changes during human gestation. All underlying code and models are released with permissive licenses as a community resource
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
Maximum margin learning of t-SPNs for cell classification with filtered input
An algorithm based on a deep probabilistic architecture referred to as a
tree-structured sum-product network (t-SPN) is considered for cell
classification. The t-SPN is constructed such that the unnormalized probability
is represented as conditional probabilities of a subset of most similar cell
classes. The constructed t-SPN architecture is learned by maximizing the
margin, which is the difference in the conditional probability between the true
and the most competitive false label. To enhance the generalization ability of
the architecture, L2-regularization (REG) is considered along with the maximum
margin (MM) criterion in the learning process. To highlight cell features, this
paper investigates the effectiveness of two generic high-pass filters: ideal
high-pass filtering and the Laplacian of Gaussian (LOG) filtering. On both
HEp-2 and Feulgen benchmark datasets, the t-SPN architecture learned based on
the max-margin criterion with regularization produced the highest accuracy rate
compared to other state-of-the-art algorithms that include convolutional neural
network (CNN) based algorithms. The ideal high-pass filter was more effective
on the HEp-2 dataset, which is based on immunofluorescence staining, while the
LOG was more effective on the Feulgen dataset, which is based on Feulgen
staining
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
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